bluuebunny/crossref_metadata_2025 huggingface dataset:
Diabetes before and after lung transplantation in patients with cystic fibrosis and other lung diseases
Authors: Belle‐van Meerkerk G. , van de Graaf E. A. , Kwakkel‐van Erp J. M. , van Kessel D. A. , Lammers J.‐W. J. , Biesma D. H. , de Valk H. W.
Published: April 2012

Diabet. Med. 29, e159–e162 (2012)

Aims  The aims of the study are to investigate the prevalence of diabetes in patients with cystic fibrosis compared with patients without cystic fibrosis, and its impact on the outcome after lung transplantation.

Methods  Data were reviewed from 77 lung transplantation recipients in our centre between 2001 and 2010; 43 patients had cystic fibrosis and 34 patients had other lung diseases (no cystic fibrosis). To define diabetes, we used the American Diabetes Association definition.

Results  Before lung transplantation, diabetes was diagnosed in 63% of patients with cystic fibrosis and 6% of patients without cystic fibrosis (P < 0.001). In both groups, approximately 60% of the patients at risk developed new‐onset diabetes after transplantation. The mortality in patients with cystic fibrosis was higher in patients with diabetes diagnosed before lung transplantation compared with those without (44 vs. 6%, P = 0.04). Diabetes remained an independent factor in multivariate analyses.

Conclusions  Diabetes diagnosed before lung transplantation has a negative effect on survival after lung transplantation in patients with cystic fibrosis. Pre‐existing diabetes is common in patients with cystic fibrosis, in contrast to patients without cystic fibrosis. Development of new‐onset diabetes after transplantation is similar in both groups.
Assessing diabetes support in adolescents: factor structure of the modified Diabetes Social Support Questionnaire (DSSQ–Friends)
Authors: Malik J. A. , Koot H. M.
Published: April 2012

Diabet. Med. 29, e232–e240 (2012)

Aims  To determine the underlying factor structure of friends’ enacted support behaviours for adolescents with Type 1 diabetes, confirm it in a second sample, delineate distinctive aspects of friends’ support and test the reliability of resulting scale.

Methods  The study included a total of 434 adolescents (54.8% girls), mean age 14.7 years, mean duration of diabetes 6.1 years.

Results  Results from the exploratory factor analysis, including data from a random half of the participants revealed a five‐factor solution explaining approximately 48.4% of the item variance. The five factors emerged Guidance and Encouragement (13 items; α = 0.91), Help in Critical Situations (7 items; α = 0.92), Nourishment (11 items; α = 0.88), Empathy (6 items; α = 0.83) and Help in Exercise (5 items; α = 0.76). Confirmatory factor analysis on the remainder of the sample showed good indices of model fit. Comparison of the factor structure across gender and age also presented an excellent fit. In a second‐order factor analysis all five factors loaded on one overall factor, Diabetes Social Support–Friends. Construct validity of the resulting scales was supported by predicted associations of Modified Diabetes Specific Support Questionnaire‐Friends scale scores with HbA1c, treatment adherence and responsibility, and well‐being.

Conclusion  The 42‐item Modified Diabetes Specific Support Questionnaire–Friends emerged as a reliable and valid scale for Dutch adolescents with Type 1 diabetes and measures five factors of diabetes‐specific support from close friends.
Desire to Dissociate: Implications for Problematic Drinking in College Students with Childhood or Adolescent Sexual Abuse Exposure
Authors: Klanecky Alicia , McChargue Dennis E. , Bruggeman Lindsay
Published: April 2012

Alcohol use to replace inadequate dissociative capabilities, or chemical dissociation, has been linked to college students with childhood or adolescent sexual abuse (CASA). Insofar as CASA‐exposed persons experience a restricted range of dissociative capabilities, what remains relatively unclear is whether some desire to achieve greater dissociative experiences. Nonclinical levels of dissociative tendencies have positively predicted alcohol‐related blackouts in CASA‐exposed students, and dissociation mediated the relations between CASA and intoxication frequency. Although alcohol (similar to dissociation) can reduce physiological and psychological responses to stress, alcohol consumption may be prompted by a desire to dissociate rather than inadequate dissociative tendencies alone. To investigate this interpretation of the chemical dissociation phenomenon, researchers examined the mediating potential of dissociative tendencies using the Dissociative Experiences Scale–II (DES‐II) as well as the desire to dissociate concept (ie, a modified version of the DES‐II) on the relations between CASA exposure and problematic alcohol use in college students (N = 298). Results indicated that dissociation scores did not replicate previous mediation findings whereas desire to dissociate scores fully mediated CASA exposure and problematic alcohol use. Implications of the results are discussed including possible reasons why prior mediation results were not replicated as well as links to experiential avoidance. (Am J Addict 2012;21:250–256)
DECOUPLING OF SHORT‐ AND LONG‐DISTANCE DISPERSAL PATHWAYS IN THE ENDEMIC NEW ZEALAND SEAWEED CARPOPHYLLUM MASCHALOCARPUM (PHAEOPHYCEAE, FUCALES)1
Authors: Buchanan Joe , Zuccarello Giuseppe C.
Published: April 2012

The processes that produce and maintain genetic structure in organisms operate at different timescales and on different life‐history stages. In marine macroalgae, gene flow occurs through gamete/zygote dispersal and rafting by adult thalli. Population genetic patterns arise from this contemporary gene flow interacting with historical processes. We analyzed spatial patterns of mitochondrial DNA variation to investigate contemporary and historical dispersal patterns in the New Zealand endemic fucalean brown alga Carpophyllum maschalocarpum (Turner) Grev. Populations bounded by habitat discontinuities were often strongly differentiated from adjoining populations over scales of tens of kilometers and intrapopulation diversity was generally low, except for one region of northeast New Zealand (the Bay of Plenty). There was evidence of strong connectivity between the northern and eastern regions of New Zealand’s North Island and between the North and South Islands of New Zealand and the Chatham Islands (separated by 650 km of open ocean). Moderate haplotypic diversity was found in Chatham Islands populations, while other southern populations showed low diversity consistent with Last Glacial Maximum (LGM) retreat and subsequent recolonization. We suggest that ocean current patterns and prevailing westerly winds facilitate long‐distance dispersal by floating adult thalli, decoupling genetic differentiation of Chatham Island populations from dispersal potential at the gamete/zygote stage. This study highlights the importance of encompassing the entire range of a species when inferring dispersal patterns from genetic differentiation, as realized dispersal distances can be contingent on local or regional oceanographic and historical processes.
A COMPARATIVE ANALYSIS OF THE VOLVOCACEAE (CHLOROPHYTA)1
Authors: Coleman A. W.
Published: April 2012

This review covers essentially all aspects of the organisms in the green algal family Volvocaceae and suggests the genetic history of the various steps in their evolution from their unicellular ancestors.
MOLECULAR PHYLOGENY OF ANTARCTIC PRASIOLA (PRASIOLALES, TREBOUXIOPHYCEAE) REVEALS EXTENSIVE CRYPTIC DIVERSITY1
Authors: Moniz Mónica B. J. , Rindi Fabio , Novis Phil M. , Broady Paul A. , Guiry Michael D.
Published: April 2012

Trebouxiophytes of the genus Prasiola are well known in Antarctica, where they are among the most important primary producers. Although many aspects of their biology have been thoroughly investigated, the scarcity of molecular data has so far prevented an accurate assessment of their taxonomy and phylogenetic position. Using sequences of the chloroplast genes rbcL and psaB, we demonstrate the existence of three cryptic species that were previously confused under Prasiola crispa (Lightfoot) Kützing. Genuine P. crispa occurs in Antarctica; its presence was confirmed by comparison with the rbcL sequence of the type specimen (from the Isle of Skye, Scotland). Prasiola antarctica Kützing is resurrected as an independent species to designate algae with gross morphology identical to P. crispa but robustly placed in a separate lineage. The third species is represented by specimens identified as P. calophylla (Carmichael ex Greville) Kützing in previous studies, but clearly separated from European P. calophylla (type locality: Argyll, Scotland); this alga is described as P. glacialis sp. nov. The molecular data demonstrated the presence of P. crispa in Maritime and Continental Antarctica. P. antarctica was recorded from the Antarctic Peninsula and Shetland Islands, and P. glacialis from the Southern Ocean islands and coast. Such unexpected cryptic diversity highlights the need for a taxonomic reassessment of many published Antarctic records of P. crispa. The results also indicate that marine species of Prasiola form a well‐supported monophyletic group, whereas the phylogenetic diversity of freshwater species is higher than previously suspected (at least three separate lineages within the genus include species living in this type of environments).
An Alexandrium Spp. Cyst Record from Sequim Bay, Washington State, USA, and its Relation to Past Climate Variability1
Authors: Feifel Kirsten M. , Moore Stephanie K. , Horner Rita A.
Published: April 2012

Since the 1970s, Puget Sound, Washington State, USA, has experienced an increase in detections of paralytic shellfish toxins (PSTs) in shellfish due to blooms of the harmful dinoflagellate Alexandrium. Natural patterns of climate variability, such as the Pacific Decadal Oscillation (PDO), and changes in local environmental factors, such as sea surface temperature (SST) and air temperature, have been linked to the observed increase in PSTs. However, the lack of observations of PSTs in shellfish prior to the 1950s has inhibited statistical assessments of longer‐term trends in climate and environmental conditions on Alexandrium blooms. After a bloom, Alexandrium cells can enter a dormant cyst stage, which settles on the seafloor and then becomes entrained into the sedimentary record. In this study, we created a record of Alexandrium spp. cysts from a sediment core obtained from Sequim Bay, Puget Sound. Cyst abundances ranged from 0 to 400 cysts · cm−3 and were detected down‐core to a depth of 100 cm, indicating that Alexandrium has been present in Sequim Bay since at least the late 1800s. The cyst record allowed us to statistically examine relationships with available environmental parameters over the past century. Local air temperature and sea surface temperature were positively and significantly correlated with cyst abundances from the late 1800s to 2005; no significant relationship was found between PDO and cyst abundances. This finding suggests that local environmental variations more strongly influence Alexandrium population dynamics in Puget Sound when compared to large‐scale changes.
DIEL VARIATIONS OF CARBOHYDRATES AND NEUTRAL LIPIDS IN NITROGEN‐SUFFICIENT AND NITROGEN‐STARVED CYCLOSTAT CULTURES OF ISOCHRYSIS SP.1
Authors: Lacour Thomas , Sciandra Antoine , Talec Amélie , Mayzaud Patrick , Bernard Olivier
Published: April 2012

The goal of this study was to investigate the time response of two major carbon (C) reserves, respectively neutral lipids (NL) and total carbohydrate (TC), in the Haptophyte Isochrysis sp. growing in nitrogen (N)‐sufficient or N‐starved conditions and under light:dark (L:D) cycles. Experiments were carried out in a cyclostat culture system that allowed the following of the dynamics of the main cell compounds at both hourly and daily time scales. Under N‐sufficient conditions, the L:D cycles cause the population to be synchronized, with most of the cells dividing at the beginning of the dark period. The C‐specific growth rate was maximal around midday and negative during the dark period due to respiration processes. NL and TC both accumulated during the day and consumed during the night. We showed that NL and TC are highly dynamic compounds, as more than three quarters of NL and TC accumulated during the light period were consumed during the dark period. In contrast to NL, phospholipid and glycolipid to C ratios remained quite stable during the light/dark cycles. The major effect of N starvation on the NL and TC dynamics was to uncouple their diel variations from the L:D cycle, in two different ways depending on their respective role during short‐term acclimation. Whereas the TC per cell ratio increased rapidly to reach a stable value in response to N starvation, NL per cell continued to oscillate, but with a pattern out of phase with the L:D cycle.
Regulation of the Activity and Expression of Aryl Hydrocarbon Receptor by Ethanol in Mouse Hepatic Stellate Cells
Authors: Zhang Hong Feng , Lin Xing Hua , Yang Hong , Zhou Li Chun , Guo Yang Lin , Barnett Joey V. , Guo Zhong Mao
Published: April 2012

Background

During the course of alcohol‐induced liver damage, hepatic stellate cells are transformed into proliferative, fibrogenic, and contractile myofibroblasts. Aryl hydrocarbon receptor (AhR) is a transcription factor that controls the expression of genes involved in the metabolism of xenobiotics, inflammation, cell proliferation, and death.

Methods

Immortal mouse hepatic stellate cells (MHSCs) were isolated from transgenic mice that expressed a thermolabile SV40 tumor antigen. Quantitative real‐time reverse transcription polymerase chain reaction assays, Western blot analysis, promoter activity assays, and chromatin immunoprecipitation analyses were performed for studying the effect of ethanol (EtOH) on AhR expression and transcriptional activity.

Results

Treatment of MHSCs with 50 to 200 mM EtOH for 6 hours induced AhR nuclear translocation, enhanced the promoter activity of cytochrome P450 (CYP) 1A1, increased the amount of AhR bound to the promoter of CYP1A1 and 1B1, and up‐regulated the mRNA expression of these AhR target genes in a dose‐dependent manner. In contrast, EtOH exposure down‐regulated AhR mRNA and protein expression. Similarly, benzo(a)pyrene (BaP) at 10 nM reduced AhR and increased CYP1A1 and 1B1 mRNAs. Pretreatment of MHSCs with 50 mM EtOH for 7 days diminished the capacity of MHSCs to express CYP1A1 and 1B1 induced by a 200 mM EtOH challenge, or by 10 nM BaP. However, the up‐regulatory effect of EtOH on solute carrier family 16, member 6 (SLC16a6) was unaffected by EtOH pretreatment. Similar to EtOH, dimethyl sulfoxide (DMSO) at concentrations of 50 to 100 mM down‐regulated AhR and up‐regulated CYP1A1 mRNA expression in a dose‐dependent manner.

Conclusions

These data, for the first time, demonstrate that EtOH activates MHSC AhR and down‐regulates its expression. Chronic EtOH pretreatment lowers the availability of AhR, and specifically diminishes the inducibility of CYP genes. The effect on AhR appears to not be an EtOH‐specific response, as DMSO alone (and possibly other organic solvents) was also able to activate AhR.
Ethanol Metabolism and Osmolarity Modify Behavioral Responses to Ethanol in C. elegans
Authors: Alaimo Joseph T. , Davis Scott J. , Song Sam S. , Burnette Christopher R. , Grotewiel Mike , Shelton Keith L. , Pierce‐Shimomura Jonathan T. , Davies Andrew G. , Bettinger Jill C.
Published: April 2012

Background

Ethanol (EtOH) is metabolized by a 2‐step process in which alcohol dehydrogenase (ADH) oxidizes EtOH to acetaldehyde, which is further oxidized to acetate by aldehyde dehydrogenase (ALDH). Although variation in EtOH metabolism in humans strongly influences the propensity to chronically abuse alcohol, few data exist on the behavioral effects of altered EtOH metabolism. Here, we used the nematode Caenorhabditis elegans to directly examine how changes in EtOH metabolism alter behavioral responses to alcohol during an acute exposure. Additionally, we investigated EtOH solution osmolarity as a potential explanation for contrasting published data on C. elegans EtOH sensitivity.

Methods

We developed a gas chromatography assay and validated a spectrophotometric method to measure internal EtOH in EtOH‐exposed worms. Further, we tested the effects of mutations in ADH and ALDH genes on EtOH tissue accumulation and behavioral sensitivity to the drug. Finally, we tested the effects of EtOH solution osmolarity on behavioral responses and tissue EtOH accumulation.

Results

Only a small amount of exogenously applied EtOH accumulated in the tissues of C. elegans and consequently their tissue concentrations were similar to those that intoxicate humans. Independent inactivation of an ADH‐encoding gene (sodh‐1) or an ALDH‐encoding gene (alh‐6 or alh‐13) increased the EtOH concentration in worms and caused hypersensitivity to the acute sedative effects of EtOH on locomotion. We also found that the sensitivity to the depressive effects of EtOH on locomotion is strongly influenced by the osmolarity of the exogenous EtOH solution.

Conclusions

Our results indicate that EtOH metabolism via ADH and ALDH has a statistically discernable but surprisingly minor influence on EtOH sedation and internal EtOH accumulation in worms. In contrast, the osmolarity of the medium in which EtOH is delivered to the animals has a more substantial effect on the observed sensitivity to EtOH.
Development of an Oral Operant Nicotine/Ethanol Co‐Use Model in Alcohol‐Preferring (P) Rats
Authors: Hauser Sheketha R. , Katner Simon N. , Deehan Gerald A. , Ding Zheng‐Ming , Toalston Jamie E. , Scott Briana J. , Bell Richard L. , McBride William J. , Rodd Zachary A.
Published: April 2012

Background

Alcohol abuse is frequently associated with nicotine (Nic) use. The current experiments were conducted to establish an oral operant ethanol + Nic (EtOH + Nic) co‐use model and to characterize some aspects of EtOH + Nic co‐use.

Methods

Rats were allowed to choose between EtOH alone or EtOH + Nic solutions. Additionally, alcohol‐preferring (P) rats were allowed to concurrently self‐administer 3 distinct EtOH solutions (10, 20, and 30%) with varying amounts of Nic (0.07, 0.14, or 0.21 mg/ml) under operant conditions. P rats were also allowed to concurrently self‐administer 2 distinct amounts of Nic (0.07 and 0.14 mg/ml) added to saccharin (Sacc; 0.025%) solutions.

Results

During acquisition, P rats responded for the EtOH + Nic solutions at the same level as for EtOH alone, and responding for EtOH + Nic solutions was present throughout all drinking conditions. P rats also readily maintained stable self‐administration behaviors for Nic + Sacc solutions. The results demonstrated that P rats readily acquired and maintained stable self‐administration behaviors for EtOH + 0.07 and EtOH + 0.14 mg/ml Nic solutions. Self‐administration of EtOH + 0.21 mg/ml Nic was established in only 50% of the subjects. P rats readily expressed seeking behaviors for the EtOH + Nic solutions and reacquired EtOH + Nic self‐administration during relapse testing. In addition, tail blood samples indicated that EtOH + Nic co‐use resulted in pharmacologically relevant levels of both EtOH and Nic in the blood.

Conclusions

Overall, the results indicate that P rats readily consume EtOH + Nic solutions concurrently in the presence of EtOH alone, express drug‐seeking behaviors, and will concurrently consume physiologically relevant levels of both drugs. These results support the idea that this oral operant EtOH + Nic co‐use model would be suitable for studying the development of co‐abuse and the consequences of long‐term chronic co‐abuse.
Microstructural and Mechanical Characterization of Pressure‐Less Sintered AlN‐polytypoid Based Composites by Compositional Design
Authors: Huang Saifang , Huang Zhaohui , Liu Yan‐gai , Fang Minghao , Yin Li , Huang Juntong
Published: April 2012

AlN‐polytypoid materials are hard to be sintered and usually need a hot‐pressing (HP) technique and very high sintering temperatures (≥1750°C). In this study, densified AlN‐polytypoid based composites were successfully fabricated in situ via a pressureless sintering method at a relatively lower temperature of 1650°C by compositional design. Moreover, the room temperature mechanical properties of the composites were comparable with those sintered by HP method. The results showed that 15R‐based composite was sintered via a transient liquid‐phase sintering mechanism with the aid of U‐phase Sialon. The pressureless‐sintered composites were mainly composed of platelet 15R, hexagonal β‐Sialon, and intergranular U‐phase Sialon grains, which exhibited both intercrystalline and transcrystalline fracture behaviors. Partial 15R grains were of twin structure, which was found to be positive for toughening of the composites.
Exposures related to hand eczema: a study of healthcare workers
Authors: Ibler Kristina S. , Jemec Gregor B. E. , Agner Tove
Published: April 2012

Background. Hand eczema is common in healthcare workers, owing to intensive exposure to wet work and skin irritants. Targeted interventions and vocational guidance based on documented exposures and risk factors are needed.

Objectives. The aims of the study were to investigate the relationship between exposures (domestic and at work) and prevalence and severity of hand eczema.

Methods. Self‐administered questionnaires were sent to 3181 healthcare workers in Denmark.

Results. Two thousand two hundred and sixty‐nine (71%) workers responded to the questionnaire. Frequent hand washing was significantly related to the presence of hand eczema. Having children < 4 years old in the household was also related to the presence of hand eczema. A lower prevalence of hand eczema was found among those using moisturizers at work, and a higher prevalence was found among those using moisturizers at home.

Conclusions. Although healthcare workers are recommended to use disinfectants when the hands are not visibly dirty, hand washing is still significantly related to hand eczema. Frequent hand washing may be a question of behavioural habits, and a focus for future guidance should be on changing hand washing habits. Attention should also be paid to healthcare workers with small children at home. The preventive effect of moisturizers used during working hours should be tested in future follow‐up studies.
Wool‐derived keratin stimulates human keratinocyte migration and types IV and VII collagen expression
Authors: Tang Ling , Sierra Jose Ollague , Kelly Rob , Kirsner Robert S. , Li Jie
Published: April 2012

Keratinocyte migration is essential for wound repair. Keratin‐based products have recently shown stimulatory effects on wound repair. This study was to test the cellular response to wool‐derived oxidized keratin in wound healing to further understand the biological mechanisms underlying observed clinical benefits of keratin‐based products as wound treatments. In vitro scratch migration assays examined the effects of oxidized keratin on the migration of human skin keratinocytes. Western blotting analysis determined the effects on the marker protein expression of type IV and type VII collagens and keratin 17. We found wool‐derived oxidized keratin promoted keratinocyte migration and induced protein expression of type IV and type VII collagens, but not keratin 17. The data suggest that the beneficial effects of keratin‐based treatment in wounds may be related to its positive effects on re‐epithelialization via stimulating keratinocyte migration and production of basement membrane proteins of types IV and VII collagens.
Ectopic production of hair keratin constitutes Rushton’s hyaline bodies in association with hematogenous deposits
Authors: Sakamoto Kei , Khanom Rumana , Hamagaki Miwako , Yamaguchi Akira
Published: April 2012

J Oral Pathol Med (2012) 41: 637–641

A Rushton’s hyaline body (HB) is a concretion occasionally found in odontogenic cysts. Unspecified substances produced by the lining epithelium or derived from blood components have been suggested as possible causes of HB formation, but the origin of HBs is still elusive. This study aimed to clarify the origin of HBs. Ten specimens with HBs were obtained from 400 odontogenic cysts. HBs were stained by orcein and Congo red. Immunohistochemical examination revealed that HBs were positive for hair keratin and keratin 17. Hair keratin was concentrated in HBs, and cells with hair keratin expression were hardly seen, while cells with keratin 17 expression were observed near HBs. HBs were also positive for hemoglobin alpha chain. The presence of hair keratin in HBs was confirmed by Western blot analysis. The present study suggests that HBs are formed as a consequence of two independent events: unusual alteration of epithelial differentiation so as to provide hair keratin, and hemorrhage so as to provide erythrocytic substances. Although the ectopic production of hair keratin appears more essential, our results reconcile the long‐standing debate between two theories, the keratin theory versus the hematogenous theory, concluding that both substances are required for the genesis of HBs, and also suggesting that they might be novel non‐pathological amyloidogenic proteins.
The impact of bacterial and viral co‐infection in severe influenza
Authors: Blyth Christopher C. , Webb Steve A. R. , Kok Jen , Dwyer Dominic E. , van Hal Sebastiaan J. , Foo Hong , Ginn Andrew N. , Kesson Alison M. , Seppelt Ian , Iredell Jonathan R. ,   on behalf of the ANZIC Influenza Investigators and COSI Microbiological Investigators
Published: April 2012

Please cite this paper as: Blyth et al. (2013) The impact of bacterial and viral co‐infection in severe influenza. Influenza and Other Respiratory Viruses 7(2) 168–176.

Background  Many questions remain concerning the burden, risk factors and impact of bacterial and viral co‐infection in patients with pandemic influenza admitted to the intensive care unit (ICU).

Objectives  To examine the burden, risk factors and impact of bacterial and viral co‐infection in Australian patients with severe influenza.

Patients/Methods  A cohort study conducted in 14 ICUs was performed. Patients with proven influenza A during the 2009 influenza season were eligible for inclusion. Demographics, risk factors, clinical data, microbiological data, complications and outcomes were collected. Polymerase chain reaction for additional bacterial and viral respiratory pathogens was performed on stored respiratory samples.

Results  Co‐infection was identified in 23·3–26·9% of patients with severe influenza A infection: viral co‐infection, 3·2–3·4% and bacterial co‐infection, 20·5–24·7%. Staphylococcus aureus was the most frequent bacterial co‐infection followed by Streptococcus pneumoniae and Haemophilus influenzae. Patients with co‐infection were younger [mean difference in age = 8·46 years (95% CI: 0·18–16·74 years)], less likely to have significant co‐morbidities (32·0% versus 66·2%, P = 0·004) and less frequently obese [mean difference in body mass index = 6·86 (95% CI: 1·77–11·96)] compared to those without co‐infection.

Conclusions  Bacterial or viral co‐infection complicated one in four patients admitted to ICU with severe influenza A infection. Despite the co‐infected patients being younger and with fewer co‐morbidities, no significant difference in outcomes was observed. It is likely that co‐infection contributed to a need for ICU admission in those without other risk factors for severe influenza disease. Empiric antibiotics with staphylococcal activity should be strongly considered in all patients with severe influenza A infection.
Channel Evolution Model of Semiarid Stream Response to Urban‐Induced Hydromodification1
Authors: Hawley Robert J. , Bledsoe Brian P. , Stein Eric D. , Haines Brian E.
Published: April 2012

Hawley, Robert J., Brian P. Bledsoe, Eric D. Stein, and Brian E. Haines, 2012. Channel Evolution Model of Semiarid Stream Response to Urban‐Induced Hydromodification. Journal of the American Water Resources Association (JAWRA) 48(4): 722‐744. DOI: 10.1111/j.1752‐1688.2012.00645.x

Abstract:  We present a novel channel evolution model (CEM) that qualitatively describes morphologic responses of semiarid channels to altered hydrologic and sediment regimes associated with urbanization (hydromodification). The CEM is based on southern California data from 83 detailed channel surveys, hundreds of synoptic surveys, and historical analyses of aerial photographs along 14 reaches. Channel evolution sometimes follows the well‐known sequence described by Schumm et al. (Incised Channels: Morphology, Dynamics, and Control, Water Resources Publications, Littleton, Colorado, 1984) for incising, single‐thread channels; however, departures from this sequence are common and include transitions of single thread to braided evolutionary endpoints, as opposed to a return to quasi‐equilibrium single‐thread planform. Thresholds and risk factors associated with observed channel response are also presented. In particular, distance to grade control and network position emerged as key controls on channel response trajectory. The CEM and quantitative extensions provide managers with a framework for understanding channel responses and rehabilitation alternatives, and may be transferable to other semiarid settings. It also offers insights regarding channel susceptibility to hydromodification, highlights key boundary conditions for high‐risk channels, and underscores critical knowledge gaps in predicting the complex, discontinuous response trajectories that are highly prevalent in urbanized watersheds.
Calibration Catchment Selection for Flood Regionalization Modeling1
Authors: Wan Jaafar Wan Zurina , Han Dawei
Published: April 2012

Wan Jaafar, Wan Zurina, and Dawei Han, 2012. Calibration Catchment Selection for Flood Regionalization Modeling. Journal of the American Water Resources Association (JAWRA) 48(4): 698‐706. DOI: 10.1111/j.1752‐1688.2012.00648.x

Abstract:  There are two unsolved problems in flood regionalization model development related to the quantity and quality of calibration catchments: (1) how many calibration catchments should be used? and (2) how to select the calibration catchments? This study explores these two questions through a case study on the median annual maximum flood (QMED) model in the United Kingdom. It has been found that the chance of developing a good QMED model decreases significantly when the number of calibration catchments drops below a critical number (e.g., 60 in the case study). However, no significant improvement is achieved if the number of calibration catchments is above it. This number could be used as a benchmark for choosing randomly selected calibration catchments. Across a broad range of calibration catchment numbers, there are good and poor calibrated models regardless of calibration catchment numbers. High quality models could be developed from a small number of calibration catchments and also poor models from a large number of calibration catchments. This indicates that the number of calibration catchments may not be the dominating factor for developing a high quality regionalization model. Instead, the information content could be more important. The study has demonstrated that the standard deviation values between the best and poorest groups are distinctive and could be used in choosing appropriate calibration catchments.
Transcription-Independent Function of Polycomb Group Protein PSC in Cell Cycle Control
Authors: Mohd-Sarip Adone , Lagarou Anna , Doyen Cecile M. , van der Knaap Jan A. , Aslan Ülkü , Bezstarosti Karel , Yassin Yasmin , Brock Hugh W. , Demmers Jeroen A. A. , Verrijzer C. Peter
Published: April 2012

Silence, Please

Polycomb group (PcG) proteins play pivotal roles in epigenetic gene control, development, and disease. PcG proteins can control cell cycle progression, but the underlying mechanisms remain unclear. PcG proteins are thought to silence transcription of target genes through modulating chromatin structure.

Mohd-Sarip
et al.

(p.
744
, published online 5 April) uncovered an unanticipated transcription-independent function for the canonical PcG protein “Posterior sex combs” in cell cycle control, through its direct regulation of cyclin B destruction.
Effects of Essential Oils on Methane Production and Fermentation by, and Abundance and Diversity of, Rumen Microbial Populations
Authors: Patra Amlan K. , Yu Zhongtang
Published: April 2012

Five essential oils (EOs), namely, clove oil (CLO), eucalyptus oil (EUO), garlic oil (GAO), origanum oil (ORO), and peppermint oil (PEO), were testedin vitroat 3 different doses (0.25, 0.50, and 1.0 g/liter) for their effect on methane production, fermentation, and select groups of ruminal microbes, including total bacteria, cellulolytic bacteria, archaea, and protozoa. All the EOs significantly reduced methane production with increasing doses, with reductions by 34.4%, 17.6%, 42.3%, 87%, and 25.7% for CLO, EUO, GAO, ORO, and PEO, respectively, at 1.0 g/liter compared with the control. However, apparent degradability of dry matter and neutral detergent fiber also decreased linearly with increasing doses by all EOs except GAO. The concentrations of total volatile fatty acids were not affected by GAO, EUO, or PEO but altered linearly and quadratically by CLO and ORO, respectively. All the EOs also differed in altering the molar proportions of acetate, propionate, and butyrate. As determined by quantitative real-time PCR, all the EOs decreased the abundance of archaea, protozoa, and major cellulolytic bacteria (i.e.,Fibrobacter succinogenes,Ruminococcus flavefaciens, andR. albus) linearly with increasing EO doses. On the basis of denaturing gradient gel electrophoresis analysis, different EOs changed the composition of both archaeal and bacterial communities to different extents. The Shannon-Wiener diversity index (H′) was reduced for archaea by all EOs in a dose-dependent manner but increased for bacteria at low and medium doses (0.25 and 0.50 g/liter) for all EOs except ORO. Due to the adverse effects on feed digestion and fermentation at high doses, a single EO may not effectively and practically mitigate methane emission from ruminants unless used at low doses in combinations with other antimethanogenic compounds.
Shell Biofilm Nitrification and Gut Denitrification Contribute to Emission of Nitrous Oxide by the Invasive Freshwater Mussel Dreissena polymorpha (Zebra Mussel)
Authors: Svenningsen Nanna B. , Heisterkamp Ines M. , Sigby-Clausen Maria , Larsen Lone H. , Nielsen Lars Peter , Stief Peter , Schramm Andreas
Published: April 2012

Nitrification in shell biofilms and denitrification in the gut of the animal accounted for N2O emission byDreissena polymorpha(Bivalvia), as shown by gas chromatography and gene expression analysis. The mussel's ammonium excretion was sufficient to sustain N2O production and thus potentially uncouples invertebrate N2O production from environmental N concentrations.
Comparative Analysis of Lactobacillus plantarum WCFS1 Transcriptomes by Using DNA Microarray and Next-Generation Sequencing Technologies
Authors: Leimena Milkha M. , Wels Michiel , Bongers Roger S. , Smid Eddy J. , Zoetendal Erwin G. , Kleerebezem Michiel
Published: April 2012

RNA sequencing is starting to compete with the use of DNA microarrays for transcription analysis in eukaryotes as well as in prokaryotes. The application of RNA sequencing in prokaryotes requires additional steps in the RNA preparation procedure to increase the relative abundance of mRNA and cannot employ the poly(T)-primed approach in cDNA synthesis. In this study, we aimed to validate the use of RNA sequencing (direct cDNA sequencing and 3′-untranslated region [UTR] sequencing) using
Lactobacillus plantarum
WCFS1 as a model organism, employing its established microarray platform as a reference. A limited effect of mRNA enrichment on genome-wide transcript quantification was observed, and comparative transcriptome analyses were performed for
L. plantarum
WCFS1 grown in two different laboratory media. Microarray analyses and both RNA sequencing methods resulted in similar depths of analysis and generated similar fold-change ratios of differentially expressed genes. The highest overall correlation was found between microarray and direct cDNA sequencing-derived transcriptomes, while the 3′-UTR sequencing-derived transcriptome appeared to deviate the most. Overall, a high similarity between patterns of transcript abundance and fold-change levels of differentially expressed genes was detected by all three methods, indicating that the biological conclusions drawn from the transcriptome data were consistent among the three technologies.
Quantitative PCR for Tracking the Megaplasmid-Borne Biodegradation Potential of a Model Sphingomonad
Authors: Hartmann Erica M. , Badalamenti Jonathan P. , Krajmalnik-Brown Rosa , Halden Rolf U.
Published: April 2012

We developed a quantitative PCR method for tracking the
dxnA1
gene, the initial, megaplasmid-borne gene in
Sphingomonas wittichii
RW1's dibenzo-
p
-dioxin degradation pathway. We used this method on complex environmental samples and report on growth of
S. wittichii
RW1 in landfill leachate, thus furnishing a novel tool for monitoring megaplasmid-borne, dioxygenase-encoding genes.
Inclusion of Chicory (Cichorium intybus L.) in Pigs' Diets Affects the Intestinal Microenvironment and the Gut Microbiota
Authors: Liu Haoyu , Ivarsson Emma , Dicksved Johan , Lundh Torbjörn , Lindberg Jan Erik
Published: April 2012

The content and composition of prebiotic plant fiber in the diet is important in promoting gut-related health. This study investigated the effects of the dietary inclusion of chicory forage and roots on the intestinal microenvironment of pigs. Thirty-seven-week-old pigs were fed 1 of 5 diets for 18 days, including a cereal-based control diet and 4 diets with the inclusion of 80 and 160 g kg
−1
of body weight chicory forage (CF80 and CF160), 80 g kg
−1
chicory root (CR80), and a mix of 80 g kg
−1
forage and 80 g kg
−1
chicory root (CFR). The animals maintained good performance and health irrespective of diet. Bacterial community structure and diversity in ileal and colonic samples was assessed using terminal restriction fragment length polymorphism (T-RFLP), combined with cloning and sequencing. Samples clustered perfectly according to gut segment with a higher bacterial diversity in colon than ileum. Distal ileum was dominated by lactic acid bacteria (LAB), and the relative amount of this group was increased by the CF160 and CFR diets. The colonic bacterial community was dominated by butyrate-producing bacteria and
Prevotella
. The increased relative abundance of butyrate-producing bacteria in the colon was positively correlated with the molar proportion of acetic acid and furthermore linked to the chicory forage diets (CF80 and CF160). Diets including chicory roots (CR80 and CFR) were correlated with a higher colonic abundance of
Megasphaera elsdenii
. The fermentation products and pH in digesta responded to diet type and were correlated with shifts in the microbiota, showing that chicory influences the intestinal microenvironment of pigs.
Functional Specificity of Extracellular Nucleases of Shewanella oneidensis MR-1
Authors: Heun Magnus , Binnenkade Lucas , Kreienbaum Maximilian , Thormann Kai M.
Published: April 2012

Bacterial species such asShewanella oneidensisMR-1 require extracellular nucleolytic activity for the utilization of extracellular DNA (eDNA) as a source of nutrients and for the turnover of eDNA as a structural matrix component during biofilm formation. We have previously characterized two extracellular nucleases ofS. oneidensisMR-1, ExeM and ExeS. Although both are involved in biofilm formation, they are not specifically required for the utilization of eDNA as a nutrient. Here we identified and characterized EndA, a third extracellular nuclease ofShewanella. The heterologously overproduced and purified protein was highly active and rapidly degraded linear and supercoiled DNAs of various origins. Divalent metal ions (Mg2+or Mn2+) were required for function.endAis cotranscribed withphoA, an extracellular phosphatase, and is not upregulated upon phosphostarvation. Deletion ofendAabolished both extracellular degradation of DNA byS. oneidensisMR-1 and the ability to use eDNA as a sole source of phosphorus. PhoA is not strictly required for the exploitation of eDNA as a nutrient. The activity of EndA prevents the formation of large cell aggregates during planktonic growth. However, in contrast to the findings for ExeM,endAdeletion had only minor effects on biofilm formation. The findings strongly suggest that the extracellular nucleases ofS. oneidensisexert specific functions required under different conditions.
Oxalyl-Coenzyme A Reduction to Glyoxylate Is the Preferred Route of Oxalate Assimilation in Methylobacterium extorquens AM1
Authors: Schneider Kathrin , Skovran Elizabeth , Vorholt Julia A.
Published: April 2012

Oxalate catabolism is conducted by phylogenetically diverse organisms, including
Methylobacterium extorquens
AM1. Here, we investigate the central metabolism of this alphaproteobacterium during growth on oxalate by using proteomics, mutant characterization, and
13
C-labeling experiments. Our results confirm that energy conservation proceeds as previously described for
M. extorquens
AM1 and other characterized oxalotrophic bacteria via oxalyl-coenzyme A (oxalyl-CoA) decarboxylase and formyl-CoA transferase and subsequent oxidation to carbon dioxide via formate dehydrogenase. However, in contrast to other oxalate-degrading organisms, the assimilation of this carbon compound in
M. extorquens
AM1 occurs via the operation of a variant of the serine cycle as follows: oxalyl-CoA reduction to glyoxylate and conversion to glycine and its condensation with methylene-tetrahydrofolate derived from formate, resulting in the formation of C3 units. The recently discovered ethylmalonyl-CoA pathway operates during growth on oxalate but is nevertheless dispensable, indicating that oxalyl-CoA reductase is sufficient to provide the glyoxylate required for biosynthesis. Analysis of an oxalyl-CoA synthetase- and oxalyl-CoA-reductase-deficient double mutant revealed an alternative, although less efficient, strategy for oxalate assimilation via one-carbon intermediates. The alternative process consists of formate assimilation via the tetrahydrofolate pathway to fuel the serine cycle, and the ethylmalonyl-CoA pathway is used for glyoxylate regeneration. Our results support the notion that
M. extorquens
AM1 has a plastic central metabolism featuring multiple assimilation routes for C1 and C2 substrates, which may contribute to the rapid adaptation of this organism to new substrates and the eventual coconsumption of substrates under environmental conditions.
Vicriviroc Resistance Decay and Relative Replicative Fitness in HIV-1 Clinical Isolates under Sequential Drug Selection Pressures
Authors: Tsibris Athe M. N. , Hu Zixin , Paredes Roger , Leopold Kay E. , Putcharoen Opass , Schure Allison L. , Mazur Natalie , Coakley Eoin , Su Zhaohui , Gulick Roy M. , Kuritzkes Daniel R.
Published: April 2012

We previously described an HIV-1-infected individual who developed resistance to vicriviroc (VCV), an investigational CCR5 antagonist, during 28 weeks of therapy (Tsibris AM et al., J. Virol.82:8210–8214, 2008). To investigate the decay of VCV resistance mutations, a standard clonal analysis of full-lengthenv(gp160) was performed on plasma HIV-1 samples obtained at week 28 (the time of VCV discontinuation) and at three subsequent time points (weeks 30, 42, and 48). During 132 days, VCV-resistant HIV-1 was replaced by VCV-sensitive viruses whose V3 loop sequences differed from the dominant pretreatment forms. A deep-sequencing analysis showed that the week 48 VCV-sensitive V3 loop form emerged from a preexisting viral variant. Enfuvirtide was added to the antiretroviral regimen at week 30; by week 48, enfuvirtide treatment selected for either the G36D or N43D HR-1 mutation. Growth competition experiments demonstrated that viruses incorporating the dominant week 28 VCV-resistantenvwere less fit than week 0 viruses in the absence of VCV but more fit than week 48 viruses. This week 48 fitness deficit persisted when G36D was corrected by either site-directed mutagenesis or week 48 gp41 domain swapping. The correction of N43D, in contrast, restored fitness relative to that of week 28, but not week 0, viruses. Virus entry kinetics correlated with observed fitness differences; the slower entry of enfuvirtide-resistant viruses corrected to wild-type rates in the presence of enfuvirtide. These findings suggest that while VCV and enfuvirtide select for resistance mutations in only oneenvsubunit, gp120 and gp41 coevolve to maximize viral fitness under sequential drug selection pressures.
A Lentiviral Vector-Based, Herpes Simplex Virus 1 (HSV-1) Glycoprotein B Vaccine Affords Cross-Protection against HSV-1 and HSV-2 Genital Infections
Authors: Chiuppesi Flavia , Vannucci Laura , De Luca Anna , Lai Michele , Matteoli Barbara , Freer Giulia , Manservigi Roberto , Ceccherini-Nelli Luca , Maggi Fabrizio , Bendinelli Mauro , Pistello Mauro
Published: April 2012

Genital herpes is caused by herpes simplex virus 1 (HSV-1) and HSV-2, and its incidence is constantly increasing in the human population. Regardless of the clinical manifestation, HSV-1 and HSV-2 infections are highly transmissible to sexual partners and enhance susceptibility to other sexually transmitted infections. An effective vaccine is not yet available. Here, HSV-1 glycoprotein B (gB1) was delivered by a feline immunodeficiency virus (FIV) vector and tested against HSV-1 and HSV-2 vaginal challenges in C57BL/6 mice. The gB1 vaccine elicited cross-neutralizing antibodies and cell-mediated responses that protected 100 and 75% animals from HSV-1- and HSV-2-associated severe disease, respectively. Two of the eight fully protected vaccinees underwent subclinical HSV-2 infection, as demonstrated by deep immunosuppression and other analyses. Finally, vaccination prevented death in 83% of the animals challenged with a HSV-2 dose that killed 78 and 100% naive and mock-vaccinated controls, respectively. Since this FIV vector can accommodate two or more HSV immunogens, this vaccine has ample potential for improvement and may become a candidate for the development of a truly effective vaccine against genital herpes.