bluuebunny/crossref_metadata_2025 huggingface dataset:
Does reservoir age influence reproductive tactics in opportunistic fishes? An analysis of Astyanax minor reproduction in water supply reservoirs of southern Brazil
Authors: Oliveira Elton C. , Muelbert Adriane E. , Silva Juliano P. A. , Ghisi Nédia C. , Fávaro Luís F.
Published: September 2014

The goal of this study was to assess the reproductive tactics of the ‘lambari tetra’ (Astyanax minor) in two reservoirs of different age (Iraí Reservoir = 5–6 years old; Passaúna Reservoir = 17–18 years old), both being located in the same geographical region in southern Brazil. Sampling took place monthly from July 2006 to June 2007 in both reservoirs. Collected specimens were identified and their morphometric data measured. The gonads were macroscopically and microscopically analysed. Gonadosomatic Index (GSI) and condition factor results indicate there was a higher reproductive investment in Passaúna Reservoir for both sexes, although with lower total condition. The occurrence of partially spawned ovaries allowed the characterization of partial spawning in both reservoirs. Higher growth rates and the largest individuals were found in Passaúna Reservoir for both sexes, according to length–weight relationships and length class distributions. Significant seasonal sexual rate differences were only detected in Passaúna Reservoir, with male predominance. Total length explained just a small fraction of GSI variability of mature females and males, supporting the hypothesis of local factor influence. It was concluded that this species uses distinct reproductive tactics in each of the two studied reservoirs and that these tactics seem to be reflective of environmental stability.
Stratification, diel and seasonal energy transfers in Malilangwe Reservoir in the south‐eastern lowveld of Zimbabwe
Authors: Dalu Tatenda , Moyo Sydney , Clegg Bruce W. , Nhiwatiwa Tamuka
Published: September 2014

This study provides a 9‐month record of Malilangwe Reservoir stratification and diel and seasonal energy transfers between February and October 2011. The reservoir was not strongly stratified during the hot‐wet season (February and March), exhibiting low dissolved oxygen concentrations of <2 mg DO L−1 in the bottom layers (<6 m depth). During the cool‐dry season, when both the air temperature and solar radiation input decreased, the water temperatures in the epilimnion and across the thermocline decreased, and the water column was very weakly stratified. In this state, the reservoir could easily be mixed, even by light winds, resulting in overturning, thereby giving the bottom water an opportunity to become aerated, as observed during the cool‐dry season. The stability was greatest when the water level was high (during midday), while it was considerably lower during the predawn hours. The calculated annual Birgean heat budget for the reservoir was 110 MJ m−2 year−1 for February to October 2011. The diurnal Birgean heat budget was consistently associated with heat loss over a 24 hour period in all seasons, mostly between 0400 and 1000 h. Spearman's correlation suggests that the DO was significantly correlated with stability for the three study months (February r = 0.69, P < 0.05; June r = −0.76, P < 0.001; October r = 0.96, P < 0.001). The results of this study suggests that warming temperatures (warmer months or seasons) will result in high Birgean heat budgets, which could potentially trigger some important changes in plankton population dynamics in small reservoir, with severe water quality implications. The nutrient concentrations varied throughout the seasons.
Multi‐Scale Geometric‐Semantic Modeling of Shield Tunnels for GIS and BIM Applications
Authors: Borrmann A. , Kolbe T.H. , Donaubauer A. , Steuer H. , Jubierre J.R. , Flurl M.
Published: September 2014

The planning of large infrastructure facilities such as inner‐city subway tracks requires the consideration of widely differing scales, ranging from the kilometer scale for the general routing of the track down to the centimeter scale for detailed design of connection points. On the one hand this implies the utilization of both, Geographic Information Systems (GIS) as well as Building Information Modeling (BIM) tools, for performing the required analysis, modeling, and visualization tasks. On the other hand, a sound foundation of handling multi‐scale representations is required. Although multi‐scale modeling is already well established in the GIS field, there are no corresponding approaches in Infrastructure BIM so far. However, multi‐scale concepts are also much needed in the BIM context, as the planning process typically provides only rough information in the early stages and increasingly detailed and fine‐grained information in later stages. To meet this demand, this article presents a comprehensive concept for incorporating multi‐scale representations with building information models, with a particular focus on the geometric‐semantic modeling of shield tunnels. Based on a detailed analysis of the data modeling methods used in CityGML and the requirements present in the context of infrastructure planning projects, we discuss potential extensions to the BIM data model Industry Foundation Classes (IFC) for incorporating multi‐scale representations of shield tunnels. Particular emphasis is put on providing means for preserving the consistency of the representation across the different Levels‐of‐Detail (LoDs), while taking into account both semantics and geometry. For realizing consistency preservation mechanisms, we propose to apply a procedural geometry description which makes it possible to define explicit dependencies between geometric entities on different LoDs. The modification of an object on a coarse level consequently results in an automated update of all dependent objects on the finer levels. Finally, we discuss the transformation of the IFC‐based multi‐scale tunnel model into a CityGML compliant tunnel representation.
Fuzzy Analytic Hierarchy Process Synthetic Evaluation Models for the Health Monitoring of Shield Tunnels
Authors: Zhang Wei , Sun Ke , Lei Changzheng , Zhang Yuncong , Li Huixin , Spencer Bill F.
Published: September 2014

Many uncertainties remain in tunnel health evaluation due to a lack of specific information, data scarcity, misleading or conflicting information due to the complex nature of geo‐materials, and even the ambiguity in the concept of tunnel health. This article addresses the fuzzy analytic hierarchy process (AHP) synthetic evaluation models, which merge different types of data from multiple sensors to map them into the health rating scores of shield tunnels. A piecewise distribution was chosen for membership functions, and an exponential scale was introduced for a better characterization of the scales for weight sets. A series of fuzzy operation symbols, namely fuzzy operators, were defined to yield the fuzzy synthetic evaluation indexes (FSEIs) for monitoring factors. The fuzzy‐AHP evaluation procedure applied to the models was demonstrated. Moreover, a case study on Nanjing Yangtze River Tunnel was presented to verify the feasibility and efficiency of the models and the procedure. The fuzzy‐AHP health evaluations for monitoring factors, segments, rings, and the whole tunnel were implemented in succession using the models and following the procedure. The calculated FSEIs were compared with the rating scales to determine the corresponding action strategies. The segments with poor health conditions can then be identified for administrative maintenance or repairing measures. Such evaluation results will enhance the knowledge of designers and aid them for optimization when they are designing similar tunnels. The investigations indicate that the proposed fuzzy‐AHP models characterize the fuzziness of tunnel health well and will be useful for clarifying the tunnel health evaluation uncertainties to both designers and administrators.
Lethality of sortase depletion in Actinomyces oris caused by excessive membrane accumulation of a surface glycoprotein
Authors: Wu Chenggang , Huang I‐Hsiu , Chang Chungyu , Reardon‐Robinson Melissa Elizabeth , Das Asis , Ton‐That Hung
Published: September 2014

Sortase, a cysteine‐transpeptidase conserved in Gram‐positive bacteria, anchors on the cell wall many surface proteins that facilitate bacterial pathogenesis and fitness. Genetic disruption of the housekeeping sortase in several Gram‐positive pathogens reported thus far attenuates virulence, but not bacterial growth. Paradoxically, we discovered that depletion of the housekeeping sortase SrtA was lethal for Actinomyces oris; yet, all of its predicted cell wall‐anchored protein substrates (AcaA‐N) were individually dispensable for cell viability. Using Tn5‐transposon mutagenesis to identify factors that upend lethality of srtA deletion, we uncovered a set of genetic suppressors harbouring transposon insertions within genes of a locus encoding AcaC and a LytR‐CpsA‐Psr (LCP)‐like protein. AcaC was shown to be highly glycosylated and dependent on LCP for its glycosylation. Upon SrtA depletion, the glycosylated form of AcaC, hereby renamed GspA, was accumulated in the membrane. Overexpression of GspA in a mutant lacking gspA and srtA was lethal; conversely, cells overexpressing a GspA mutant missing a membrane‐localization domain were viable. The results reveal a unique glycosylation pathway in A. oris that is coupled to cell wall anchoring catalysed by sortase SrtA. Significantly, this novel phenomenon of glyco‐stress provides convenient cell‐based assays for developing a new class of inhibitors against Gram‐positive pathogens.
Controlling DNA degradation from a distance: a new role for the Mu transposition enhancer
Authors: Choi Wonyoung , Saha Rudra P. , Jang Sooin , Harshey Rasika M.
Published: September 2014

Phage Mu is unique among transposable elements in employing a transposition enhancer. The enhancer DNA segment is the site where the transposase MuA binds and makes bridging interactions with the two Mu ends, interwrapping the ends with the enhancer in a complex topology essential for assembling a catalytically active transpososome. The enhancer is also the site at which regulatory proteins control divergent transcription of genes that determine the phage lysis‐lysogeny decision. Here we report a third function for the enhancer – that of regulating degradation of extraneous DNA attached to both ends of infecting Mu. This DNA is protected from nucleases by a phage protein until Mu integrates into the host chromosome, after which it is rapidly degraded. We find that leftward transcription at the enhancer, expected to disrupt its topology within the transpososome, blocks degradation of this DNA. Disruption of the enhancer would lead to the loss or dislocation of two non‐catalytic MuA subunits positioned in the transpososome by the enhancer. We provide several lines of support for this inference, and conclude that these subunits are important for activating degradation of the flanking DNA. This work also reveals a role for enhancer topology in phage development.
Identification of Trypanosoma brucei components involved in trypanolysis by normal human serum
Authors: Lecordier Laurence , Uzureau Pierrick , Tebabi Patricia , Pérez‐Morga David , Nolan Derek , Schumann Burkard Gabriela , Roditi Isabel , Pays Etienne
Published: September 2014

Normal human serum (NHS) confers human resistance to infection by the parasite Trypanosoma brucei owing to the trypanolytic activity of apolipoprotein L1 (APOL1), present in two serum complexes termed Trypanolytic Factors (TLF‐1 and ‐2). In order to identify parasite components involved in the intracellular trafficking and activity of TLFs, an inducible RNA interference (RNAi) genomic DNA library constructed in bloodstream form T. brucei was subjected to RNAi induction and selection for resistant parasites under NHS conditions favouring either TLF‐1 or TLF‐2 uptake. While TLF‐1 conditions readily selected the haptoglobin‐haemoglobin (HP‐HB) surface receptor TbHpHbR as expected, given its known ability to bind TLF‐1, under TLF‐2 conditions no specific receptor for TLF‐2 was identified. Instead, the screen allowed the identification of five distinct factors expected to be involved in the assembly of the vacuolar proton pump V‐ATPase and consecutive endosomal acidification. These data confirm that lowering the pH during endocytosis is required for APOL1 toxic activity.
Rapid recovery of Dutch gray seal colonies fueled by immigration
Authors: Brasseur Sophie M. J. M. , van Polanen Petel Tamara D. , Gerrodette Tim , Meesters Erik H.W.G. , Reijnders Peter J. H. , Aarts Geert
Published: September 2014

Gray seals were first observed breeding in the Dutch Wadden Sea in 1985, after centuries of absence. The breeding colony there is now the largest on the European continent. We describe the changes in gray seal numbers and their geographical expansion, and estimate how these processes were influenced by immigration from other colonies. Counts of hauled out animals were carried out between 1985 and 2013, monitoring three different periods of the seals' annual cycle. Using priors determined for the UK population, a Bayesian demographic model was fitted to pup numbers to estimate the population parameters driving the growth. This included immigration of subadults into the breeding population, which contributed to an average growth rate in the pup counts of 19%/yr, much higher than expected in a closed population. This immigration may account for approximately 35% of the total annual growth. In addition, at least 200 gray seals from the UK visit the area temporarily. Recovery of the population in the Netherlands occurred more than 50 yr after gray seals were protected in the UK. These time scales should be taken into account when studying long living marine mammals, e.g., in impact and conservation studies.
Host‐iron assimilation: pathogenesis and novel therapies of mucormycosis
Authors: Ibrahim Ashraf S.
Published: September 2014

Mucormycosis is a fungal infection caused by organisms belonging to the orderMucorales. Although considered uncommon, mucormycosis has been steadily increasing in incidents for the last two decades. Mortality of the disease is unacceptably high despite antifungal therapy and surgical interventions. The lack of understanding of the pathogenesis of the disease and the absence of rapid diagnostic assay contribute to the poor prognosis of mucormycosis. The hyper susceptibility of patients with elevated available serum iron points to the critical role of the ability ofMucoralesto acquire host iron as a critical virulence factor. Specifically patients with deferoxamine‐therapy, hyperglycaemic with or without ketoacidosis, or other forms of acidosis are uniquely predisposed to mucormycosis. In this review, we discuss the molecular mechanisms of infection in these patient categories in an attempt to identify novel therapies for a disease with poor prognosis. Emphasis on the effect of glucose and free iron on host–pathogen interactions are also covered.
Effectiveness of zonisamide in a patient with Parkinson's disease and various levodopa‐induced psychotic symptoms
Authors: Yabe Ichiro , Ohta Midori , Egashira Toshiaki , Sato Kazunori , Kano Takahiro , Hirotani Makoto , Kunieda Yasuyuki , Sasaki Hidenao
Published: September 2014

Levodopa and dopamine agonists are useful as Parkinson's disease medications. However, they often induce persistent psychotic symptoms and motor complications, which make Parkinson's disease treatment difficult. This is a case report of a patient with advanced Parkinson's disease accompanied by exacerbation of motor symptoms and psychotic symptoms derived from prolonged use of conventional anti‐Parkinson's disease drugs, and in whom adjunctive therapy with a new anti‐Parkinson's disease drug, zonisamide, was shown to improve motor symptoms with no exacerbation of psychotic symptoms.
Simplification of the modified Gallyas method
Authors: Kuninaka Nobuo , Kawaguchi Minato , Ogawa Masaru , Sato Ayako , Arima Kunimasa , Murayama Shigeo , Saito Yuko
Published: September 2014

The Gallyas method is a silver impregnation technique that is essential in the field of neuropathology because of its high sensitivity for the detection of argentophilic inclusion bodies in the central nervous system. In Japan, the Gallyas method has improved and is widely used as the “modified Gallyas method”. However, this method is not popularly used in general pathology laboratories because of the need for special reagents, several staining processes, and skilled techniques. The objective of the current study was to provide a simplified Gallyas method. We omitted the lanthanum nitrate step from the staining process and verified the adequacy in comparison with the original method as well as immunohistochemistry, using specimens from patients of Alzheimer's disease, argyrophilic grain disease, multiple system atrophy, Pick's disease, and Lewy body disease. The simplified method provided good staining to all the structures in archival tissues, compared with the modified Gallyas method in a significantly shorter staining time. The lanthanum nitrate step can be omitted from the modified Gallyas method, resulting in reduction in the number of reagents required and shortening of the staining time.
Potentially malignant oral disorders and high‐risk habits in liver cirrhosis and lung cancer patients
Authors: Salarić I , Povrzanović I , Brajdić D , Lukšić I , Macan D
Published: September 2014

Objectives

To analyze the role of smoking, drinking, and their synergistic effect in the occurrence of potentially malignant oral disorders (PMOD).

Subjects and methods

We examined three groups: 50 patients with lung cancer, 50 patients with liver cirrhosis, and 50 patients with clear medical history. Scores were developed for drinking, smoking, drinking & smoking, and PMOD.

Results

All four scores were the lowest in the control group. The lung cancer group showed the highest Smoking, Alcohol & Smoking and Lesions score, while the liver cirrhosis group had the Alcohol score the highest. Compared with the control group, lung cancer group is more likely to develop a PMOD than the liver cirrhosis group (OR = 12.31/OR = 6.71). Statistical significance between the groups was found in the Lesions score (χ2 = 15.34; P = 0.001).

Conclusions

The patients with lung cancer and liver cirrhosis represent a high‐risk group for PMOD. Patients with lung cancer and liver cirrhosis have never, to our knowledge, been categorized as high‐risk patients for PMOD. After diagnosed, patients with lung cancer and liver cirrhosis should have a routine oral cavity examination, as they present a high‐risk group for PMOD and oral cancer.
‘To me, it's like a little box of tricks’: Breaking the depressive interlock as a programme participant in mindfulness‐based cognitive therapy
Authors: Murphy Helen , Lahtinen Marika
Published: September 2014

Objectives

Mindfulness meditation practices have become increasingly popular in clinical therapies, changing patterns of depressogenic thinking for individuals who experience consecutive episodes of depression. We were interested in finding out how mindfulness‐based cognitive therapy (MBCT) worked for programme participants by focussing on how meditative practices changed their relationships with their thoughts.

Design

Data for the study came from six semi‐structured research interviews carried out with individuals who had taken part in an 8‐week MBCT programme.

Methods

We used interpretative phenomenological analysis to analyse the experiential accounts.

Results

We report on two superordinate themes – Engaging the Neutral Mind (with subordinate themes ‘breaking the paralysis of worry’ and ‘choosing to think differently’) and Experiencing the Neutral Mind (with subordinate themes of ‘reflection on previous thinking styles’ and ‘becoming psychologically self‐reliant’).

Conclusions

Themes from the present study offer support to the assertion that mindfulness meditation helps facilitate a different mode of meta‐cognitive processing with which to handle depression‐related cognitions.

Practitioner points

Participants reported that they experienced an enhanced capacity to differentiate between their thought processes, experiencing an ability to tolerate some more uncomfortable thoughts, and experiencing a/more choice in how to respond to thoughts.

Participants recognized that ruminating over negative thoughts was related to depressive states and experienced a shift in meta‐cognitive processes that actively challenged depressogenic cognitions.

Participants became more psychologically self‐reliant and therapeutically independent following MBCT.

Integrating mindfulness‐based practices in therapy may be a mediating factor in sustaining psychological well‐being and may help clients develop self‐compassion.

Future research looks to examining exit cases to understand elements of MBCT which are experienced as less successful by clients.
Health‐related quality of life in pediatric intestinal transplantation
Authors: Andres A. M. , Alameda A. , Mayoral O. , Hernandez F. , Dominguez E. , Martinez Ojinaga E. , Ramos E. , Prieto G. , Lopez Santamaría M. , Tovar J. A.
Published: September 2014

To determine HRQOL after pediatric intestinal transplantation. Thirty‐four IT survivors from 1999 to 2012 were asked to complete age‐specific HRQOL non‐disease‐specific questionnaires: TAPQOL (0–4 yr), KINDL‐R (5–7 yr; 8–12 yr; 13–17 yr), and SF‐36v2 (>18 yr), all validated with Spanish population. Primary caregiver completed a SF‐36 questionnaire and CBI. Thirty‐one participants were included. Median age was 10.2 yr (1–29) and time after transplant 4.4 yr (0–13). Overall patient scores were 78.2 ± 10.6 (n = 8), 83.3 ± 9.7 (n = 6), 72.2 ± 9.21 (n = 6), 80.5 ± 12.4 (n = 7), and 82.2 ± 12.4 (n = 4) for each age group. Highest scores were obtained for vitality (group I), self‐esteem (group IV), and physical and social functioning and emotions (group V). Lowest scores were obtained in appetite and behavior (I), family and school (III), and chronic disease perception (III, IV). No significant differences were found between caregivers and their children. CBI showed stress in 52%. SF‐36 for caregivers was lower than general population. No significant differences were found depending on relevant clinical and sociodemographic data. HRQOL was acceptable and improved with age and time since transplantation. Parents had a slighter own QOL and worse perception of health than their children. When successful, intestinal transplantation allows a normal life in most patients and can be offered as an attractive option.
Disease Mongering in Direct‐to‐Consumer Advertising and the Expansion of the Antidepressant Market
Authors: Arney Jennifer , Menjivar Cecilia
Published: September 2014

The recent trend toward health care consumerism is largely the product of market practices, which have instilled the notion of health care as a product to be purchased by informed, empowered consumers, rather than a service bestowed upon a patient by a paternalistic provider. In recent years, health care consumerism has been facilitated by direct‐to‐consumer advertising (DTCA) of pharmaceutical products. In this paper, we use the case ofDTCAfor antidepressant medications to examine medicalization techniques used to promote consumerism and establish and expand the antidepressant market. We used content analysis ofDTCAfrom the 1997–2006 issues of a broad sample of women's, men's, and common readership magazines to identify techniques of medicalization, and we analyzed in‐depth interviews with magazine readers and antidepressant users to examine how such messages are received. Findings are presented within a framework of economic sociology, which allowed us to unveil the links between emotions and social action that undergird responses to medicalization techniques and consumption of advertised products.
Network Governance and Programme Steering – Rationales and Tensions in Planning Child and Youth Policies
Authors: Määttä Mirja , Eriksson Kai
Published: September 2014

This article examines the underlying rationales and tensions of network governance and programme steering in policy planning processes by closely examining their practical implementation in the national and municipal child and youth welfare planning. It is asserted that a fundamental gap exists not only between the ideals and actual practices of networked planning, but also (despite being seen as forming a natural alliance) between network governance and programme steering. This gap is mainly because the former emphasizes governmental openness, whereas the latter tends to be connected to administrative centralization and control. In order to be successful, the article concludes, both need elements of political exclusion albeit for different reasons.
A cross‐sectional study of tetanus and diphtheria antibody concentrations post vaccination among lung transplant patients compared with healthy individuals
Authors: Rohde K.A. , Cunningham K.C. , Henriquez K.M. , Nielsen A.R. , Worzella S.L. , Hayney M.S.
Published: September 2014

Background

Lung transplant (LuTx) patients are routinely immunized against tetanus and diphtheria. However, few studies have been done to measure serologic immunity in the transplant population.

Objectives

The primary objective of this study was to compare tetanus and diphtheria antibody concentrations in LuTx vs. healthy subjects.

Methods

Serum was used from an available sample of 111 total individuals (n = 36 healthy;n = 75 LuTx). Tetanus and diphtheria antibody concentrations were measured using an enzyme‐linked immunosorbant assay method.

Results

A statistically significant difference in both tetanus and diphtheria antibody concentrations was found between the groups. The median concentration of tetanus antibody was higher for healthy individuals compared with the LuTx group (3.2 IU/mL [1.2–5.2 interquartile range {IQR}] vs. 1.3 IU/mL [0.4–2.6IQR], respectively;P = 0.0001). No difference in time was found since the last tetanus‐diphtheria vaccine or tetanus‐diphtheria‐pertussis vaccine dose between the groups (healthy 76.5 months [16–114IQR] vs. LuTx 74.5 months [45–118IQR];P = 0.44).

Conclusions

Tetanus and diphtheria immunizations are recommended for LuTx patients to reduce the risk of infection. Because the LuTx group has lower antibody concentrations, further studies should investigate the possible need for more frequent tetanus and diphtheria boosters.
Production of human monoclonal anti‐Jk3, recognising an epitope including the Jka/Jkb polymorphic site of the Kidd glycoprotein
Authors: Toyoda C. , Suzuki Y. , Tsuneyama H. , Onodera T. , Masuno A. , Yabe R. , Ogasawara K. , Okuda M. , Nakajima K. , Uchikawa M.
Published: September 2014

Background and objectives

The Kidd blood group system consists of polymorphic antigens, Jka (JK1) and Jkb (JK2), and a high‐incidence antigen, Jk3. Anti‐Jk3 is often observed in immunised Jk(a−b−) individuals. In this study, we aimed to establish a human hybridoma cell line secreting monoclonal anti‐Jk3 (HIRO‐294).

Materials and methods

Peripheral blood lymphocytes of a Filipino woman with the Jk(a−b−) phenotype having anti‐Jk3 were transformed with Epstein‐Barr virus and then hybridised with the myeloma cell line JMS‐3 using the polyethylene glycol (PEG) method. The reactivity and specificity of the anti‐Jk3 were examined by serology and flow cytometry.

Results

Four hybridoma clones secreting anti‐Jk3 were established and the antibody from one of these clones, HIRO‐294, was examined. The reactivity of HIRO‐294 was positive with 227 Jk(a+b−) red blood cells (RBCs), 298 Jk(a−b+) RBCs, and 1043 Jk(a+b+) RBCs, but was negative with 21 Jk(a−b−) RBCs. Eluates from Jk(a+b−) RBCs and Jk(a−b+) RBCs sensitised with the anti‐Jk3 were cross‐reacted with Jk(a−b+) RBCs and Jk(a+b−) RBCs, respectively. The reactivity of HIRO‐294 was enhanced by the treatment of RBCs with ficin, trypsin, pronase and α‐chymotrypsin, but was not changed by their treatment with neuraminidase, dithiothreitol and ethylenediaminetetraacetic acid (EDTA) glycine acid (GA). The RBCs sensitised by the anti‐Jk3 were not agglutinated with the commercial reagents of anti‐Jka and anti‐Jkb by saline test, whereas the nonsensitised RBCs or those sensitised by monoclonal anti‐D [HIRO‐3, immunoglobulin G (IgG) class] were agglutinated with those reagents.

Conclusions

We established a human hybridoma cell line secreting monoclonal anti‐Jk3 (HIRO‐294). This antibody had unique specificity, recognising the Kidd glycoprotein including the Jka/Jkb polymorphic site.
Young but not relatively old retrotransposons are preferentially located in gene‐rich euchromatic regions in tomato (Solanum lycopersicum) plants
Authors: Xu Yingxiu , Du Jianchang
Published: September 2014

Long terminal repeat (LTR) retrotransposons are the major DNA components of flowering plants. They are generally enriched in pericentromeric heterochromatin regions of their host genomes, which could result from the preferential insertion of LTR retrotransposons and the low effectiveness of purifying selection in these regions. To estimate the relative importance of the actions of these two factors on their distribution pattern, the LTR retrotransposons in Solanum lycopersicum (tomato) plants were characterized at the genome level, and then the distribution of young elements was compared with that of relatively old elements. The current data show that old elements are mainly located in recombination‐suppressed heterochromatin regions, and that young elements are preferentially located in the gene‐rich euchromatic regions. Further analysis showed a negative correlation between the insertion time of LTR retrotransposons and the recombination rate. The data also showed there to be more solo LTRs in genic regions than in intergenic regions or in regions close to genes. These observations indicate that, unlike in many other plant genomes, the current LTR retrotransposons in tomatoes have a tendency to be preferentially located into euchromatic regions, probably caused by their severe suppression of activities in heterochromatic regions. These elements are apt to be maintained in heterochromatin regions, probably as a consequence of the pericentromeric effect in tomatoes. These results also indicate that local recombination rates and intensities of purifying selection in different genomic regions are largely responsible for structural variation and non‐random distribution of LTR retrotransposons in tomato plants.
Comparative expression profiling reveals gene functions in female meiosis and gametophyte development in Arabidopsis
Authors: Zhao Lihua , He Jiangman , Cai Hanyang , Lin Haiyan , Li Yanqiang , Liu Renyi , Yang Zhenbiao , Qin Yuan
Published: September 2014

Megasporogenesis is essential for female fertility, and requires the accomplishment of meiosis and the formation of functional megaspores. The inaccessibility and low abundance of female meiocytes make it particularly difficult to elucidate the molecular basis underlying megasporogenesis. We used high‐throughput tag‐sequencing analysis to identify genes expressed in female meiocytes (FMs) by comparing gene expression profiles from wild‐type ovules undergoing megasporogenesis with those from the spl mutant ovules, which lack megasporogenesis. A total of 862 genes were identified as FMs, with levels that are consistently reduced in spl ovules in two biological replicates. Fluorescence‐assisted cell sorting followed by RNA‐seq analysis of DMC1:GFP‐labeled female meiocytes confirmed that 90% of the FMs are indeed detected in the female meiocyte protoplast profiling. We performed reverse genetic analysis of 120 candidate genes and identified four FM genes with a function in female meiosis progression in Arabidopsis. We further revealed that KLU, a putative cytochrome P450 monooxygenase, is involved in chromosome pairing during female meiosis, most likely by affecting the normal expression pattern of DMC1 in ovules during female meiosis. Our studies provide valuable information for functional genomic analyses of plant germline development as well as insights into meiosis.
Comparison of two platelet transfusion strategies to minimize ABO‐nonidentical transfusion, outdating, and shortages using a computer‐simulated “virtual blood bank”
Authors: Jackups Ronald , Kymes Steven
Published: September 2014

Background

Transfusion of ABO‐incompatible platelets (PLTs) is associated with reduced PLT recovery and a risk of transfusion reactions. However, a policy of transfusing only ABO‐identical PLTs may increase wastage due to product outdating. A prospective study attempting to compare the effects of different ABO compatibility strategies could be costly and disruptive to a blood bank's operations.

Study Design and Methods

We designed a “virtual blood bank,” a stochastic computer program that models the stocking and release of products to meet demand for PLT transfusion in a simulated hospital population. ABO‐nonidentical transfusions (ABOni), outdates, and inventory shortages were recorded and compared under two different transfusion strategies: ABO‐First, a strategy that prioritizes transfusion of ABO‐identical PLTs, and Age‐First, a strategy that minimizes outdating by transfusing products closest to expiration.

Results

The ABO‐First strategy resulted in fewer ABOni but more outdates than the Age‐First strategy. Under conditions that mimic a large hospital blood bank, the ABO‐First strategy was more cost‐effective overall than the Age‐First strategy if avoiding an ABOni is valued at more than $19 to $26. For a small blood bank, the ABO‐First strategy was more cost‐effective if avoiding an ABOni is valued at more than $104 to $123.

Conclusion

Based on a virtual blood bank computer simulation, the cost of avoiding an ABOni using the ABO‐First strategy varies greatly by size of institution. Individual blood banks must carefully consider these management strategies to determine the most cost‐effective solution.
Science Signaling
Podcast: 2 September 2014
Authors: Michaeli Shulamit , VanHook Annalisa M.
Published: September 2014

The kinase PK3 inhibits new protein production in
Trypanosoma brucei
in response to endoplasmic reticulum stress.
TRIMs for Autophagy
Authors: VanHook Annalisa M.
Published: September 2014

TRIM5α stimulates bulk autophagy and acts as a cargo receptor for selective autophagy.
T and B Cells’ Intricate Molecular Dance
Authors: Mueller Kristen L.
Published: September 2014

Live-cell imaging in mice reveals the molecular details of B cell selection in germinal centers.
Diverse Bacterial Microcompartment Organelles
Authors: Chowdhury Chiranjit , Sinha Sharmistha , Chun Sunny , Yeates Todd O. , Bobik Thomas A.
Published: September 2014

Bacterial microcompartments (MCPs) are sophisticated protein-based organelles used to optimize metabolic pathways. They consist of metabolic enzymes encapsulated within a protein shell, which creates an ideal environment for catalysis and facilitates the channeling of toxic/volatile intermediates to downstream enzymes. The metabolic processes that require MCPs are diverse and widely distributed and play important roles in global carbon fixation and bacterial pathogenesis. The protein shells of MCPs are thought to selectively control the movement of enzyme cofactors, substrates, and products (including toxic or volatile intermediates) between the MCP interior and the cytoplasm of the cell using both passive electrostatic/steric and dynamic gated mechanisms. Evidence suggests that specialized shell proteins conduct electrons between the cytoplasm and the lumen of the MCP and/or help rebuild damaged iron-sulfur centers in the encapsulated enzymes. The MCP shell is elaborated through a family of small proteins whose structural core is known as a bacterial microcompartment (BMC) domain. BMC domain proteins oligomerize into flat, hexagonally shaped tiles, which assemble into extended protein sheets that form the facets of the shell. Shape complementarity along the edges allows different types of BMC domain proteins to form mixed sheets, while sequence variation provides functional diversification. Recent studies have also revealed targeting sequences that mediate protein encapsulation within MCPs, scaffolding proteins that organize lumen enzymes and the use of private cofactor pools (NAD/H and coenzyme A [HS-CoA]) to facilitate cofactor homeostasis. Although much remains to be learned, our growing understanding of MCPs is providing a basis for bioengineering of protein-based containers for the production of chemicals/pharmaceuticals and for use as molecular delivery vehicles.
Latent Tuberculosis Infection: Myths, Models, and Molecular Mechanisms
Authors: Dutta Noton K. , Karakousis Petros C.
Published: September 2014

The aim of this review is to present the current state of knowledge on human latent tuberculosis infection (LTBI) based on clinical studies and observations, as well as experimentalin vitroand animal models. Several key terms are defined, including “latency,” “persistence,” “dormancy,” and “antibiotic tolerance.” Dogmas prevalent in the field are critically examined based on available clinical and experimental data, including the long-held beliefs that infection is either latent or active, that LTBI represents a small population of nonreplicating, “dormant” bacilli, and that caseous granulomas are the haven for LTBI. The role of host factors, such as CD4+and CD8+T cells, T regulatory cells, tumor necrosis factor alpha (TNF-α), and gamma interferon (IFN-γ), in controlling TB infection is discussed. We also highlight microbial regulatory and metabolic pathways implicated in bacillary growth restriction and antibiotic tolerance under various physiologically relevant conditions. Finally, we pose several clinically important questions, which remain unanswered and will serve to stimulate future research on LTBI.
Systems Biology Perspectives on Minimal and Simpler Cells
Authors: Xavier Joana C. , Patil Kiran Raosaheb , Rocha Isabel
Published: September 2014

The concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. This broad concept encompasses extreme reductions of genomes, the last universal common ancestor (LUCA), the creation of semiartificial cells, and the design of protocells and chassis cells. Here we review these different areas of research and identify common and complementary aspects of each one. We focus on systems biology, a discipline that is greatly facilitating the classical top-down and bottom-up approaches toward minimal cells. In addition, we also review the so-called middle-out approach and its contributions to the field with mathematical and computational models. Owing to the advances in genomics technologies, much of the work in this area has been centered on minimal genomes, or rather minimal gene sets, required to sustain life. Nevertheless, a fundamental expansion has been taking place in the last few years wherein the minimal gene set is viewed as a backbone of a more complex system. Complementing genomics, progress is being made in understanding the system-wide properties at the levels of the transcriptome, proteome, and metabolome. Network modeling approaches are enabling the integration of these different omics data sets toward an understanding of the complex molecular pathways connecting genotype to phenotype. We review key concepts central to the mapping and modeling of this complexity, which is at the heart of research on minimal cells. Finally, we discuss the distinction between minimizing the number of cellular components and minimizing cellular complexity, toward an improved understanding and utilization of minimal and simpler cells.
Bilateral pneumothoraces in a patient with laryngeal carcinoma following tracheostomy for stridor
Authors: Lodhia Joshil Vinod , Ismail Iyad , Christensen Thomas D
Published: September 2014

A pneumothorax following a tracheostomy is a known but rare complication. Bilateral pneumothoraces are rarer still and very few are described in the literature. We present a case of bilateral pneumothoraces following an emergency tracheostomy in a female patient with known laryngeal carcinoma. She was managed with bilateral intercostal chest drains (ICDs) with good result. Anatomical integrity of the oesophagus was confirmed using barium swallow. Prior to removal of the drains a CT scan of the thorax was performed that showed disease progression and led to a change in the initial curative plan. We emphasise the importance in early diagnosis of this complication with a low index of suspicion. We suggest regular monitoring and a low threshold for treatment with bilateral ICDs.
Clinical handovers between prehospital and hospital staff: literature review
Authors: Wood Kate , Crouch Robert , Rowland Emma , Pope Catherine
Published: September 2014

Background

Clinical handover plays a vital role in patient care and has been investigated in hospital settings, but less attention has been paid to the interface between prehospital and hospital settings. This paper reviews the published research on these handovers.

Methods

A computerised literature search was conducted for papers published between 2000 and 2013 using combinations of terms: ‘handover’, ‘handoff’, ‘prehospital’, ‘ambulance’, ‘paramedic’ and ‘emergency’ and citation searching. Papers were assessed and included if determined to be at least moderate quality with a primary focus on prehospital to hospital handover.

Findings

401 studies were identified, of which 21 met our inclusion criteria. These revealed concerns about communication and information transfer, and themes concerning context, environment and interprofessional relationships. It is clear that handover exchanges are complicated by chaotic and noisy environments, lack of time and resources. Poor communication is linked to behaviours such as not listening, mistrust and misunderstandings between staff. While standardisation is offered as a solution, notably in terms of the use of mnemonics (alphabetical memory aids), evidence for benefit appears inconclusive.

Conclusions

This review raises concerns about handovers at the interface between prehospital and hospital settings. The quality of existing research in this area is relatively poor and further high-quality research is required to understand this important part of emergency care. We need to understand the complexity of handover better to grasp the challenges of context and interprofessional relationships before we reach for tools and techniques to standardise part of the handover process.
Non-adenomatous forms of gastro-oesophageal epithelial dysplasia: an under-recognised entity?
Authors: Serra Stefano , Chetty Runjan
Published: September 2014

Foveolar dysplasia is an uncommon form of dysplasia that is encountered in the stomach and oesophagus in the context of Barrett's oesophagus. Glands displaying foveolar dysplasia also show architectural abnormalities that are similar to those encountered in adenomatous dysplasia. However, from a cytological point of view, foveolar dysplasia glands are lined by low-cuboidal to columnar epithelium, the cytoplasm is often clear with round-to-oval nuclei. Nuclear stratification as seen in adenomatous dysplasia is not common, although there is loss of nuclear polarity, pleomorphism and mitotic activity. It is important to distinguish low-grade foveolar dysplasia from regenerative change.
Astragalusmembranaceusmodulates Th1/2 immune balance and activates PPARγ in a murine asthma model
Authors: Chen Shih-Ming , Tsai Yau-Sheng , Lee Su-Wen , Liu Ya-Hui , Liao Shuen-Kuei , Chang Wen-Wei , Tsai Pei-Jane
Published: September 2014

Astragalus membranaceus, a traditional Chinese herb, has been used to improve airway inflammation and asthma. The present study investigated whether A. membranaceus has immunotherapeutic effects on asthma, a chronic inflammatory mucosal disease that is associated with excess production of IgE, eosinophilia, T helper 2 (Th2) cytokines, and bronchial hyperresponsiveness. An ovalbumin (OVA)-induced, chronic inflammatory airway murine asthma model was used to examine the status of pulmonary inflammation after the administration of A. membranaceus. The IgE levels in serum and bronchoalveolar lavage fluid showed a tendency to decrease after the administration of A. membranaceus. The number of eosinophils decreased and infiltration of inflammatory cells and collagen deposition declined in lung sections after A. membranaceus administration. The RNA and protein levels of Th2 cytokines and the ratio of the GATA3/T-bet mRNA levels decreased after A. membranaceus treatment. Furthermore, the mRNA level of peroxisome proliferator-activated receptor γ (PPARγ), a nuclear hormone receptor, increased in the lung tissues of A. membranaceus–treated mice. Finally, an A. membranaceus water extract activated PPARγ activity in either human embryonic kidney 293 (HEK293) or A549 cells in a PPARγ-responsive element-containing luciferase reporter assay. These results indicate that A. membranaceus has an inhibitory effect on airway inflammation in a murine model of asthma through modulating the imbalanced relationship between Th1 and Th2 cytokines.
Validation of a model to predict fish passage mortality in pumping stations
Authors: van Esch B.P.M. , Spierts I.L.Y.
Published: September 2014

A total of 1253 live cyprinids and eel were exposed to a centrifugal pump to study fish damage rates in a wide operating range. The observed types of injuries were consistent with a mechanical cause of damage. The measured mortality rates for cyprinids show a fair agreement with a blade strike model based on empirical data by Electric Power Research Institute. Analysis of the experiments with eel led to a new correlation for the blade mortality ratio for this species; lethal injury rate is shown to be zero up to a strike velocity of 8 m·s–1 and increases linearly to 42% for a strike velocity of 15 m·s–1. Use was made of video recordings that provided valuable information on the orientation and distribution of fish approaching the impeller. Results are presented using a new method to visualize fish mortality from a pump in its entire operating range using graphs of pressure head versus flow rate. The theory of pump hydrodynamics is used to derive a method to scale results of fish damage rate, obtained either by a model or by experiments, to different pump sizes, shaft speeds, or fish lengths. This will prove essential for a valid interpretation of pump experiments with fish.
Linking individual size and wild and hatchery ancestry to survival and predation risk of threatened steelhead (Oncorhynchus mykiss)
Authors: Osterback Ann-Marie K. , Frechette Danielle M. , Hayes Sean A. , Bond Morgan H. , Shaffer Scott A. , Moore Jonathan W.
Published: September 2014

We examined the role of individual size and origin (wild versus hatchery) to predation risk and marine survival for threatened juvenile steelhead (Oncorhynchus mykiss) in a coastal California watershed. In this study, we found that individual size and origin were strongly associated with increased predation risk of steelhead by a generalist avian predator (western gull, Larus occidentalis) and associated with survival to reproduction by tracking the fate of juvenile steelhead tagged with passive integrated transponder (PIT) tags. Across six cohorts (2005–2010), larger steelhead (>170 mm fork length (FL)) experienced marine survival rates at least 60 times higher than the smallest individuals. Predation risk by western gulls was highest for intermediate-sized fish (145–190 mm FL), which was at least ten times higher than the predation risk of the smallest individuals and four times higher than the predation risk of the largest individuals. Wild steelhead experienced both higher predation risk and higher survival rates than hatchery fish of the same size. Although gulls disproportionately remove intermediate-sized wild steelhead from the population, they also remove large wild individuals that may otherwise experience the highest adult return rates. Instead of focusing on population size alone, conservation measures could also be guided towards the recovery of larger and wild individuals, whose survival is paramount for population recovery.