bluuebunny/crossref_metadata_2025 huggingface dataset:
“So tell me what happened!”
Authors: Böser Ursula
Published: July 2013

This article investigates the impact of interpreting within the discursive frame of the free recall element in forensic interview formats. The delivery of a prompted free recall has been shown to yield evidence of a better quality than that obtained through elicited accounts; free recall, therefore, constitutes a central technique in investigative interviewing. Police institutional discourse associates specific discursive behavior and conversational resources with free recall. Drawing on experimental data, this paper analyzes several effects of interpreting on achieving and maintaining free recall. The following topics are feature in this paper: the frame transition from the interviewer-led opening section to the delivery of a free narrative; the meta-talk that arises regarding interpreting; and the segmentation of the interpreted free recall and the coordination of turn-taking. The article discusses instances of misalignment between the functional goals of free recall and the interpreting-related strategies the interviewer and the interpreter adopt. This analysis demonstrates the contextual nature of “quality” as defined in institutional face-to-face interpreting and highlights discursive expertise as a central component in the professionalization of Public Service Interpreting.
Helpful processes in psychological therapy for patients with primary cancers: A qualitative interview study
Authors: Omylinska-Thurston Joanna , Cooper Mick
Published: July 2013

Aims: The purpose of this study was to identify what patients with primary cancers found helpful in therapy. Method: In‐depth qualitative interviews were conducted with eight patients who had completed a course of psychological therapy within an NHS psychology service for cancer patients. Data were analysed using thematic analysis. Results: The participants identified a range of helpful processes in therapy: talking and expressing their feelings to someone outside of the family; forming a relationship with their therapist; normalisation through the therapists' expert knowledge; problem‐solving and CBT. Limitations: As with all qualitative studies, the small sample and size and dependence on participant recall limits generalisability of the findings. Implications: The findings of this study are consistent with a pluralistic perspective: that multiple therapeutic processes ‐ aligned to a range of different orientations ‐ can be of value to patients with primary cancers. This supports the provision of a range of therapeutic interventions and strategies for this patient group.
The TAL1 complex targets the FBXW7 tumor suppressor by activating miR-223 in human T cell acute lymphoblastic leukemia
Authors: Mansour Marc R. , Sanda Takaomi , Lawton Lee N. , Li Xiaoyu , Kreslavsky Taras , Novina Carl D. , Brand Marjorie , Gutierrez Alejandro , Kelliher Michelle A. , Jamieson Catriona H.M. , von Boehmer Harald , Young Richard A. , Look A. Thomas
Published: July 2013

The oncogenic transcription factor TAL1/SCL is aberrantly expressed in 60% of cases of human T cell acute lymphoblastic leukemia (T-ALL) and initiates T-ALL in mouse models. By performing global microRNA (miRNA) expression profiling after depletion of TAL1, together with genome-wide analysis of TAL1 occupancy by chromatin immunoprecipitation coupled to massively parallel DNA sequencing, we identified the miRNA genes directly controlled by TAL1 and its regulatory partners HEB, E2A, LMO1/2, GATA3, and RUNX1. The most dynamically regulated miRNA was miR-223, which is bound at its promoter and up-regulated by the TAL1 complex. miR-223 expression mirrors TAL1 levels during thymic development, with high expression in early thymocytes and marked down-regulation after the double-negative-2 stage of maturation. We demonstrate that aberrant miR-223 up-regulation by TAL1 is important for optimal growth of TAL1-positive T-ALL cells and that sustained expression of miR-223 partially rescues T-ALL cells after TAL1 knockdown. Overexpression of miR-223 also leads to marked down-regulation of FBXW7 protein expression, whereas knockdown of TAL1 leads to up-regulation of FBXW7 protein levels, with a marked reduction of its substrates MYC, MYB, NOTCH1, and CYCLIN E. We conclude that TAL1-mediated up-regulation of miR-223 promotes the malignant phenotype in T-ALL through repression of the FBXW7 tumor suppressor.
Immune history shapes specificity of pandemic H1N1 influenza antibody responses
Authors: Li Yang , Myers Jaclyn L. , Bostick David L. , Sullivan Colleen B. , Madara Jonathan , Linderman Susanne L. , Liu Qin , Carter Donald M. , Wrammert Jens , Esposito Susanna , Principi Nicola , Plotkin Joshua B. , Ross Ted M. , Ahmed Rafi , Wilson Patrick C. , Hensley Scott E.
Published: July 2013

Human antibody responses against the 2009 pandemic H1N1 (pH1N1) virus are predominantly directed against conserved epitopes in the stalk and receptor-binding domain of the hemagglutinin (HA) protein. This is in stark contrast to pH1N1 antibody responses generated in ferrets, which are focused on the variable Sa antigenic site of HA. Here, we show that most humans born between 1983 and 1996 elicited pH1N1 antibody responses that are directed against an epitope near the HA receptor–binding domain. Importantly, most individuals born before 1983 or after 1996 did not elicit pH1N1 antibodies to this HA epitope. The HAs of most seasonal H1N1 (sH1N1) viruses that circulated between 1983 and 1996 possess a critical K133 amino acid in this HA epitope, whereas this amino acid is either mutated or deleted in most sH1N1 viruses circulating before 1983 or after 1996. We sequentially infected ferrets with a 1991 sH1N1 virus and then a pH1N1 virus. Sera isolated from these animals were directed against the HA epitope involving amino acid K133. These data suggest that the specificity of pH1N1 antibody responses can be shifted to epitopes near the HA receptor–binding domain after sequential infections with sH1N1 and pH1N1 viruses that share homology in this region.
Domain IV voltage-sensor movement is both sufficient and rate limiting for fast inactivation in sodium channels
Authors: Capes Deborah L. , Goldschen-Ohm Marcel P. , Arcisio-Miranda Manoel , Bezanilla Francisco , Chanda Baron
Published: July 2013

Voltage-gated sodium channels are critical for the generation and propagation of electrical signals in most excitable cells. Activation of Na+ channels initiates an action potential, and fast inactivation facilitates repolarization of the membrane by the outward K+ current. Fast inactivation is also the main determinant of the refractory period between successive electrical impulses. Although the voltage sensor of domain IV (DIV) has been implicated in fast inactivation, it remains unclear whether the activation of DIV alone is sufficient for fast inactivation to occur. Here, we functionally neutralize each specific voltage sensor by mutating several critical arginines in the S4 segment to glutamines. We assess the individual role of each voltage-sensing domain in the voltage dependence and kinetics of fast inactivation upon its specific inhibition. We show that movement of the DIV voltage sensor is the rate-limiting step for both development and recovery from fast inactivation. Our data suggest that activation of the DIV voltage sensor alone is sufficient for fast inactivation to occur, and that activation of DIV before channel opening is the molecular mechanism for closed-state inactivation. We propose a kinetic model of sodium channel gating that can account for our major findings over a wide voltage range by postulating that DIV movement is both necessary and sufficient for fast inactivation.
Incidence Trends in Pathogen-Specific Central Line–Associated Bloodstream Infections in US Intensive Care Units, 1990–2010
Authors: Fagan Ryan P. , Edwards Jonathan R. , Park Benjamin J. , Fridkin Scott K. , Magill Shelley S.
Published: July 2013

Objective.

To quantify historical trends in rates of central line-associated bloodstream infections (CLABSIs) in US intensive care units (ICUs) caused by major pathogen groups, includingCandidaspp.,Enterococcusspp., specified gram-negative rods, andStaphylococcus aureus.

Design.

Active surveillance in a cohort of participating ICUs through the Centers for Disease Control and Prevention, the National Nosocomial Infections Surveillance system during 1990–2004, and the National Healthcare Safety Network during 2006–2010.

Setting.

ICUS.

Participants.

Patients who were admitted to participating ICUs.

Results.

The CLABSI incidence density rate forS. aureusdecreased annually starting in 2002 and remained lower than for other pathogen groups. Since 2006, the annual decrease forS. aureusCLABSIs in nonpediatric ICU types was −18.3% (95% confidence interval [CI], −20.8% to −15.8%), whereas the incidence density rate forS. aureusamong pediatric ICUs did not change. The annual decrease for all ICUs combined since 2006 was −17.8% (95% CI, −19.4% to −16.1%) forEnterococcusspp., −16.4% (95% CI, −18.2% to −14.7%) for gram-negative rods, and −13.5% (95% CI, −15.4% to −11.5%) forCandidaspp.

Conclusions.

Patterns of ICU CLABSI incidence density rates among major pathogen groups have changed considerably during recent decades. CLABSI incidence declined steeply since 2006, except for CLABSI due toS. aureusin pediatric ICUs. There is a need to better understand CLABSIs that still do occur, on the basis of microbiological and patient characteristics. New prevention approaches may be needed in addition to central line insertion and maintenance practices.
RACER: Rapid and accurate correction of errors in reads
Authors: Ilie Lucian , Molnar Michael
Published: July 2013

Motivation: High-throughput next-generation sequencing technologies enable increasingly fast and affordable sequencing of genomes and transcriptomes, with a broad range of applications. The quality of the sequencing data is crucial for all applications. A significant portion of the data produced contains errors, and ever more efficient error correction programs are needed.

Results: We propose RACER (Rapid and Accurate Correction of Errors in Reads), a new software program for correcting errors in sequencing data. RACER has better error-correcting performance than existing programs, is faster and requires less memory. To support our claims, we performed extensive comparison with the existing leading programs on a variety of real datasets.

Availability: RACER is freely available for non-commercial use at www.csd.uwo.ca/∼ilie/RACER/.

Contact:  ilie@csd.uwo.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
Leaf Surface Colonization of Sugarcane byXanthomonas albilineansand Subsequent Disease Progress Vary According to the Host Cultivar
Authors: Daugrois Jean Heinrich , Boisne-Noc Rosiane , Rott Philippe
Published: July 2013

Spread of leaf scald in modern sugarcane cultivars in Guadeloupe occurs through aerial dissemination of Xanthomonas albilineans. However, the importance of host genotype on the foliar spread of leaf scald has never been investigated. To explore this, we followed two trials used to screen sugarcane cultivars for resistance to leaf scald under natural inoculum pressure. Leaf scald epidemic characteristics were studied by measuring epiphytic populations of X. albilineans, leaf symptom incidence and severity, and the number of infected stalks. In both trials, epiphytic X. albilineans populations and incidence of foliar symptoms varied between sugarcane cultivars (P < 0.001 in each trial for both traits) and differences in stalk infection between cultivars was also observed (P < 0.002 and P < 0.07 for trials A and B, respectively). Part of the cultivar resistance that minimizes epiphytic bacterial populations is correlated to resistance to internal leaf tissue infection as expressed by leaf symptoms. No correlation was found between epiphytic X. albilineans populations of cultivar and the incidence of stalk infection. However, foliar symptom incidence was inconsistently correlated with stalk infection. Resistance of sugarcane to leaf scald appears to involve several traits, including limiting size of epiphytic X. albilineans populations and limiting the capacity of the pathogen to produce leaf necrotic symptoms by invading the leaf vascular system or to move from the leaf into the stalk.
Susceptibility of Cultivated and WildVitisspp. to Wood Infection by Fungal Trunk Pathogens
Authors: Travadon Renaud , Rolshausen Philippe E. , Gubler Walter D. , Cadle-Davidson Lance , Baumgartner Kendra
Published: July 2013

Cultivars of European grapevine, Vitis vinifera, show varying levels of susceptibility to Eutypa dieback and Esca, in terms of foliar symptoms. However, little is known regarding cultivar susceptibility of their woody tissues to canker formation. Accordingly, we evaluated the relative susceptibility of V. vinifera cultivars (‘Cabernet Franc’, ‘Cabernet Sauvignon’, ‘Chardonnay’, ‘Merlot’, ‘Riesling’, ‘Petite Syrah’, and ‘Thompson Seedless’) and species or interspecific hybrids of North American Vitis (Vitis hybrid ‘Concord’, V. arizonica ‘b42-26’, V. rupestris × V. cinerea ‘Ill547-1’, and Fennell 6 [V. aestivalis] × Malaga [V. vinifera] ‘DVIT0166’) to canker formation by seven trunk pathogens (Neofusicoccum parvum, Lasiodiplodia theobromae, Phaeomoniella chlamydospora, Togninia minima, Phomopsis viticola, Eutypa lata, and an undescribed Eutypa sp.). Susceptibility was based on the length of wood discoloration (LWD) in the woody stems of rooted plants in duplicate greenhouse experiments. Cultivars of V. vinifera and Concord did not vary significantly in susceptibility to N. parvum or L. theobromae (LWD of 21 to 88 mm at 14 weeks post inoculation; P > 0.16), suggesting that they are similarly susceptible to Botryosphaeria dieback. The table-grape Thompson Seedless was most susceptible to P. viticola (mean LWD of 61 mm at 11 months post inoculation; P < 0.0001). V. vinifera cultivars and Concord showed similar susceptibility to the Esca pathogens, Phaeomoniella chlamydospora and T. minima. Susceptibility to E. lata was greatest in V. arizonica b42-26 (mean LWD of 96 mm at 11 months post inoculation; P < 0.03). In fact, all four American Vitis spp. were more susceptible to Eutypa dieback than the V. vinifera cultivars. Our findings suggest that no one cultivar is likely to provide resistance to the range of trunk pathogens but that certain cultivars may be promising candidates for commercially relevant host resistance in grape-production systems where the dominant cultivars are very susceptible.
First Report of Rice yellow mottle virus on Rice in the Democratic Republic of Congo
Authors: Hubert J. G. , Pinel-Galzi A. , Dibwe D. , Cinyabuguma E. , Kaboré A. , Fargette D. , Silué D. , Hébrard E. , Séré Y.
Published: July 2013

Rice yellow mottle virus (RYMV), genus Sobemovirus, is a widespread rice pathogen reported in nearly all rice-growing countries of Africa. Although the virus was detected in Cameroon, Chad, Tanzania, Rwanda, Burundi, and Uganda (2,3), RYMV has never been described in the Democratic Republic of Congo (DRC). In July 2012, plants with leaf yellowing and mottling symptoms were observed in large irrigated rice production schemes 30 km south of Bukavu, in eastern DRC, and in lowland subsistence fields in the surroundings of Bukavu. Several dozen hectares affected by the disease were abandoned by the farmers. Symptomatic leaf samples were collected in different farmer fields. Back-inoculations to susceptible rice variety IR64 resulted in the same yellowing and mottling symptoms 7 to 9 days post-inoculation. Infected leaves gave positive results using double antibody sandwich (DAS)-ELISA tests with polyclonal antisera (as described in [1]), indicating for the first time the presence of RYMV in DRC. Triple antibody sandwich (TAS)-ELISA tests with discriminant monoclonal antibodies (1) revealed that they all belong to serotype 4 found in the neighboring region in Rwanda. Total RNA of three samples from South Kivu was extracted with the RNeasy Plant Mini kit (Qiagen, Germany). The 720 nucleotide coat protein (CP) gene was amplified by reverse transcription (RT)-PCR with primers 5′CTCCCCCACCCATCCCGAGAATT3′ and 5′CAAAGATGGCCAGGAA3′ (1). The sequences were deposited in GenBank (Accessions KC788208, KC788209, and KC788210). A set of CP sequences of 45 isolates representative of the RYMV diversity in Africa, including the sequences of the DRC samples, were used for phylogenetic reconstruction by maximum-likelihood method. The isolates from South Kivu belonged to strain S4-lv, mainly found around Lake Victoria. Specifically, within the S4-lv strain, the South Kivu isolates clustered with isolates from eastern and southern provinces of Rwanda and Burundi, respectively (2), suggesting a recent spread from these countries. Recently, efforts have been directed to shift from the traditional upland system to lowland and irrigated systems in which water availability allows sequential planting and maintenance of higher crop intensity. This agricultural change may increase insect vectors and alternate host plant populations which may result in higher RYMV incidence in DRC (3). Similar yellowing and mottling symptoms have been observed in Bas-Congo and Equateur provinces of the country, which would justify further surveys and characterisation of RYMV in the DRC.

References: (1) D. Fargette et al. Arch. Virol. 147:583, 2002. (2) I. Ndikumana et al. Plant Dis. 96:1230, 2012. (3) O. Traoré et al. Mol. Ecol. 14:2097, 2005.
Effect of Operator Experience and Frequency of Procedure Performance on Complication Rate After Ultrasound‐Guided Percutaneous Liver Biopsies
Authors: Westheim Birgitte H. , Aagenæs Ingegerd , Østensen Anniken B. , Sanengen Truls , Almaas Runar
Published: July 2013

Objective:

The aim of the present study was to assess whether the complication rate after ultrasound‐guided percutaneous liver biopsies in children is affected by how frequently the procedure is performed by the operator.

Methods:

Medical charts and ultrasound descriptions of 311 ultrasound‐guided percutaneous liver biopsy procedures performed by 18 radiologists at a single center from 2000 to 2011 were reviewed. Postbiopsy ultrasound the following day was performed after 97% of the procedures.

Results:

There were no differences in the procedure‐associated rate of major bleeding incidents (2.2% vs 0.8%, P = 0.38), minor bleeding incidents (15.2% vs 10.2%, P = 0.31), or abdominal pain (13.0% vs 10.6%, P = 0.61) among operators who performed ≤10 procedures and those who performed >10 procedures during the study period. A higher rate of minor bleeding incidents were recorded after liver biopsy when operators had performed <10 biopsies compared with operators who had performed >20 pediatric liver biopsies during the study period (odds ratio 3.4 [1.3–9.1], P = 0.02). No association between the number of biopsies performed by the operator during the 2 years preceding the date of the biopsy and complications was found.

Conclusions:

Major complications are infrequent after pediatric liver biopsies and no relation between operator experience and major complications was found. We found a significant, but minor, effect of operator procedure frequency on the rate of minor bleeding incidents after ultrasound‐guided pediatric liver biopsies.
Donor Human Milk for Preterm Infants
Authors:   ESPGHAN Committee on Nutrition, Arslanoglu Sertac , Corpeleijn Willemijn , Moro Guido , Braegger Christian , Campoy Cristina , Colomb Virginie , Decsi Tamas , Domellöf Magnus , Fewtrell Mary , Hojsak Iva , Mihatsch Walter , Mølgaard Christian , Shamir Raanan , Turck Dominique , van Goudoever Johannes
Published: July 2013

The Committee on Nutrition of the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition aims to document the existing evidence of the benefits and common concerns deriving from the use of donor human milk (DHM) in preterm infants. The comment also outlines gaps in knowledge and gives recommendations for practice and suggestions for future research directions. Protection against necrotizing enterocolitis is the major clinical benefit deriving from the use of DHM when compared with formula. Limited data also suggest unfortified DHM to be associated with improved feeding tolerance and with reduced cardiovascular risk factors during adolescence. Presence of a human milk bank (HMB) does not decrease breast‐feeding rates at discharge, but decreases the use of formula during the first weeks of life. This commentary emphasizes that fresh own mother's milk (OMM) is the first choice in preterm infant feeding and strong efforts should be made to promote lactation. When OMM is not available, DHM is the recommended alternative. When neither OMM nor DHM is available, preterm formula should be used. DHM should be provided from an established HMB, which follows specific safety guidelines. Storage and processing of human milk reduces some biological components, which may diminish its health benefits. From a nutritional point of view, DHM, like HM, does not meet the requirements of preterm infants, necessitating a specific fortification regimen to optimize growth. Future research should focus on the improvement of milk processing in HMB, particularly of heat treatment; on the optimization of HM fortification; and on further evaluation of the potential clinical benefits of processed and fortified DHM.
A framework for assessing frequency domain causality in physiological time series with instantaneous effects
Authors: Faes Luca , Erla Silvia , Porta Alberto , Nollo Giandomenico
Published: July 2013

We present an approach for the quantification of directional relations in multiple time series exhibiting significant zero-lag interactions. To overcome the limitations of the traditional multivariate autoregressive (MVAR) modelling of multiple series, we introduce an extended MVAR (eMVAR) framework allowing either exclusive consideration of time-lagged effects according to the classic notion of Granger causality, or consideration of combined instantaneous and lagged effects according to an extended causality definition. The spectral representation of the eMVAR model is exploited to derive novel frequency domain causality measures that generalize to the case of instantaneous effects the known directed coherence (DC) and partial DC measures. The new measures are illustrated in theoretical examples showing that they reduce to the known measures in the absence of instantaneous causality, and describe peculiar aspects of directional interaction among multiple series when instantaneous causality is non-negligible. Then, the issue of estimating eMVAR models from time-series data is faced, proposing two approaches for model identification and discussing problems related to the underlying model assumptions. Finally, applications of the framework on cardiovascular variability series and multichannel EEG recordings are presented, showing how it allows one to highlight patterns of frequency domain causality consistent with well-interpretable physiological interaction mechanisms.
Prevalence, seasonality and severity of disease caused by pathogenic Escherichia coli in children with diarrhoea in Bolivia
Authors: Gonzales Lucia , Joffre Enrique , Rivera Rosario , Sjöling Åsa , Svennerholm Ann-Mari , Iñiguez Volga
Published: July 2013

The prevalence of infection caused by different categories of diarrhoeagenicE. coli(DEC) strains, including enteroaggregative (EAEC), enteropathogenic (EPEC), enterotoxigenic (ETEC), enteroinvasive (EIEC) and enterohaemorrhagic (EHEC)E. coli, in children who suffered from diarrhoea (n = 3943) or did not have diarrhoea (n = 1026) were analysed in two areas in Bolivia over a period of 4 years. We also analysed the seasonality of DEC infections and severity of diarrhoea in children with DEC infection and compared antibiotic resistance in DEC strains isolated from children with and without diarrhoea. Stool samples were analysed for the presence of DEC by culturing followed by PCR. The most prevalent DEC categories in samples from the children were: EAEC (11.2 %); ETEC (6.6 %); EPEC (5.8 %); and EIEC and EHEC (<1 %). DEC strains were isolated significantly more often from diarrhoea cases (21.6 %) than from controls (17.6 %;P = 0.002). The number of children with diarrhoea associated with EAEC, EPEC and ETEC infections peaked in the Bolivian winter (April–September), although the proportion of DEC-positive stool samples was higher during the warm rainy season (October–March). High levels of antibiotic resistance were detected among the DEC strains. In particular, resistance to tetracycline and sulfamethoxazole–trimethoprim was significantly higher in strains isolated from individuals with diarrhoea than in samples from controls. The severity of disease in children infected with EAEC, EPEC and ETEC varied from mild to severe diarrhoea, although disease severity did not differ significantly between the different DEC categories. ETEC, EPEC and EAEC are commonly found in Bolivia and may cause severe disease in children.
Dengue virus envelope domain III immunization elicits predominantly cross-reactive, poorly neutralizing antibodies localized to the AB loop: implications for dengue vaccine design
Authors: Li Xiao-Quan , Qiu Li-Wen , Chen Yue , Wen Kun , Cai Jian-Piao , Chen Jing , Pan Yu-Xian , Li Jie , Hu Dong-Mei , Huang Yan-Fen , Liu Li-Dong , Ding Xi-Xia , Guo Yong-hui , Che Xiao-Yan
Published: July 2013

Dengue virus (DENV) is a mosquito-borne virus that causes severe health problems. An effective tetravalent dengue vaccine candidate that can provide life-long protection simultaneously against all four DENV serotypes is highly anticipated. A better understanding of the antibody response to DENV envelope protein domain III (EDIII) may offer insights into vaccine development. Here, we identified 25 DENV cross-reactive mAbs from immunization with Pichia pastoris-expressed EDIII of a single or all four serotype(s) using a prime–boost protocol, and through pepscan analysis found that 60 % of them (15/25) specifically recognized the same highly conserved linear epitope aa 309–320 of EDIII. All 15 complex-reactive mAbs exhibited significant cross-reactivity with recombinant EDIII from all DENV serotypes and also with C6/36 cells infected with DENV-1, -2, -3 and -4. However, neutralization assays indicated that the majority of these 15 mAbs were either moderately or weakly neutralizing. Through further epitope mapping by yeast surface display, two residues in the AB loop, Q316 and H317, were discovered to be critical. Three-dimensional modelling analysis suggests that this epitope is surface exposed on EDIII but less accessible on the surface of the E protein dimer and trimer, especially on the surface of the mature virion. It is concluded that EDIII as an immunogen may elicit cross-reactive mAbs toward an epitope that is not exposed on the virion surface, therefore contributing inefficiently to the mAbs neutralization potency. Therefore, the prime–boost strategy of EDIII from a single serotype or four serotypes mainly elicited a poorly neutralizing, cross-reactive antibody response to the conserved AB loop of EDIII.
In vitro responses of neurofibroma fibroblasts, mast cells and Schwann cells obtained from patients with neurofibromatosis 1 to 308‐nm excimer light and/or vitamin D3
Authors: Nakayama Juichiro , Sato Chiemi , Imafuku Shinichi
Published: July 2013

Fibroblasts, mast cells and Schwann cells were isolated from neurofibromas of patients with neurofibromatosis 1, and their responses to 308‐nm excimer light irradiation and/or vitamin D3 or an analog (tacalcitol; 1,24‐dihydroxyvitamin D3) were examined in vitro. Excimer light irradiation (300 mJ/cm2) suppressed the growth of all three cell types. Exposure to 10−7 mol/L of 1α,25(OH)2D3 (VD3) or tacalcitol suppressed the growth of fibroblasts and mast cells, but not Schwann cells. These results suggest that the different neurofibroma cell types show different responses to VD3. A combination of excimer light irradiation and VD3 is necessary to suppress the growth of neurofibroma cells in vivo.
One size fits all: Eurasian lynx females share a common optimal litter size
Authors: Gaillard Jean‐Michel , Nilsen Erlend B. , Odden John , Andrén Henrik , Linnell John D. C.
Published: July 2013

Lack proposed that the average clutch size of altricial species should be determined by the average maximum number of young the parents can raise such that all females in a given population should share a common optimal clutch size. Support for this model remains equivocal and recent studies have suggested that intra‐population variation in clutch size is adaptive because each female has its own optimal clutch size associated with its intrinsic ability to raise offspring.

Although Lack litter size and condition‐dependent litter size are presented as two competing models, both are based on the concept of individual optimization. We propose a unified optimal litter size model (called ‘adaptive litter size’) and identify a set of conditions under which a common vs. a state‐dependent optimal litter size should be observed.

We test whether females of Eurasian lynx (Lynx lynx) have a common optimal litter size, or whether they adjust their litter size according to their state. We used a detailed individual‐based data set collected from contrasting populations of Eurasian lynx in Scandinavia.

Observed reproductive patterns in female lynx provide strong support for the existence of a common optimal litter size. Litter size did not vary according to female body mass or reproductive category, or among contrasted populations and years. A litter size of 2 was associated with a higher fitness than both smaller and larger litters, and thus corresponded to the ‘adaptive litter size’ for female lynx.

We suggest that the reproductive pattern of female lynx might correspond to a risk avoidance tactic common to all individuals, which has evolved in response to strong environmental constraints generated by a highly unpredictable food supply during lactation.
Agricultural soil and drilosphere as reservoirs of new and unusual assimilators of 2,4‐dichlorophenol carbon
Authors: Dallinger Anja , Horn Marcus A.
Published: July 2013

2,4‐Dichlorophenol (2,4‐DCP) is a potential soil and groundwater contaminant. Earthworms modulate growth and activities of soil microbiota. Thus, active 2,4‐DCP degraders in agricultural soil and drilosphere (i.e. burrow walls, gut content and cast) were identified by comparative amplicon pyrosequencing‐based 16S rRNA stable isotope probing in soil columns. In situ relevant concentrations of [U‐13C]2,4‐DCP were consumed in soil within 19 and 41 days in the presence and absence of the endogeic earthworm Aporrectodea caliginosa, respectively. [U‐14C]2,4‐DCP mineralization was higher in cast, burrow wall and soil from columns with than without earthworms. [U‐14C]2,4‐DCP mineralization was lowest in gut contents. Data indicated a strong impact of earthworms on the active microbial community. Novosphingobium, Comamonas and Desulfitobacterium sp. assimilated 2,4‐DCP‐[13C] in the absence of earthworms. Pseudomonas, Flavobacterium and Clostridium sp. assimilated 2,4‐DCP‐[13C] in the drilosphere. Novosphingobium‐ and Variovorax‐related taxa dominated [U‐13C]2,4‐DCP consumers in soil slurries with drilosphere and bulk soil material. 16S rRNA sequences suggested species level novelty. The collective data demonstrates that new Bacteroidetes and Alphaproteobacteria/Betaproteobacteria were involved in 2,4‐DCP‐C transformation and indicated that diverse and hitherto unknown microbes associated with carbon flow from 2,4‐DCP are shaped by earthworms.
A think‐aloud study of strategy use by EFL college readers reading Chinese and English texts
Authors: Lin Lu‐Chun , Yu Wan‐Yu
Published: July 2013

This study used a think‐aloud approach to compare reading strategy use in the first language (L1) and non‐native language (L2) among 36 English as a foreign language (EFL) college students at different reading levels. The participants took an English proficiency test and participated in two individual sessions in which a reading test and a think‐aloud task were administered separately in Chinese and English. Cross‐language transfer theory and the linguistic threshold hypothesis were used to conceptualise the similarities and differences in L1 and L2 reading strategies. This study found more frequent and diverse strategy use in English than in Chinese. Similar patterns of meta‐cognitive strategy use were evident in both languages. The applications of certain meta‐cognitive and support strategies served as indicators that differentiated more‐proficient from less‐proficient readers. The present study extended previous questionnaire studies and suggested that English reading instruction should be informed by this line of research to provide instruction on effective reading strategy use for EFL learners.
Making and justifying health claims
Authors: Lalor Fiona , Wall Patrick G.
Published: July 2013

The regulatory hurdles that exist to bring a functional food to market often prove the greatest challenge for the food industry. Different regulatory approaches exist worldwide, with the European Union having one of the tightest regimes of all. EU Regulation 1924/2006 sets out the framework for nutrition and health claims, and the system has been slow at approving claims. In recent years, the European Food Safety Authority has published Guidance Notes to aid industry with the application process. However, among other things, the fact that not one probiotic has received approval has left the food industry critical of the system. It is likely that an approval pattern will emerge in the future, and once the pathway to approval identified, the industry will emerge stronger and with more integrity than before.
Professional development in international schools; issues of inclusion identified by a group of international school teaching assistants
Authors: Tarry Estelle , Cox Anna
Published: July 2013

With the growth in numbers of teaching assistants (TAs) in the UK, it has been identified through research carried out on behalf of the Council of British International Schools (COBIS) research that TAs in British international schools have specific and unmet training needs. Following the development of a course for TAs in international contexts, COBIS and the University of Northampton provided a Professional Development Programme for TAs working in British international schools. The 2‐day event took place in a European city, with participants from three further European cities. The impact of this training on subsequent professional practice was investigated. An initial questionnaire was completed at the conference, and follow‐up questionnaires were distributed at 6 weeks, post‐event. Responses came from participants and from head teachers of the British international schools in which they worked. This paper focuses upon issues of inclusion, which arose from the feedback received, both during the event and afterwards. Group discussions during the event revealed concern among the group that they had insufficient knowledge to provide the level of inclusion support that they felt should be available. Data from the questionnaires provided more detail about these issues and allowed some first conclusions to be drawn, providing further focus and direction for subsequent training for international school TAs.
Generalizing Observational Study Results: Applying Propensity Score Methods to Complex Surveys
Authors: DuGoff Eva H. , Schuler Megan , Stuart Elizabeth A.
Published: July 2013

Objective

To provide a tutorial for using propensity score methods with complex survey data.

Data Sources

Simulated data and the 2008 Medical Expenditure Panel Survey.

Study Design

Using simulation, we compared the following methods for estimating the treatment effect: a naïve estimate (ignoring both survey weights and propensity scores), survey weighting, propensity score methods (nearest neighbor matching, weighting, and subclassification), and propensity score methods in combination with survey weighting. Methods are compared in terms of bias and 95 percent confidence interval coverage. In Example 2, we used these methods to estimate the effect on health care spending of having a generalist versus a specialist as a usual source of care.

Principal Findings

In general, combining a propensity score method and survey weighting is necessary to achieve unbiased treatment effect estimates that are generalizable to the original survey target population.

Conclusions

Propensity score methods are an essential tool for addressing confounding in observational studies. Ignoring survey weights may lead to results that are not generalizable to the survey target population. This paper clarifies the appropriate inferences for different propensity score methods and suggests guidelines for selecting an appropriate propensity score method based on a researcher's goal.
Comparison of molecular species identification for North Sea calanoid copepods (Crustacea) using proteome fingerprints and DNA sequences
Authors: Laakmann S. , Gerdts G. , Erler R. , Knebelsberger T. , Martínez Arbizu P. , Raupach M.J.
Published: July 2013

Calanoid copepods play an important role in the pelagic ecosystem making them subject to various taxonomic and ecological studies, as well as indicators for detecting changes in the marine habitat. For all these investigations, valid identification, mainly of sibling and cryptic species as well as early life history stages, represents a central issue. In this study, we compare species identification methods for pelagic calanoid copepod species from the North Sea and adjacent regions in a total of 333 specimens. Morphologically identified specimens were analysed on the basis of nucleotide sequences (i.e. partial mitochondrial cytochrome c oxidase subunit I (COI) and complete 18S rDNA) and on proteome fingerprints using the technology of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS). On all three molecular approaches, all specimens were classified to species level indicated by low intraspecific and high interspecific variability. Sequence divergences in both markers revealed a second Pseudocalanus species for the southern North Sea identified as Pseudocalanus moultoni by COI sequence comparisons to GenBank. Proteome fingerprints were valid for species clusters irrespective of high intraspecific variability, including significant differences between early developmental stages and adults. There was no effect of sampling region or time; thus, trophic effect, when analysing the whole organisms, was observed in species‐specific protein mass spectra, underlining the power of this tool in the application on metazoan species identification. Because of less sample preparation steps, we recommend proteomic fingerprinting using the MALDI‐TOF MS as an alternative or supplementary approach for rapid, cost‐effective species identification.
The association of pre‐operative STOP‐BANG scores with postoperative critical care admission
Authors: Chia P. , Seet E. , Macachor J. D. , Iyer U. S. , Wu D.
Published: July 2013

The STOP‐BANG questionnaire screens for obstructive sleep apnoea. We retrospectively analysed the independent association of pre‐operative variables with postoperative critical care admission using multivariable logistic regression for patients undergoing elective surgery from January to December 2011. Of 5432 patients, 338 (6.2%) were admitted postoperatively to the critical care unit. In multivariate analysis, the odds ratios (95% CI) for critical care admission were: 2.2 (1.1–4.6), p = 0.037; 3.2 (1.2–8.1), p = 0.017; and 5.1 (1.8–14.9), p = 0.002, for STOP‐BANG scores of 4, 5 and ≥ 6, respectively. The odds ratio was also independently increased for: each year of age, 1.015 (1.004–1.026), p = 0.019; asthma, 1.6 (1.1–2.4), p = 0.016; obstructive sleep apnoea, 3.2 (1.9–5.6), p < 0.001; and for ASA physical status 2, 3 and ≥ 4, 2.1 (1.4–3.3), 6.5 (3.9–11.0), 6.3 (2.9–13.8), respectively, p < 0.001 for all.
Evaluating the value and impact of the Victorian Audit of Surgical Mortality
Authors: Retegan Claudia , Russell Colin , Harris Darren , Andrianopoulos Nick , Beiles C. Barry
Published: July 2013

Introduction

Since the Victorian Audit of Surgical Mortality (VASM) commenced in 2007, 95% of Victorian Fellows have agreed to participate and have provided data on the deaths of patients receiving surgical care. All public, and the majority of private, hospitals involved in the delivery of surgical services in Victoria have been submitting data on deaths associated with surgery. De‐identified reports on this data are distributed in regular annual reports and case note review booklets. Although informal feedback on the perceived value of the audit was encouraging, a formal review of all aspects of the audit was felt necessary.

Methods

An independent formal review of VASM governance, documentation, datasets and data analysis was performed, in addition to a survey of 257 individuals (surgeons and other stakeholders) on the perceived impact of VASM.

Results

The review confirmed increasing participation and acceptance by surgeons since the inception of the project. Governance mechanisms were found to be effective and acknowledged by stakeholders and collaborators. Robust participation rates have been achieved, and stakeholders were generally satisfied with the quality of feedback. Suggestions for improvement were provided by some surgeons and hospitals.

Conclusion

External review of VASM processes and procedures confirmed that the audit was operating effectively, with robust quality control and achieving the trust of stakeholders. The educational value of the audit to the surgical community was acknowledged and areas for future improvement have been identified.
Mechanistic Analysis of Challenge–Response Experiments
Authors: Shotwell M. S. , Drake K. J. , Sidorov V. Y. , Wikswo J. P.
Published: July 2013

We present an application of mechanistic modeling and nonlinear longitudinal regression in the context of biomedical response‐to‐challenge experiments, a field where these methods are underutilized. In this type of experiment, a system is studied by imposing an experimental challenge, and then observing its response. The combination of mechanistic modeling and nonlinear longitudinal regression has brought new insight, and revealed an unexpected opportunity for optimal design. Specifically, the mechanistic aspect of our approach enables the optimal design of experimental challenge characteristics (e.g., intensity, duration). This article lays some groundwork for this approach. We consider a series of experiments wherein an isolated rabbit heart is challenged with intermittent anoxia. The heart responds to the challenge onset, and recovers when the challenge ends. The mean response is modeled by a system of differential equations that describe a candidate mechanism for cardiac response to anoxia challenge. The cardiac system behaves more variably when challenged than when at rest. Hence, observations arising from this experiment exhibit complex heteroscedasticity and sharp changes in central tendency. We present evidence that an asymptotic statistical inference strategy may fail to adequately account for statistical uncertainty. Two alternative methods are critiqued qualitatively (i.e., for utility in the current context), and quantitatively using an innovative Monte‐Carlo method. We conclude with a discussion of the exciting opportunities in optimal design of response‐to‐challenge experiments.
Allergy to illicit drugs and narcotics
Authors: Swerts S. , Van Gasse A. , Leysen J. , Faber M. , Sabato V. , Bridts C. H. , Jorens P. G. , De Clerck L. S. , Ebo D. G.
Published: July 2013

Despite their frequent use, allergy to illicit drugs and narcotics is rarely reported in literature. We present a review of the different classes of drugs of abuse that might be involved in allergies: central nervous system (CNS) depressants (such as cannabis, opioids and kava), CNS stimulants (cocaine, amphetamines, khat and ephedra) and hallucinogens such as ketamine and nutmeg. Diagnosis of drug and narcotic allergy generally relies upon careful history taking, complemented with skin testing eventually along with quantification of sIgE. However, for various reasons, correct diagnosis of most of these drug allergies is not straightforward. For example, the native plant material applied for skin testing and sIgE antibody tests might harbour irrelevant IgE‐binding structures that hamper correct diagnosis. Diagnosis might also be hampered due to uncertainties associated with the non‐specific histamine releasing characteristics of some compounds and absence of validated sIgE tests. Whether the introduction of standardized allergen components and more functional tests, that is, basophil activation and degranulation assays, might be helpful to an improved diagnosis needs to be established. It is anticipated that due to the rare character of these allergies further validation is although necessary.
Body composition assessment in overweight women: validation of air displacement plethysmography
Authors: Wingfield Hailee L. , Smith‐Ryan Abbie E. , Woessner Mary N. , Melvin Malia N. , Fultz Sarah N. , Graff Rachel M.
Published: July 2013

Purpose

The purpose of this study was to evaluate the validity and reliability of air displacement plethysmography (ADP) compared to a dual energy x‐ray absorptiometry (DXA) criterion for body composition measurement in overweight and obese women (BMI ≥ 25·0 kg m2).

Subjects/Methods

Twenty‐four overweight and obese women (Mean ± SD; Age: 36·6 ± 12·0 years; Height: 166·4 ± 5·8 cm; Weight: 86·5 ± 14·2 kg; Body Fat: 38·5 ± 3·7%; BMI: 31·3 ± 5·5 kg m2) were tested after an 8‐h fast. Fat mass (FM), fat‐free mass (FFM) and percent body fat (%BF) were measured by ADP and compared to values determined by the DXA criterion. FFM from DXA was calculated as lean mass plus bone mineral content. A paired samples t‐test was used to test for significant differences in the body composition variables between methods. A one‐way ANOVA along with intraclass correlation coefficient (ICC), SEM,%SEM and MD was used to represent reliability.

Results

Validity data comparing ADP and DXA demonstrated no significant difference in FM (ADP‐DXA FM = 0·99 kg; P = 0·113), FFM (0·98 kg; P = 0·115) and %BF (1·56%; P = 0·540). Reliability data for ADP between the first and second trials showed no significant difference in FM (P = 0·168; ICC = 0·994; SEM = 0·668), FFM (P = 0·058; ICC = 0·973; SEM = 0·892) or %BF (P = 0·121; ICC = 0·971; SEM = 0·813).

Conclusions

For overweight and obese women, ADP was found to be a valid measure of FM, FFM and %BF when compared with DXA. The reliability of ADP was supported for all body composition variables.