bluuebunny/crossref_metadata_2025 huggingface dataset:
Habitat persistence for sedentary organisms in managed rivers: the case for the federally endangered dwarf wedgemussel (Alasmidonta heterodon) in the Delaware River
Authors: MALONEY KELLY O. , LELLIS WILLIAM A. , BENNETT RANDY M. , WADDLE TERRY J.
Published: April 2012

1. To manage the environmental flow requirements of sedentary taxa, such as mussels and aquatic insects with fixed retreats, we need a measure of habitat availability over a variety of flows (i.e. a measure of persistent habitat). Habitat suitability measures in current environmental flow assessments are measured on a ‘flow by flow’ basis and thus are not appropriate for these taxa. Here, we present a novel measure of persistent habitat suitability for the dwarf wedgemussel (Alasmidonta heterodon), listed as federally endangered in the U.S.A., in three reaches of the Delaware River.

2. We used a two‐dimensional hydrodynamic model to quantify suitable habitat over a range of flows based on modelled depth, velocity, Froude number, shear velocity and shear stress at three scales (individual mussel, mussel bed and reach). Baseline potentially persistent habitat was quantified as the sum of pixels that met all thresholds identified for these variables for flows ≥40 m3 s−1, and we calculated the loss of persistently suitable habitat by sequentially summing suitable habitat estimates at lower flows. We estimated the proportion of mussel beds exposed at each flow and the amount of change in the size of the mussel bed for one reach.

3. For two reaches, mussel beds occupied areas with lower velocity, shear velocity, shear stress and Froude number than the reach average at all flows. In the third reach, this was true only at higher flows. Together, these results indicate that beds were possible refuge areas from the effects of these hydrological parameters. Two reaches showed an increase in the amount of exposed mussel beds with decreasing flow.

4. Baseline potentially persistent habitat was less than half the areal extent of potentially suitable habitat, and it decreased with decreasing flow. Actually identified beds and modelled persistent habitat showed good spatial overlap, but identified beds occupied only a portion of the total modelled persistent habitat, indicating either that additional suitable habitat is available or the need to improve habitat criteria. At one site, persistent beds (beds where mussels were routinely collected) were located at sites with stable substratum, whereas marginal beds (beds where mussels were infrequently collected or that were lost following a large flood event) were located in scoured areas.

5. Taken together, these model results support a multifaceted approach, which incorporates the effects of low and high flow stressors, to quantify habitat suitability for mussels and other sedentary taxa. Models of persistent habitat can provide a more holistic environmental flow assessment of rivers.
Seasonal and spatial hydrological variability drives aquatic biodiversity in a flood‐pulsed, sub‐tropical wetland
Authors: DAVIDSON THOMAS A. , MACKAY ANSON W. , WOLSKI PIOTR , MAZEBEDI RICHARD , MURRAY‐HUDSON MIKE , TODD MARTIN
Published: April 2012

1. Flood‐pulsed wetlands make vital contributions to local and global biodiversity. However, the patterns and controls of spatial and temporal variation in aquatic biodiversity in flood‐pulsed wetlands are not well understood. We analysed the relationship between variation in hydrological regime and the patterns of aquatic biodiversity in a large pristine flood‐pulsed wetland, the Okavango Delta, Botswana.

2. Surveys of water chemistry, diatoms and macroinvertebrates were conducted over the seasonal phases of the flood pulse. Hydrological variables of flood frequency and hydroperiod class were collated from 16 years of satellite images. Multivariate regression trees and generalised least squares regression were used to determine the chief controls of community composition and taxon richness.

3. Hydroperiod class, phase of the flood and conductivity explained 32% and 43% of the variation in diatom and invertebrate taxon richness, respectively. There was a negative relationship between hydroperiod class and invertebrate taxon richness on the rising, peak and receding flood, whereas at low flood there was no significant relationship. Multivariate regression tree analysis revealed hydroperiod class, phase of the flood and conductivity as the dominant forces shaping invertebrate and diatom community composition.

4. Seasonal and spatial variation in hydrological conditions are the principal drivers of variation in aquatic biodiversity in flood‐pulsed wetlands. In pristine flood‐pulsed wetlands, increased productivity caused by the arrival of the flood waters appears to override disturbance and connectivity in shaping taxon richness and community composition. Thus, these data suggest that the maintenance of a rich mosaic of habitats covering a broad range of hydroperiod is the key to preserving aquatic biodiversity and natural ecosystem function in flood‐pulsed wetlands.
Improvement of bixin extraction yield and extraction quality from annatto seed by modification and combination of different extraction methods
Authors: Van Chuyen Hoang , Hoi Nguyen Thi Ngoc , Eun Jong‐Bang
Published: April 2012

Bixin from annatto seed was extracted by submerging the seeds in acetone and by combined extractions using sodium hydroxide and soybean oil in the dark to improve extraction yield and reduce content of volatile compounds in annatto extracts. The exclusion of light from acetone extraction did not significantly improve bixin extraction yield (68.5%) compared to the process carried out under daylight (67.3%), but it remarkably reduced contents of toluene and m‐xylene in annatto extracts. Combined extraction using sodium hydroxide solution at 50 °C for 40 min and soybean oil at 100 °C for 20 min resulted in very low level of volatile compounds. Significantly higher extraction yield (53.7%) could be achieved by such a process as compared to a single extraction sodium hydroxide (31.8%) or soybean oil (42.9%) alone. In conclusion, the exclusion of light from acetone extraction and combined extraction significantly reduced concentration of undesirable volatile compounds. The combined extraction significantly improved bixin yield compared to the original extraction methods.
Characterisation of physical, chemical and antimicrobial properties of allicin–chitosan complexes
Authors: Pirak Tantawan , Jangchud Anuvat , Jantawat Pantipa
Published: April 2012

Formation of allicin (freshly used after prepared from fresh garlic cloves) and chitosan (78%DD with 1100 kDa, and 88%DD and 1020 kDa) complexes were conducted under the optimum conditions. After complete complexation (pH 4.5–4.8, 4 °C, and 48 h), the optimum weight ratio was resulted (1:1). The highest yield after freeze drying was 64.98%. The light yellow complexes (L* 81.0–87.3, a* 0.4–2.2 and b* 16.8–21.2) can be dissolved in wide pH range (3–11). Scanning electron micrographs revealed the round shape complexes with diameter between 5 and 15 μm. The FT‐IR analysis showed the main functional groups, including alkyl group, alkyl group‐hydroxy or possibly amino substituent, hydroxyl or amino compound, and aliphatic alcohol with carbonyl substitution. XRD results showed that the complex crystalinity was amorphous. The clear zone results and MIC (mg mL−1) revealed that allicin–chitosan complexes exhibited the antibacterial activity against spoilage bacteria indicated the possibility to use as antimicrobial agent in foods.
How to define ‘best practice’ for use in Knowledge Translation research: a practical, stepped and interactive process
Authors: Bosch Marije , Tavender Emma , Bragge Peter , Gruen Russell , Green Sally
Published: April 2012

Objectives  Defining ‘best practice’ is one of the first and crucial steps in any Knowledge Translation (KT) research project. Without a sound understanding of what exactly should happen in practice, it is impossible to measure the extent of existing gaps between ‘desired’ and ‘actual’ care, set implementation goals, and monitor performance. The aim of this paper is to present a practical, stepped and interactive process to develop best practice recommendations that are actionable, locally applicable and in line with the best available research‐based evidence, with a view to adapt these into process measures (quality indicators) for KT research purposes.

Methods  Our process encompasses the following steps: (1) identify current, high‐quality clinical practice guidelines (CPGs) and extract recommendations; (2) select strong recommendations in key clinical management areas; (3) update evidence and create evidence overviews; (4) discuss evidence and produce agreed ‘evidence statements’; (5) discuss the relevance of the evidence with local stakeholders; and (6) develop locally applicable actionable best practice recommendations, suitable for use as the basis of quality indicators.

Conclusions  Actionable definitions of local best practice are a prerequisite for doing KT research. As substantial resources go into rigorously synthesizing evidence and developing CPGs, it is important to make best use of such available resources. We developed a process for efficiently developing locally applicable actionable best practice recommendations from existing high‐quality CPGs that are in line with current research evidence.
The impact of the National Denture Service on oral health‐related quality of life among poor elders
Authors: HA J. E. , HEO Y. J. , JIN B. H. , PAIK D. I. , BAE K. H.
Published: April 2012

Summary  The objective of this study was to assess the effects of the Korean National Denture Service (NDS) for poor elderly people requiring dentures on oral health‐related quality of life (OHRQOL). Data from follow‐up studies were collected from 439 subjects at eight public health centres who answered every question of a questionnaire, and the OHRQOL was measured at the baseline and at 3‐month follow‐up after receiving the NDS according to the type of denture provision. The multivariate linear mixed model with a public health centre as a random effect for the score change of Oral Health Impact Profile (OHIP)‐14K was carried out to confirm the factors related to the improvement in OHRQOL. The mean OHIP‐14K was 28·60 at the baseline time points, and there was a decrease in the OHIP‐14 scores to 21·14 ± 12·52 at the 3‐month follow‐up of the removable partial denture beneficiaries. The changes in OHIP‐14K among complete denture beneficiaries were 21·53 ± 12·01 for previously dentate subjects and 22·54 ± 11·12 for edentate subjects. The multivariate linear mixed model of dentate subjects demonstrated that the improvement in the OHRQOL was associated with the number of remaining teeth, satisfaction with denture and self‐reported oral health status after 3 months. In the case of the edentate model, satisfaction with denture was the only factor related to the improvement in OHRQOL. This study revealed considerable improvement in OHRQOL among poor elderly people after NDS. Satisfaction with provision of dentures was associated with improvement in the OHRQOL.
Rehabilitation of occlusion – science or art?
Authors: KOYANO K. , TSUKIYAMA Y. , KUWATSURU R.
Published: April 2012

Summary  The primary objective of rehabilitating occlusion is to improve stomatognathic function in patients experiencing dysfunction in mastication, speech, and swallowing as a consequence of tooth loss. The procedure of occlusal treatment involves improving the morphology and the stomatognathic function. Several practical methods and morphological endpoints have been described in occlusal rehabilitation. We made a selection of these (mandibular position, occlusal plane, occlusal guidance, occlusal contact, face‐bow transfer, use of an adjustable articulator and occlusal support) and performed a literature review to verify the existence of compelling scientific evidence for each of these. A literature search was conducted using Medline/PubMed in March 2011. Over 400 abstracts were reviewed, and more than 50 manuscripts selected. An additional hand search was also conducted. Of the many studies investigating stomatognathic function in relation to specific occlusal schemes, most studies were poorly designed and of low quality, thus yielding ambiguous results. Overall, there is no scientific evidence that supports any specific occlusal scheme being superior to others in terms of improving stomatognathic function, nor that sophisticated methods are superior to simpler ones in terms of clinical outcomes. However, it is obvious that the art of occlusal rehabilitation requires accurate, reproducible, easy and quick procedures to reduce unnecessary technical failures and/or the requirement for compensatory adjustments. Therefore, despite the lack of scientific evidence for specific treatments, the acquisition of these general skills by dentists and attaining profound knowledge and skills in postgraduate training will be necessary for specialists in charge of complicated cases.
The future of environmental DNA in ecology
Authors: YOCCOZ NIGEL G.
Published: April 2012

The contributions of environmental DNA to ecology are reviewed, focusing on diet, trophic interactions, species distributions and biodiversity assessment. Environmental DNA has the potential to dramatically improve quantitative studies in these fields. Achieving this, however, will require large investments of time and money into developing the relevant databases, models, and software.
New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems
Authors: EPP LAURA S. , BOESSENKOOL SANNE , BELLEMAIN EVA P. , HAILE JAMES , ESPOSITO ALFONSO , RIAZ TIAYYBA , ERSÉUS CHRISTER , GUSAROV VLADIMIR I. , EDWARDS MARY E. , JOHNSEN ARILD , STENØIEN HANS K. , HASSEL KRISTIAN , KAUSERUD HÅVARD , YOCCOZ NIGEL G. , BRÅTHEN KARI ANNE , WILLERSLEV ESKE , TABERLET PIERRE , COISSAC ERIC , BROCHMANN CHRISTIAN
Published: April 2012

Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds. The ability of these metabarcodes to amplify the target groups was systematically evaluated by (i) in silico PCRs using all standard sequences in the EMBL public database as templates, (ii) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway and (iii) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late‐Pleistocene age (∼16 000–50 000 years bp) from two Siberian sites, Duvanny Yar and Main River. Comparison of the results from the in silico PCR with those obtained in vitro showed that the in silico approach offered a reliable estimate of the suitability of a marker. All target groups were detected in the environmental DNA, but we found large variation in the level of detection among the groups and between modern and ancient samples. Success rates for the Pleistocene samples were highest for fungal DNA, whereas bryophyte, beetle and bird sequences could also be retrieved, but to a much lesser degree. The metabarcoding approach has considerable potential for biodiversity screening of modern samples and also as a palaeoecological tool.
Next‐generation sequencing technologies for environmental DNA research
Authors: SHOKRALLA SHADI , SPALL JENNIFER L. , GIBSON JOEL F. , HAJIBABAEI MEHRDAD
Published: April 2012

Since 2005, advances in next‐generation sequencing technologies have revolutionized biological science. The analysis of environmental DNA through the use of specific gene markers such as species‐specific DNA barcodes has been a key application of next‐generation sequencing technologies in ecological and environmental research. Access to parallel, massive amounts of sequencing data, as well as subsequent improvements in read length and throughput of different sequencing platforms, is leading to a better representation of sample diversity at a reasonable cost. New technologies are being developed rapidly and have the potential to dramatically accelerate ecological and environmental research. The fast pace of development and improvements in next‐generation sequencing technologies can reflect on broader and more robust applications in environmental DNA research. Here, we review the advantages and limitations of current next‐generation sequencing technologies in regard to their application for environmental DNA analysis.
Bioinformatic challenges for DNA metabarcoding of plants and animals
Authors: COISSAC ERIC , RIAZ TIAYYBA , PUILLANDRE NICOLAS
Published: April 2012

Almost all empirical studies in ecology have to identify the species involved in the ecological process under examination. DNA metabarcoding, which couples the principles of DNA barcoding with next generation sequencing technology, provides an opportunity to easily produce large amounts of data on biodiversity. Microbiologists have long used metabarcoding approaches, but use of this technique in the assessment of biodiversity in plant and animal communities is under‐explored. Despite its relationship with DNA barcoding, several unique features of DNA metabarcoding justify the development of specific data analysis methodologies. In this review, we describe the bioinformatics tools available for DNA metabarcoding of plants and animals, and we revisit others developed for DNA barcoding or microbial metabarcoding. We also discuss the principles and associated tools for evaluating and comparing DNA barcodes in the context of DNA metabarcoding, for designing new custom‐made barcodes adapted to specific ecological question, for dealing with PCR and sequencing errors, and for inferring taxonomical data from sequences.
Postglacial colonization of Europe by the barbastelle bat: agreement between molecular data and past predictive modelling
Authors: REBELO HUGO , FROUFE ELSA , BRITO JOSÉ C. , RUSSO DANILO , CISTRONE LUCA , FERRAND NUNO , JONES GARETH
Published: April 2012

The barbastelle (Barbastella barbastellus) is a rare forest bat with a wide distribution in Europe. Here, we combine results from the analysis of two mtDNA fragments with species distribution modelling to determine glacial refugia and postglacial colonization routes. We also investigated whether niche conservatism occurs in this species. Glacial refugia were identified in the three southern European peninsulas: Iberia, Italy and the Balkans. These latter two refugia played a major role in the postglacial colonization process, with their populations expanding to England and central Europe, respectively. Palaeo‐distribution models predicted that suitable climatic conditions existed in the inferred refugia during the last glacial maximum (LGM). Nevertheless, the overlap between the current and the LGM distributions was almost inexistent in Italy and in the Balkans, meaning that B. barbastellus populations were forced to shift range between glacial and interglacial periods, a process that probably caused some local extinctions. In contrast, Iberian populations showed a ‘refugia within refugium’ pattern, with two unconnected areas containing stable populations (populations that subsisted during both glacial and interglacial phases). Moreover, the match between LGM models and the refugial areas determined by molecular analysis supported the hypothesis of niche conservatism in B. barbastellus. We argue that geographic patterns of genetic structuring, altogether with the modelling results, indicate the existence of four management units for conservation: Morocco, Iberia, Italy and UK, and Balkans and central Europe. In addition, all countries sampled possessed unique gene pools, thus stressing the need for the conservation of local populations.
Large‐scale study of the interactions between proteins involved in type IV pilus biology in Neisseria meningitidis: characterization of a subcomplex involved in pilus assembly
Authors: Georgiadou Michaella , Castagnini Marta , Karimova Gouzel , Ladant Daniel , Pelicic Vladimir
Published: April 2012

The functionally versatile type IV pili (Tfp) are one of the most widespread virulence factors in bacteria. However, despite generating much research interest for decades, the molecular mechanisms underpinning the various aspects of Tfp biology remain poorly understood, mainly because of the complexity of the system. In the human pathogen Neisseria meningitidis for example, 23 proteins are dedicated to Tfp biology, 15 of which are essential for pilus biogenesis. One of the important gaps in our knowledge concerns the topology of this multiprotein machinery. Here we have used a bacterial two‐hybrid system to identify and quantify the interactions between 11 Pil proteins from N. meningitidis. We identified 20 different binary interactions, many of which are novel. This represents the most complex interaction network between Pil proteins reported to date and indicates, among other things, that PilE, PilM, PilN and PilO, which are involved in pilus assembly, indeed interact. We focused our efforts on this subset of proteins and used a battery of assays to determine the membrane topology of PilN and PilO, map the interaction domains between PilE, PilM, PilN and PilO, and show that a widely conserved N‐terminal motif in PilN is essential for both PilM–PilN interactions and pilus assembly. Finally, we show that PilP (another protein involved in pilus assembly) forms a complex with PilM, PilN and PilO. Taken together, these findings have numerous implications for understanding Tfp biology and provide a useful blueprint for future studies.
Genotyping of HPA‐1 to ‐7 and ‐15 in the Thai population using multiplex PCR
Authors: Kengkate M. , Butthep P. , Kupatawintu P. , Kanunthong S. , Chantratita W. , Nathalang O.
Published: April 2012

Background: Different polymerase chain reaction (PCR) techniques for human platelet antigens (HPA) genotyping have been implemented, in order to diagnose the clinical syndromes of patients with thrombocytopaenia and provide effective HPA‐matched platelet donors.

Objectives: The aim of this study is to develop an in‐house multiplex PCR for HPA‐1 to ‐7 and ‐15 genotyping in the Thai population.

Methods: One hundred DNA samples of known HPA genotyping by the PCR with sequence‐specific primers (PCR‐SSP), as previously described, were tested with the multiplex PCR. Additionally, 300 DNA samples of group O donors were tested for HPA‐1 to ‐7 and ‐15 genotyping using multiplex PCR.

Results: The comparison of HPA‐1 to ‐7 and ‐15 genotype results between multiplex PCR and PCR‐SSP technique was in 100% concordance. Interestingly, HPA‐2b2b genotype was found in two samples; however, other low‐incidence genotypes such as HPA‐1b1b, HPA‐5b5b, HPA‐6b6b and HPA‐7b7b were not found in this study. Moreover, 30 samples were randomly tested twice for HPA genotyping using the multiplex PCR and demonstrated reproducible results.

Conclusions: This study shows that the in‐house multiplex PCR is simple, cost‐effective and suitable for HPA genotyping for routine laboratories in other developing countries. Nevertheless, a large‐scale evaluation of this technique through multicentre analysis is suggested.
Community participation and voice mechanisms under performance‐based financing schemes in Burundi
Authors: Falisse Jean‐Benoît , Meessen Bruno , Ndayishimiye Juvénal , Bossuyt Michel
Published: April 2012

Objective  Community participation is often described as a key for primary health care in low‐income countries. Recent performance‐based financing (PBF) initiatives have renewed the interest in this strategy by questioning the accountability of those in charge at the health centre (HC) level. We analyse the place of two downward accountability mechanisms in a PBF scheme: health committees elected among the communities and community‐based organizations (CBOs) contracted as verifiers of health facilities’ performance.

Method  We evaluated 100 health committees and 79 CBOs using original data collected in six Burundi provinces (2009–2010) and a framework based on the literature on community participation in health and New Institutional Economics.

Results  Health committees appear to be rather ineffective, focusing on supporting the medical staff and not on representing the population. CBOs do convey information about the concerns of the population to the health authorities; yet, they represent only a few users and lack the ability to force changes. PBF does not automatically imply more ‘voice’ from the population, but introduces an interesting complement to health committees with CBOs. However, important efforts remain necessary to make both mechanisms work. More experiments and analysis are needed to develop truly efficient ‘downward’ mechanisms of accountability at the HC level.
A novel HLA‐A*31 allele, A*31:57, identified by sequence‐based typing
Authors: Lim A. H. , Song S. N. , Lee J. Y. , Cho N. S. , Kwon S. Y.
Published: April 2012

The novel allele A*31:57 allele showed a single nucleotide difference with A*31:01:02 at nt 235 G>C in exon 2.
Full‐length coding sequences of the two novel HLA‐C alleles, C*14:36 and C*01:02:15
Authors: Lee K. W.
Published: April 2012

Full‐length coding sequences of C*14:36 and C*01:02:15 differ from C*14:02:01 and C*01:02:01 by one nucleotide in exons 3 and 4, respectively.
Identification of a novel HLA‐A*23 variant allele, A*23:50
Authors: Ferriola D. , Heron S. , Lind C. , Monos D. S.
Published: April 2012

HLA‐A*23:50 differs from HLA‐A*23:01:01 by one nucleotide at position 112 resulting in an amino acid change, Arginine to Tryptophan, at codon 14 of exon 2.
Genotypes and haplotypes in the 3′ untranslated region of the HLA‐G gene and their association with clinical outcome of hematopoietic stem cell transplantation for beta‐thalassemia
Authors: Sizzano F. , Testi M. , Zito L. , Crocchiolo R. , Troiano M. , Mazzi B. , Turchiano G. , Torchio M. , Pultrone C. , Gregori S. , Chiesa R. , Gaziev J. , Sodani P. , Marktel S. , Amoroso A. , Roncarolo M. G. , Lucarelli G. , Ciceri F. , Andreani M. , Fleischhauer K.
Published: April 2012

Polymorphisms in the 3′ untranslated region (3′UTR) of HLA‐G, an important player in immunological tolerance, could be involved in post‐transcriptional expression control, and their association with different clinical immune‐related conditions including autoimmunity and transplantation is of mounting interest. Most studies have focused on a 14 base pair (bp) insertion/deletion (ins/del), while additional single‐nucleotide polymorphisms (SNPs) in the HLA‐G 3′UTR have been described but not extensively investigated for their clinical relevance. Here we have comparatively studied the association between 3′UTR haplotypes of HLA‐G, or the 14 bp ins/del, with clinical outcome of HLA‐identical sibling hematopoietic stem cell transplantation (HSCT) in 147 Middle Eastern beta‐thalassemia patients. Sequence based typing of 3′UTR HLA‐G polymorphisms in the patients and in 102 healthy Italian blood donors showed strong linkage disequilibrium between the 14 bp ins/del and five 3′UTR SNPs, which together could be arranged into eight distinct haplotypes based on expectation‐maximization studies, with four predominant haplotypes (UTRs1–4). After HSCT, we found a moderate though not significant association between the presence of UTR‐2 in double dose and protection from acute graft versus host disease (hazard ratio (HR) 0.45, 95% confidence intervals (CI): 0.14–1.45; P = 0.18), an effect that was also seen when the corresponding 14 bp ins/ins genotype was considered alone (HR 0.42, 95% CI: 0.16–1.06; P = 0.07). No association was found with rejection or survival. Taken together, our data show that there is no apparent added value of considering entire 3′UTR HLA‐G haplotypes for risk prediction after allogeneic HSCT for beta‐thalassemia.
Closing the gap: discrimination of the expression profile of HLA questionable alleles by a cytokine‐induced secretion approach using HLA‐A*32:11Q
Authors: Föll D. , Hinrichs J. , Tischer S. , Battermann A. , Schambach A. , Figueiredo C. , Immenschuh S. , Blasczyk R. , Eiz‐Vesper B.
Published: April 2012

Matching of human leukocyte antigen (HLA) alleles between donors and recipients plays a major role in hematopoietic stem cell transplantation (HSCT). Null or questionably expressed HLA allelic variants are a major issue in HLA matching, because the aberrant expression of such alleles can have a major impact on the outcome of HSCT and/or its complications such as graft‐versus‐host disease. The goal of this study was to investigate the potential of a recently developed cytokine‐induced secretion assay to differentiate the expression levels of HLA‐A*32:11Q (questionable) into a null (N) or low (L) expression variant. An amino acid mutation at position 164 of HLA‐A*32:11Q disrupts the disulfide bridge in the α2 domain. HLA‐A*32:11Q is not detectable by standard microlymphocytotoxicity assay. To this end, we cloned soluble HLA‐A*32:11Q and a reference allele (HLA‐A*32:01) into expression vectors and transfected/transduced HEK293 and K562 cells. Allele‐expressing K562 cells were simultaneously transfected/transduced with a β2‐microglobulin (B2M)‐encoding vector to ensure the intact HLA structure with B2M. After treatment with proinflammatory cytokines, secreted soluble HLA molecules were determined by enzyme‐linked immunosorbent assay in the supernatant and intracellular accumulation of the recombinant proteins by flow cytometry. HLA‐A*32:11Q was nearly undetectable in untreated transfectants. Cytokine treatment increased the secretion of HLA‐A*32:11Q to detectable levels and resulted in intracellular accumulation of the allele. There was no difference in mRNA transcription between the A*32 alleles. On the basis of these results, we recommend reclassification of HLA‐A*32:11Q as a low expression (L) variant.
Evidence of recombination producing allelic diversity in MHC class I Mafa‐B and ‐A alleles in cynomolgus macaques
Authors: Orysiuk D. , Lawrence J. , Prashar T. , Spangelo L. , Pilon R. , Fournier J. , Rud E. , Sandstrom P. , Plummer F. A. , Luo M.
Published: April 2012

The MHC class I‐A and ‐B genes of cynomolgus macaques are highly polymorphic. These genes encode proteins presenting peptides to CD8+ T cells to initiate adaptive immune response. Recombination events are one way the diversity of these alleles can be increased. Such events have been well characterized in humans, but have not been as well characterized in macaques. In order to identify and examine recombinations that create new alleles, it is important to analyze intron sequences. Intron sequences have been shown to be important to understand the evolutionary mechanisms involved in the generation of major histocompatibility complex (MHC) alleles and loci. Thus far, there have been relatively few intron sequences reported for MHC class I alleles in macaques, and this has hampered the understanding of MHC organization and evolution in macaques. In this study, we present evidence of a gene conversion event generating the Mafa‐B*099 allele lineage by the combination of Mafa‐B*054 and Mafa‐B*095 allele lineages. A potential recombination between the Mafa‐A3*13 and Mafa‐A4:14 lineages was also observed, but it is less clear due to lack of intron 2 sequence. This report stresses the role that recombination can play in MHC class I diversity in cynomologus macaques, and the importance of introns in identifying and analyzing such events.
Somatic mutations in the HLA genes of patients with hematological malignancy
Authors: Smith A. G. , Fan W. , Regen L. , Warnock S. , Sprague M. , Williams R. , Nisperos B. , Zhao L. P. , Loken M. R. , Hansen J. A. , Pereira S.
Published: April 2012

Somatic mutations and genomic alterations are frequent events in the clonal evolution of hematologic malignancies. Recent studies have reported copy neutral loss of heterozygosity (LOH) for the mismatched human leukocyte antigen (HLA) haplotype in patients relapsed after haploidentical hematopoietic cell transplantation (HCT) for a hematologic malignancy. Herein, we report 15 cases of somatic mutations in the HLA genes of patients with a variety of hematologic diseases, including acute myelogenous leukemia, acute lymphocytic leukemia, chronic lymphocytic leukemia, chronic myeloid leukemia, myelodysplastic syndrome, and non‐Hodgkin's lymphoma, encountered at our institute over the past decade. While two of the cases were identified in patient relapse specimens collected post‐HCT, 13 cases were found in peripheral blood specimens submitted for HLA typing prior to transplantation. Ten patients exhibited acquired LOH for all or part of one HLA haplotype. Five other cases involved somatic mutations in the nucleotide sequences of common HLA‐A or HLA‐B alleles. Since they are not systematically evaluated prior to HCT, acquired mutations in HLA genes are likely under reported. Beyond the implications for accurate HLA typing and donor selection, alternations that result in the loss of HLA expression may allow escape from immune surveillance and adversely impact transplant outcome.
Recombinant factor VIIa as last‐resort treatment of desperate haemorrhage
Authors: PALMASON R. , VIDARSSON B. , SIGVALDASON K. , INGIMARSSON J. P. , GUDBJARTSSON T. , SIGURDSSON G. H. , ONUNDARSON P. T.
Published: April 2012

Introduction

Studies are inconclusive regarding clinical outcomes after administration of recombinant activated coagulation factor VII (rFVIIa) during severe haemorrhage. The circumstances encountered during desperate haemorrhage make it difficult to include the most critically ill patients that could possibly benefit the most from such treatment into randomized controlled trials. We report our experience with rFVIIa as last‐resort treatment of desperate haemorrhage when all standard treatment has failed.

Materials and Methods

Hospital charts of all consecutive patients treated with rFVIIa for desperate non‐haemophilic bleeding over a 10‐year period at the single institution administering rFVIIa were surveyed for treatment indications, clinical outcome, transfusion need and coagulation profiles.

Results

Fifty‐five rFVIIa treatment occasions of desperate bleeding were identified in 54 patients (median age 54 years). A single rFVIIa dose was used in 86%, and haemorrhage was considered effectively contained by immediate clinical response on 81% of occasions. Overall, 38 patients (71%) survived for over 30 days. Two thromboembolic events occurred (3.6%). The 24‐h mortality in 45 rFVIIa immediate clinical responders and 10 non‐responders was 2% and 50%, respectively (P = 0.0004), and the 30‐day mortality was 25% and 60%, respectively (P = 0.05). Blood product use decreased with rFVIIa (P < 0.01) as did the prothrombin time (20.0‐13.3 s, P < 0.0001).

Conclusions

The majority of unselected consecutive patients receiving rFVIIa as last‐resort treatment for desperate haemorrhage were considered to have immediate clinical response as well as reduced transfusion requirements and correction of coagulation parameters. An immediate clinical response to rFVIIa may possibly be predictive of survival.
Improvement of the photosynthetic characteristics of transgenic wheat plants by transformation with the maize C4 phosphoenolpyruvate carboxylase gene
Authors: Hu Lin , Li Yan , Xu Weigang , Zhang Qingchen , Zhang Lei , Qi Xueli , Dong Haibin
Published: April 2012

With 7 figures and 2 tables

Attempts have been made to transform C3 crops with C4 genes to improve the photosynthetic rate of C3 plants. In our study, a full‐length cDNA for phosphoenolpyruvate carboxylase gene (pepc) was isolated from Zea mays by PCR. The pepc gene was introduced into wheat plants (Triticum aestivum) by particle bombardment transformation. The integration, transcription and expression of the pepc gene were confirmed by Southern blot, RT‐PCR and Western blot analysis. Physiological studies showed that phosphoenolpyruvate carboxylase activity in the transgenic plants was 140% higher than that of the untransformed plants. The highest rate of photosynthesis in the transgenic plants was 31.95 μmol CO2/m2/s, which was 26% greater than the rate in untransformed plants. The light saturation point and carboxylation efficiency of pepc transgenic wheat were 20% and 22.57% higher, respectively, than those of untransformed wheat. As a result, the weight of seed per spike and thousand‐grain weight were 0.23 g and 1.21 g higher than those of untransformed wheat. Our research will facilitate the further study of the function of the pepc gene in wheat plants.
Improving in vivo maize doubled haploid production efficiency through early detection of false positives
Authors: Choe Eunsoo , Carbonero Christine Hayot , Mulvaney Kelly , Rayburn A. Lane , Mumm Rita H.
Published: April 2012

With 1 figure and 2 tables

In vivo doubled haploid (DH) technology provides a means of creating new maize inbred lines relatively quickly; however, productivity is limited by false‐positive (FP) plants for haploidy and for dihaploidy, which consume resources of space and labour until detected. This work examines the potential for using stomata guard cell length measurement as a means for early detection of FP plants. We found that the true haploid and DH plants could be differentiated from FP and untreated diploid controls as early as Leaf 2 stage by stomata guard cell length measurement. Furthermore, DH plants were distinguishable from haploid and other diploid plants by the Leaf 7 growth stage. Results suggest that, when used together with screening through the anthocyanin colour marker system and flower fertility, stomata guard cell measurement is an easy, non‐destructive, early screening method that may lead to a greater efficiency in DH production systems and optimization of resource allocation for space and labour.
Evidence of the existence of a toxic form of Cylindrospermopsis raciborskii (Nostocales, Cyanobacteria) in Japan
Authors: Zarenezhad Saghar , Sano Tomoharu , Watanabe Makoto M. , Kawachi Masanobu
Published: April 2012

Cylindrospermopsis raciborskii is a common, bloom‐forming, planktonic, freshwater cyanobacterium. Toxic populations producing cylindrospermopsin can cause water‐safety problems. Although C. raciborskii is distributed worldwide, the presence of cylindrospermopsin‐producing strains of C. raciborskii was initially reported only in Australia and recently in Thailand. Here, we report the isolation of a toxic strain of C. raciborskii (ISG9) from a freshwater sample collected in Okinawa in 2008. This is the first report describing toxin expression in this species in Japan, detected from a subtropical area. The C. raciborskii species is known to produce cylindrospermopsin as a dominant toxin; however, in this new isolate, the dominant toxin expressed was deoxy‐cylindrospermopsin. The discovery of a toxic strain of C. raciborskii in southern Japan emphasizes the need for basic monitoring schemes for this species in water supplies located in the temperate regions of Japan because of its possible expansion and distribution to other geographic areas.
Prospective evaluation of the optimal number of 25‐gauge needle passes for endoscopic ultrasound‐guided fine‐needle aspiration biopsy of solid pancreatic lesions in the absence of an onsite cytopathologist
Authors: Suzuki Rei , Irisawa Atsushi , Bhutani Manoop S. , Hikichi Takuto , Takagi Tadayuki , Sato Ai , Sato Masaki , Ikeda Tsunehiko , Watanabe Ko , Nakamura Jun , Tasaki Kazuhiro , Obara Katsutoshi , Ohira Hiromasa
Published: April 2012

Introduction:  A prior study with 22‐gauge needles recommended more than seven needle passes for endoscopic ultrasound‐guided fine‐needle aspiration biopsy (EUS‐FNA) of solid pancreatic lesions (SPL) without onsite cytopathology for optimal acquisition of cytopathological diagnosis. The feasibility of this recommendation should be re‐evaluated considering the later development and popularity of 25‐gauge EUS‐FNA needles. We aimed to determine the optimal number of needle passes for cytopathological specimen acquisition with 25‐gauge needles for EUS‐FNA of SPL.

Methods:  A preliminary prospective study of 22 patients with an onsite cytopathology technician showed a sensitivity of 93.3% and a specificity of 100% with four needle passes that was not statistically different from five needle passes. Based on our preliminary study, we fixed the number of needle passes to four (Group A). As a control group, we carried out sampling in consecutive patients using 25‐gauge needles with an onsite cytopathologist (Group B). Sampling rate, diagnostic value and complications were evaluated.

Results:  We enrolled 20 patients in each group. Sampling rate was higher in Group B (20/20, 100%) than in Group A (19/20, 95%), but there was no statistical difference between them (P‐value = 0.31). In Group A, sensitivity, specificity and accuracy were 100% among 19. In Group B, sensitivity was 94.1%, specificity 100%, accuracy 95%. There were also no statistical differences between the groups. No complications were seen.

Conclusion:  Our study suggests that four needle passes using a 25‐gauge needle may be sufficient for EUS‐FNA of SPL where onsite cytology is not available.
The value of coordinated management of interacting ecosystem services
Authors: White Crow , Costello Christopher , Kendall Bruce E. , Brown Christopher J.
Published: April 2012

Ecology Letters (2012)

Coordinating decisions and actions among interacting sectors is a critical component of ecosystem‐based management, but uncertainty about coordinated management’s effects is compromising its perceived value and use. We constructed an analytical framework for explicitly calculating how coordination affects management decisions, ecosystem state and the provision of ecosystem services in relation to ecosystem dynamics and socio‐economic objectives. The central insight is that the appropriate comparison strategy to optimal coordinated management is optimal uncoordinated management, which can be identified at the game theoretic Nash equilibrium. Using this insight we can calculate coordination’s effects in relation to uncoordinated management and other reference scenarios. To illustrate how this framework can help identify ecosystem and socio‐economic conditions under which coordination is most influential and valuable, we applied it to a heuristic case study and a simulation model for the California Current Marine Ecosystem. Results indicate that coordinated management can more than double an ecosystem’s societal value, especially when sectors can effectively manipulate resources that interact strongly. However, societal gains from coordination will need to be reconciled with observations that it also leads to strategic simplification of the ecological food web, and generates both positive and negative impacts on individual sectors and non‐target species.
Environment‐dependent selection on mate choice in a natural population of birds
Authors: Robinson Matthew R. , Sander van Doorn G. , Gustafsson Lars , Qvarnström Anna
Published: April 2012

Female mate choice acts as an important evolutionary force, yet the influence of the environment on both its expression and the selective pressures acting upon it remains unknown. We found consistent heritable differences between females in their choice of mate based on ornament size during a 25‐year study of a population of collared flycatchers. However, the fitness consequences of mate choice were dependent on environmental conditions experienced whilst breeding. Females breeding with highly ornamented males experienced high relative fitness during dry summer conditions, but low relative fitness during wetter years. Our results imply that sexual selection within a population can be highly variable and dependent upon the prevailing weather conditions experienced by individuals.
Does increasing mortality change the response of fish populations to environmental fluctuations?
Authors: Rouyer Tristan , Sadykov Alexander , Ohlberger Jan , Stenseth Nils Chr.
Published: April 2012

Ecology Letters (2012) 15: 658–665

Fluctuations of fish populations abundances are shaped by the interplay between population dynamics and the stochastic forcing of the environment. Age‐structured populations behave as a filter of the environment. This filter is characterised by the species‐specific life cycle and life‐history traits. An increased mortality of mature individuals alters these characteristics and may therefore induce changes in the variability of populations. The response of a generic age‐structured model was analysed to investigate the expected changes in the fluctuations of fish populations in response to decreased adult survival. These expectations were then tested on an extensive dataset. In accordance with theory, the analyses revealed that decreased adult survival and mean age of spawners were linked to an increase in the relative importance of short‐term fluctuations. It suggests that intensive exploitation can lead to a change in the variability of fish populations, an issue of central interest from both conservation and management perspectives.
WHAT DOES RESPECT FOR THE PATIENT'S AUTONOMY REQUIRE?
Authors: CHENG KAM‐YUEN
Published: April 2012

Personal autonomy presupposes the notion of rationality. What is not so clear is whether, and how, a compromise of rationality to various degrees will diminish a person's autonomy. In bioethical literature, three major types of threat to the rationality of a patient's medical decision are identified: insufficient information, irrational beliefs/desires, and influence of different framing effects. To overcome the first problem, it is suggested that patients be provided with information about their diseases and treatment choices according to the objective standard. I shall explain how this should be finessed. Regarding the negative impact of irrational beliefs/desires, some philosophers have argued that holding irrational beliefs can still be an expression of autonomy. I reject this argument because the degree of autonomy of a decision depends on the degree of rationality of the beliefs or desires on which the decision is based. Hence, to promote patient autonomy, we need to eliminate irrational beliefs by the provision of evidence and good arguments. Finally, I argue that the way to smooth out the framing effects is to present the same information in different perspectives: it is too often assumed that medical information can always be given in a complete and unadorned manner. This article concludes with a cautionary note that the protection of patient autonomy requires much more time and effort than the current practice usually allows.
OPEN HOUSE? FREEDOM OF INFORMATION AND ITS IMPACT ON THE UK PARLIAMENT
Authors: HAZELL ROBERT , BOURKE GABRIELLE , WORTHY BENJAMIN
Published: April 2012

Not all parliaments are subject to Freedom of Information (FOI), and no one has studied what difference it makes to the working of a parliament. This article evaluates the impact of FOI on the UK Parliament by reference to its main objectives. It finds that FOI has made Westminster slightly more open and accountable; but it has not increased public understanding, participation, or trust. Westminster was already very open and other initiatives have helped increase participation. Trust was badly damaged by the MPs' expenses scandal, triggered by FOI requests. The House of Commons' hesitant response to those requests revealed problems of corporate governance.