bluuebunny/crossref_metadata_2025 huggingface dataset:
Biological and operational determinants of the effectiveness and efficiency of biodiversity conservation programs
Authors: Laycock Helen F. , Moran Dominic , Raffaelli David G. , White Piran C. L.
Published: May 2013

Context
Comprehensive evaluation of biodiversity conservation programs is essential for informing their development as well as the design of future programs. Such evaluations should not be limited to whether targets have been met, but should also assess the cost and efficiency of meeting targets, and any factors contributing to success or failure.

Aims
We aimed to evaluate the effectiveness and efficiency of individual-species conservation programs, and the biological and operational factors affecting these. We used the species action plans (SAPs) within the UK Biodiversity Action Plan as our case study.

Methods
We used cost–effectiveness analysis, cost–utility analysis and threat-reduction assessment to evaluate the effectiveness and efficiency of individual SAPs. Then we used statistical models to investigate the relative importance of biological and operational factors affecting cost, effectiveness and efficiency.

Key results
Conservation plan success was affected by both biological and operational factors. Invertebrate plans tended to be less effective, whereas vertebrate plans were less efficient. Plans for widely distributed species with longer generation times tended to be less efficient. Of the three different evaluation approaches, cost-effectiveness analysis offered the best combination of ease of data collection and accuracy of data content.

Conclusions
The most successful SAPs concerned species with short generation times and narrow distributions. Operationally, the most successful SAPs were concise and focussed and showed clear lines of responsibility for implementation.

Implications
Techniques such as cost–effectiveness analysis, cost-utility analysis and threat reduction assessment should be used to inform decisions on maximising the rate of return on conservation investments, although broader ecological implications and socio-cultural benefits should also be considered. The success of conservation plans is influenced by both biological and operational factors. Because biological factors cannot be controlled or altered, where species exhibit characteristics that are likely to make their conservation less effective or efficient, it is critical that operational factors are optimised. High-quality data are necessary to underpin prioritisation decisions, and monitoring to deliver reliable data on both the benefits and costs of conservation should form a core component of conservation programs.
Planning impact avoidance and biodiversity offsetting using software for spatial conservation prioritisation
Authors: Moilanen Atte
Published: May 2013

Context
Impact avoidance and biodiversity offsetting are measures that can be used for alleviating environmental impacts of economic development projects. Offsetting is frequently implemented via habitat restoration. Biodiversity offsets should be designed in a cost-effective manner.

Aims
To investigate how spatial conservation prioritisation methods, most commonly used for reserve network design, could be used for informing impact avoidance and biodiversity offsetting.

Methods
Zonation is a publicly available framework and software for grid-based, large-scale, high-resolution spatial conservation prioritisation. Zonation produces a hierarchical, balanced, and complementarity-based priority ranking through the landscape, identifying areas of both highest and lowest conservation value in one analysis. It is shown how these capabilities can be utilised in the context of impact avoidance and offsetting.

Key results
Impact avoidance can be implemented by focusing environmentally harmful activity into low-priority areas of the spatial priority ranking. Offsets can be implemented via a more complicated analysis setup. First, identify development areas unavailable for conservation, which leads to a decrease in the quality of conservation value achievable in the landscape. Second, develop compensation layers that describe the difference made by allocation of extra conservation action. Running a spatial prioritisation, integrating information about where species are (representation), what areas and features are damaged (reduced condition and negative connectivity effects), and the difference made by remedial action, allows identification of areas where extra conservation effort maximally compensates for damage. Factors such as connectivity and costs can be included in this analysis. Impact avoidance and offsetting can also be combined in the procedure.

Conclusions
Spatial conservation-prioritisation methods can inform both impact avoidance and offsetting design.

Implications
Decision support tools that are commonly associated with reserve selection can be used for planning of impact avoidance and offsetting, conditional on the availability of high-quality data about the distributions of biodiversity features (e.g. species, habitat type, ecosystem services).
Ten principles for a landscape approach to reconciling agriculture, conservation, and other competing land uses
Authors: Sayer Jeffrey , Sunderland Terry , Ghazoul Jaboury , Pfund Jean-Laurent , Sheil Douglas , Meijaard Erik , Venter Michelle , Boedhihartono Agni Klintuni , Day Michael , Garcia Claude , van Oosten Cora , Buck Louise E.
Published: May 2013

“Landscape approaches” seek to provide tools and concepts for allocating and managing land to achieve social, economic, and environmental objectives in areas where agriculture, mining, and other productive land uses compete with environmental and biodiversity goals. Here we synthesize the current consensus on landscape approaches. This is based on published literature and a consensus-building process to define good practice and is validated by a survey of practitioners. We find the landscape approach has been refined in response to increasing societal concerns about environment and development tradeoffs. Notably, there has been a shift from conservation-orientated perspectives toward increasing integration of poverty alleviation goals. We provide 10 summary principles to support implementation of a landscape approach as it is currently interpreted. These principles emphasize adaptive management, stakeholder involvement, and multiple objectives. Various constraints are recognized, with institutional and governance concerns identified as the most severe obstacles to implementation. We discuss how these principles differ from more traditional sectoral and project-based approaches. Although no panacea, we see few alternatives that are likely to address landscape challenges more effectively than an approach circumscribed by the principles outlined here.
Assessment of multidrug resistance on cell coculture patterns using scanning electrochemical microscopy
Authors: Kuss Sabine , Polcari David , Geissler Matthias , Brassard Daniel , Mauzeroll Janine
Published: May 2013

The emergence of resistance to multiple unrelated chemotherapeutic drugs impedes the treatment of several cancers. Although the involvement of ATP-binding cassette transporters has long been known, there is no in situ method capable of tracking this transporter-related resistance at the single-cell level without interfering with the cell’s environment or metabolism. Here, we demonstrate that scanning electrochemical microscopy (SECM) can quantitatively and noninvasively track multidrug resistance-related protein 1–dependent multidrug resistance in patterned adenocarcinoma cervical cancer cells. Nonresistant human cancer cells and their multidrug resistant variants are arranged in a side-by-side format using a stencil-based patterning scheme, allowing for precise positioning of target cells underneath the SECM sensor. SECM measurements of the patterned cells, performed with ferrocenemethanol and [Ru(NH
3
)
6
]
3+
serving as electrochemical indicators, are used to establish a kinetic “map” of constant-height SECM scans, free of topography contributions. The concept underlying the work described herein may help evaluate the effectiveness of treatment administration strategies targeting reduced drug efflux.
Ninjurin1, a target of p53, regulates p53 expression and p53-dependent cell survival, senescence, and radiation-induced mortality
Authors: Cho Seong-Jun , Rossi Andrea , Jung Yong-Sam , Yan Wensheng , Liu Gang , Zhang Jin , Zhang Min , Chen Xinbin
Published: May 2013

The tumor suppressor protein p53 plays a crucial role in coordinating cellular processes, such as cell cycle arrest, apoptosis, and senescence. The nerve injury-induced protein 1 (Ninjurin1, Ninj1) is a homophilic adhesion molecule and involved in nerve regeneration. Interestingly, Ninj1 is found to be overexpressed in human cancer, but its role in tumorigenesis is not clear. Here, we found thatNinj1is transcriptionally regulated by p53 and can be induced by DNA damage in a p53-dependent manner. We also found that knockout or knockdown of Ninj1 increases p53 expression potentially through enhanced p53 mRNA translation. In addition, we found that Ninj1 deficiency suppresses cell proliferation but enhances apoptosis and premature senescence in a p53-dependent manner. Consistent with this, we found that mice heterozygous inninj1are hypersensitive to ionizing radiation-induced lethality, along with increased expression of p53 in thymus. Taken together, we provided evidence that Ninj1 is a p53 target and modulatesp53mRNA translation and p53-dependent premature senescence, cell proliferation, apoptosis, and radiation-induced mortality in vitro and in vivo. Thus, we postulate that as a membrane adhesion molecule, Ninj1 is an ideal target to regulate p53 activity via the p53-Ninj1 loop.
Regulation of T cell function by the ubiquitin-specific protease USP9X via modulating the Carma1-Bcl10-Malt1 complex
Authors: Park Yoon , Jin Hyung-seung , Liu Yun-Cai
Published: May 2013

The ubiquitin conjugation system plays an important role in immune regulation; however, the ubiquitin-specific proteases (USPs) that carry out deubiquitination of cellular substrates are poorly understood. Here we show that in vivo knockdown of the deubiquitinating enzyme USP9X attenuates T-cell proliferation. In addition, naïve CD4
+
T cells from USP9X knockdown chimeric mice display decreased cytokine production and T helper cell differentiation in vitro, which we confirmed in vivo by performing adoptive transfer of transgenic T cells and subsequent immunization. USP9X silencing in both a human T-cell line and mouse primary T cells reduced T-cell receptor (TCR) signaling-induced NF-κB activation. Mechanistically, USP9X interacts with Bcl10 of the Carma1-Bcl10-Malt1 (CBM) complex and removes the TCR-induced ubiquitin chain from Bcl10, which facilitates the association of Carma1 with Bcl0-Malt1. These results demonstrate that USP9X is a crucial positive regulator of the TCR signaling pathway and is required for T-cell function through the modulation of CBM complex formation.
Interplay of physics and evolution in the likely origin of protein biochemical function
Authors: Skolnick Jeffrey , Gao Mu
Published: May 2013

The intrinsic ability of protein structures to exhibit the geometric and sequence properties required for ligand binding without evolutionary selection is shown by the coincidence of the properties of pockets in native, single domain proteins with those in computationally generated, compact homopolypeptide, artificial (ART) structures. The library of native pockets is covered by a remarkably small number of representative pockets (∼400), with virtually every native pocket having a statistically significant match in the ART library, suggesting that the library is complete. When sequences are selected for ART structures based on fold stability, pocket sequence conservation is coincident to native. The fact that structurally and sequentially similar pockets occur across fold classes combined with the small number of representative pockets in native proteins implies that promiscuous interactions are inherent to proteins. Based on comparison of PDB (real, single domain protein structures found in the Protein Data Bank) and ART structures and pockets, the widespread assumption that the co-occurrence of global structure, pocket similarity, and amino acid conservation demands an evolutionary relationship between proteins is shown to significantly underestimate the random background probability. Indeed, many features of biochemical function arise from the physical properties of proteins that evolution likely fine-tunes to achieve specificity. Finally, our study suggests that a repertoire of thermodynamically (marginally) stable proteins could engage in many of the biochemical reactions needed for living systems without selection for function, a conclusion with significant implications for the origin of life.
In vitro reconstitution of lipid-dependent dual topology and postassembly topological switching of a membrane protein
Authors: Vitrac Heidi , Bogdanov Mikhail , Dowhan William
Published: May 2013

Phospholipids could exert their effect on membrane protein topology either directly by interacting with topogenic signals of newly inserted proteins or indirectly by influencing the protein assembly machinery. In vivo lactose permease (LacY) of
Escherichia coli
displays a mixture of topological conformations ranging from complete inversion of the N-terminal helical bundle to mixed topology and then to completely native topology as phosphatidylethanolamine (PE) is increased from 0% to 70% of membrane phospholipids. These topological conformers are interconvertible by postassembly synthesis or dilution of PE in vivo. To investigate whether coexistence of multiple topological conformers is dependent solely on the membrane lipid composition, we determined the topological organization of LacY in an in vitro proteoliposome system in which lipid composition can be systematically controlled before (liposomes) and after (fliposomes) reconstitution using a lipid exchange technique. Purified LacY reconstituted into preformed liposomes of increasing PE content displayed inverted topology at low PE and then a mixture of inverted and proper topologies with the latter increasing with increasing PE until all LacY adopted its native topology. Interconversion between topological conformers of LacY was observed in a PE dose-dependent manner by either increasing or decreasing PE levels in proteoliposomes postreconstitution of LacY, clearly demonstrating that membrane protein topology can be changed simply by changing membrane lipid composition independent of other cellular factors. The results provide a thermodynamic-based lipid-dependent model for shifting the equilibrium between different conformational states of a membrane protein.
Natural language change or prescriptive influence?
Authors: Anderwald Lieselotte
Published: May 2013

This paper investigates five morphological Americanisms in their diachronic development since 1810 on the basis of data from the Corpus of Historical American English, namely the past tense forms of THRIVE, DIVE, PLEAD, DRAG, and SNEAK. THRIVE is a clear case of an irregular verb becoming regular; in the other four lexemes (DIVE, PLEAD, DRAG and SNEAK), the irregular forms are actually a new development, as the corpus analysis can show. Present-day Americanisms can thus be the result of different historical processes that diverge from British English: differential speed in the same process, or change in a different direction. In both cases of change, it is a valid question to ask whether they might have been the result of prescriptive pressure. In order to investigate the question in how far prescriptive grammars may have influenced this trend towards more regular or towards newly irregular forms, my corpus-linguistic data is correlated with changing recommendations in historical grammar books of English, based on a quantitative investigation of my collection of 258 grammars. I propose that prescriptive influence both on the regularization of THRIVE and on the process of ‘irregularization’ of DIVE, PLEAD, DRAG and SNEAK is minimal, and that we are most likely dealing with genuine changes from below. These changes are then, with some time lag, reflected in the (not so) prescriptive grammars of the time.
Intelligibility and attitudes
Authors: Tan Ying-Ying , Castelli Christina
Published: May 2013

This paper investigates international responses to Singapore English (SgE), in terms of both intelligibility and attitudes toward the speaker, and compares it to responses to American English (AmE). It surveys 200 respondents from over 20 countries as they listen to a set of 15 sound recordings, including read SgE, spontaneous SgE, and read AmE. The results suggest that the intelligibility of SgE and AmE does differ between informants from different regions. However, the intelligibility of the test stimuli does not correlate simply to positive and negative attitudes. While SgE elicits generally positive attitudes, what is interesting is that the judgments of respondents from South-East Asia and East Asia are often more negative than those of English speakers of Inner Circle varieties. This seems to suggest not only an impenetrable mindset of these traditionally “non-native” English speakers, who seem to be still clamoring to speak an idealized “standard”, but also an inferiority complex over their own varieties of English.
Temporal adverbials and the present perfect/past tense alternation
Authors: Werner Valentin
Published: May 2013

Specification by certain temporal adverbials has been shown to be one of the typical triggers of the present perfect in British English. Often, however, L2 varieties display different patterns of temporal co-occurrence, especially using the simple past tense. This study is based on corpus data from twelve components of the International Corpus of English and analyzes the distribution between present perfect and past tense for a number of co-occurring temporal adverbials. In addition, it establishes three measures of similarity across the varieties (hierarchical cluster analysis, phylogenetic networks and a distribution-based measure). On the basis of 6 353 adverbials in total, this paper suggests (1) that there is a L1–L2 divide, (2) that the difference between “traditional” and “transplanted” L1 varieties is less pronounced, (3) that L2 varieties allow more variation, which indicates that in these varieties, the present perfect is partly used as a tense (sensu Quirk et al. 1985), and (4) that some temporal adverbials are less categorically attached to either present perfect or past tense than others. Finally, some conclusions with regard to the importance of geographical and socio-cultural proximity of certain varieties can be drawn.
A systemic typology of existential and possessive constructions
Authors: Wang Yong , Xu Jie
Published: May 2013

In this article, we examine locational constructions (including existentials, locatives, and possessives) in a number of languages. Morpho-syntactically, locationals resemble or are related to one another in word order, in case marking, and in the choice of verbs. In semantics, the relatedness lies in the definiteness effect, in the locative feature, and in the mutually defining relationship between the semantic elements within each construction. As is recognized by Heine (1997), Stassen (2001) and others, the existential is one of the major sources from which possessives are derived. Basically, possessive constructions are existentials whose locative elements are prototypically human. We argue that locational constructions are relational processes and that they can be integrated into a systemic network with respect to two semantic features, i.e., the definiteness of the existent element and the humanness of the locative element. This systemic relationship between locationals has implications for the description and comparison of languages within the Systemic Functional Grammar framework, particularly where locationals are concerned.
Metonymy in grammar
Authors: Park Chongwon
Published: May 2013

This article focuses on the conceptual structures of Korean Multiple Object Constructions (MOCs), which exhibit various types of meanings. I argue that these various meanings are systematically explained when we adopt the notion of reference point. I claim that the accusative-marked nominals in the constructions are metonymically connected; outer accusative-marked nominals function as reference points. More specifically, NP1, in the schematic configuration [NP-Nom [NP1-Acc [NP2-Acc [PRED]]]], functions as a reference point in relation to the complex verb [NP2-PRED], where NP1 provides access to the target. In other words, the function of Korean MOCs is to provide mental access to a target, similar to English possessive constructions. For example, since one natural mental path of access is by following a taxonomic hierarchy from general to specific, the metonymic meaning of the Type-Token construction arises. The same mechanism is then recursively applied to explain the case of multiply-occurring accusative-marked nominals. In order to provide technical analyses of my claim, Langacker’s Cognitive Grammar is adopted as a theoretical framework as it accurately captures the properties of the constructions without additional unnecessary mechanisms.
Distinguishing causative and permissive readings of the Swedish verb låta
Authors: Rawoens Gudrun , Egan Thomas
Published: May 2013

In this paper an account is given of the semantics of the Present-day Swedish verb låta ‘let’ in constructions with an infinitival complement. It is generally assumed that the verb låta in this construction type can encode either causation or permission. From a synchronic perspective, the relationship between the two meanings has been described by some scholars as inclusive, whereas others have adduced possible criteria for distinguishing between them. Using corpus data, it is shown that the two semantic categories can be disentangled by means of a number of syntactic and semantic criteria, the most important of which relates to the semantic features of the central arguments in the sequence. Other criteria have to do with the occurrence of an object in the matrix clause, the Aktionsart of the complement predicate and the various degrees of autonomy of the object. The outcome of the empirical study reveals that the two constructions constitute comparably substantial categories in Present-day Swedish.
Gender assignment and gender agreement in adult bilinguals and second language learners of French
Authors: Kupisch Tanja , Akpinar Deniz , Stöhr Antje
Published: May 2013

This paper is concerned with gender marking in adult French. Four groups of subjects are compared: German-French simultaneous bilinguals (2L1ers) who grew up in France, German-French 2L1ers who grew up in Germany, advanced second language learners (L2ers) who are resident either in France or in Germany at the time of testing. The major goal of the study is to investigate whether differences in input conditions (acquisition in a minority vs. a majority language context) and differences in age of onset affect gender assignment and gender agreement in the same way or differently. Furthermore, we investigate whether successful acquisition of gender is dependent on influence from German. Two experiments, an acceptability judgment task and an elicited production task, are carried out. Results show successful acquisition of agreement in all groups. By contrast, gender assignment may be mildly affected if French is acquired in a minority language context or as an L2.
Whose stuff is it?
Authors: Lwin Soe Marlar
Published: May 2013

In this study, I investigate how one museum storyteller engaged her audience at different stages of producing a narrative and how museum exhibits were incorporated into her narrative in the process. The analysis focuses on the interplay among various verbal, vocal and visual features emanating from the teller at different storytelling moments and the audience’s outward responses. The study extends our understanding of the ways museum storytelling can enhance the audience’s interest in the displayed artefacts as well as in the life and culture of the people associated with these artefacts.
Doing indiscipline in narrative performances
Authors: Archakis Argiris
Published: May 2013

The present paper concentrates on the narrative management of the teacher-student relationship. Focusing on students’ identities, the present study draws upon the social constructionism paradigm, thus considering identities as social constructs via discourse. The analysis of representative narrative extracts shows how students construct themselves as powerful enough to challenge teachers’ authority which is expressed in the Initiation–Response–Feedback structure. Their resistance is indicative of their will to free themselves from their teachers’ expectations, even if this can only take place during their conversations with their peers. In this context, narratives allow them to achieve interactional goals which may not always be fulfilled in class.
How do narrative and language skills relate to each other?
Authors: Kang Jennifer Yusun
Published: May 2013

Past studies on narratives have identified two main dimensions of narrative production: the story-related narrative quality, which relates to the narrative structure and evaluations, and the language-related quality, which relates to the appropriate use of linguistic devices that contribute to the overall discourse cohesion. Although studies on the language development of monolinguals and bilinguals have demonstrated the developmental nature of the two different narrative dimensions, little attention has been paid to the potential relationship between them. Thus, this study aimed to identify the interrelationship between the two main narrative quality skills and explored the role of cross-language facilitations for performance on each of these narrative dimensions. Oral Frog Story narratives produced by 70 six-year-old Korean English as a Foreign Language (EFL) learners were analyzed. The findings indicated that the two narrative sub-dimensions play facilitative roles for each other within English (L2), and that there are cross-language contributions for only the linguistic quality of narratives. The findings are discussed in relation to the bilingual children’s language proficiency and the degree of differences in narrative conventions across the two languages.
Gypsy-Traveller narratives: Making sense of place
Authors: Convery Ian , O'Brien Vincent
Published: May 2013

Using a co-ethnographic approach to focus on one person’s story, we explore how a sense of place may be evident in self constructed Gypsy-Traveller identity and narrative. Mary’s recounting of her experiences of living and growing up in the Caldewgate district of Carlisle (UK) illustrates the place of family relations as a key element of Gypsy-Traveller self identity and suggests, we believe, the centrality of family and internal relationships as a strong feature in the construction of personal notions and narratives of place for Gypsy-Traveller people.
“What we’re going to be doing”
Authors: Heinrichsmeier Rachel
Published: May 2013

A growing body of work charts and explicates the way participants in interactions constitute the context and their respective identities as ‘institutional’ through differences in a number of dimensions to ‘everyday’ talk. The role played by stories, particularly non-canonical or ‘small stories’, in this context-creating and identity-orientating work has been largely overlooked, although there is an expanding collection of studies into the affordances offered by different narrative types in terms of identity performance. Building on and combining existing research into institutional interaction on the one hand and narrative and identity on the other, the research discussed here starts to address the gap identified. Using fine-grained linguistic analysis and drawing on narrative positioning theory in a detailed analysis of two narratives recorded as part of a wider study, this paper aims to explicate the way participants — in this case guides in a working visitor attraction — may use different narrative types to orientate to their institutionally-ascribed identity of ‘guide’. The paper also highlights the benefits in terms of added nuance and depth of interpretation to be gained from using the tools of narrative analysis in investigating institutional contexts and identity.
The cognitive turn
Authors: Clark Matthew
Published: May 2013

Corresponding to the “narrative turn” in the human and cultural sciences, this paper advocates a “cognitive turn” in the study of literary narratives. The representation of the self in literary narratives, for example, is in some ways similar to the representation of the self represented in philosophic, psychological, and sociological theory, but the narrative models extend and enrich the understanding of the self. The tradition of literary narrative includes the monadic, dyadic, and triadic models of the self, as well as representations of agent, patient, experiencer, witness, instrumental, and locative selves. Narrative is thus a kind of worldmaking, and the making of complex worlds, such as the worlds of the self, lead towards narrative.
Parts of speech in Russian Sign Language
Authors: Kimmelman Vadim
Published: May 2013

In this paper, we present data that shed light on the parts of speech system of Russian Sign Language (RSL), in particular, the noun-verb distinction. An experimental study revealed that in RSL, specific phonological differences distinguish between nouns and verbs; these include differences in movement, handshape, orientation, location, and mouthing. The attested differences, which are subject to variation among the signers, can co-occur with each other. The patterns we found cannot be accounted for by models that have previously been proposed for other sign languages (e.g. American Sign Language and Australian Sign Language). We argue that these differences may result from the higher iconicity of verbs and the higher economy of nouns.
Infection Control Assessment after an Influenza Outbreak in a Residential Care Facility for Children and Young Adults with Neurologic and Neurodevelopmental Conditions
Authors: Azofeifa Alejandro , Yeung Lorraine F. , Peacock Georgina , Moore Cynthia A. , Rodgers Loren , DiOrio Mary , Page Shannon L. , Fowler Brian , Stone Nimalie D. , Finelli Lyn , Jhung Michael A.
Published: May 2013

Objective.

To assess the knowledge, attitudes, and practices of infection control among staff in a residential care facility for children and young adults with neurologic and neurodevelopmental conditions.

Design.

Self-administered survey.

Setting.

Residential care facility (facility A).

Participants.

Facility A staff (N = 200).

Methods.

We distributed a survey to staff at facility A. We classified staff with direct care responsibilities as clinical (ie, physicians, nurses, and therapists) or nonclinical (ie, habilitation assistants, volunteers, and teachers) and used X2 tests to measure differences between staff agreement to questions.

Results.

Of 248 surveys distributed, 200 (81%) were completed; median respondent age was 36 years; 85% were female; and 151 were direct care staff (50 clinical, 101 nonclinical). Among direct care staff respondents, 86% agreed they could identify residents with respiratory symptoms, 70% stayed home from work when ill with respiratory infection, 64% agreed that facility administration encouraged them to stay home when ill with respiratory infection, and 72% reported that ill residents with respiratory infections were separated from well residents. Clinical and nonclinical staff differed in agreement about using waterless hand gel as a substitute for handwashing (96% vs 78%; P = .005) and whether handwashing was done after touching residents (92% vs 75%; P = .04).

Conclusions.

Respondents' knowledge, attitudes, and practices regarding infection control could be improved, especially among nonclinical staff. Facilities caring for children and young adults with neurologic and neurodevelopmental conditions should encourage adherence to infection control best practices among all staff having direct contact with residents.
Specificity control for read alignments using an artificial reference genome-guided false discovery rate
Authors: Giese Sven H. , Zickmann Franziska , Renard Bernhard Y.
Published: May 2013

Motivation: Accurate estimation, comparison and evaluation of read mapping error rates is a crucial step in the processing of next-generation sequencing data, as further analysis steps and interpretation assume the correctness of the mapping results. Current approaches are either focused on sensitivity estimation and thereby disregard specificity or are based on read simulations. Although continuously improving, read simulations are still prone to introduce a bias into the mapping error quantitation and cannot capture all characteristics of an individual dataset.

Results: We introduce ARDEN (artificial reference driven estimation of false positives in next-generation sequencing data), a novel benchmark method that estimates error rates of read mappers based on real experimental reads, using an additionally generated artificial reference genome. It allows a dataset-specific computation of error rates and the construction of a receiver operating characteristic curve. Thereby, it can be used for optimization of parameters for read mappers, selection of read mappers for a specific problem or for filtering alignments based on quality estimation. The use of ARDEN is demonstrated in a general read mapper comparison, a parameter optimization for one read mapper and an application example in single-nucleotide polymorphism discovery with a significant reduction in the number of false positive identifications.

Availability: The ARDEN source code is freely available at http://sourceforge.net/projects/arden/.

Contact:  renardb@rki.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
A Human Volunteer Study to Identify Variability in Performance in the Cognitive Domain of the Postoperative Quality of Recovery Scale
Authors: Royse Colin F. , Newman Stanton , Williams Zelda , Wilkinson David J.
Published: May 2013

Background:

The Postoperative Quality of Recovery Scale found lower than anticipated recovery in the cognitive domain. The definition of cognitive recovery did not allow for performance variability, and may have been too sensitive. This study aimed to examine variability in cognitive performance in volunteers.

Methods:

One hundred forty-three volunteers completed the cognitive domain questions at baseline, after 15 min and 40 min, and on days 1 and 3. Delivery via face-to-face interview was conducted for the first three measurements, and then randomized for day 1 and 3 measurements (face-to-face only, telephone only, telephone then face-to-face, face-to-face then telephone).

Results:

All volunteers answered orientation correctly. Mean change scores for other tests were positive, indicating a modest learning effect. There were no significant differences between methods of delivery (all P > 0.05). Due to variability in volunteers’ performances, the authors propose a new scoring system to introduce a tolerance factor in scoring cognitive recovery. The proposed revised change from baseline scores are: orientation 0 or higher, digits forward −2 or higher, digits back −1 or higher, word recall −3 or higher, and word generation −3 or higher. This resulted in approximately 95% volunteers classed as “recovered” for each test item, and recovery for the domains ranged from 82.6 to 89.1%. The initial feasibility study was reanalyzed and cognitive recovery increased at all assessment times. At 3 days, cognitive recovery was found to increase from 33.5 to 86.4%.

Conclusion:

The authors recommend adoption of the new method for scoring cognitive recovery in the Postoperative Quality of Recovery Scale. Telephone or face-to-face delivery was equivalent and either method can be reliably applied.
Esophageal Impedance Baseline Is Age Dependent
Authors: Salvatore Silvia , Salvatoni Alessandro , Van Berkel Marieke , Van Steen Kristel , Unmarino Dario , Ghanma Abdallah , Hauser Bruno , Vandenplas Yvan
Published: May 2013

Objective:

Esophageal impedance (multichannel intraluminal impedance [MII]) baseline (impedance baseline [IB]) has been recently considered to be related to esophageal integrity. The aim of this study was to analyze the age effect on IB in a large population of pediatric patients.

Design:

A total of 816 children with symptoms of gastroesophageal reflux and submitted to MII were included. Mean IB was automatically calculated in the different MII channels (Chs) throughout 24‐hour tracings by the specific software without removing any episode of increased/decreased IB. Acid and nonacid reflux parameters and age subgroups analysis were performed. Unpaired t test, Spearman rank correlation, polynomial and regression plot, multiple regression analysis, factorial analysis of variance, and the least mean squares method were used for statistical analysis and age‐related percentile curves. P < 0.05 was considered as statistically significant.

Results:

Mean IB was significantly (P < 0.001) lower in younger compared with older children up to 48 months. The mean increase of IB per month was 2.9 Ω in Ch 1 and 2.3 Ω in Ch 6, but much higher in the first 36 months of life (47.5 Ω in Ch 1 and 29.9 Ω in Ch 6, respectively). From 48 months onward, there was no significant increase of the mean IB (P = 0.73). In the multiple regression analysis, only age and reflux index (but no other reflux parameters) significantly correlated with IB. Distal IB was significantly (P < 0.05) lower in patients with esophagitis and in subjects taking proton pump inhibitors compared with subjects off (any) treatment. Percentiles of IB in proximal and distal Chs were provided according to different age groups.

Conclusions:

IB is significantly lower in infants (especially in the first months of life) compared with older children. Low IB in both proximal and distal esophagus in young infants may be related to anatomical and functional difference other than the presence of esophagitis.
Advice to a young researcher: with reminiscences of a life in science
Authors: Thompson J. Michael T.
Published: May 2013

This paper provides an informal guide to young researchers in science and engineering as they progress for their first 10 or so years from the time that they first started thinking about doing a PhD. This advice is drawn, with examples and anecdotes, from my own research career which started at the Cambridge Engineering Department in 1958, and progressed through 48 years at University College London to a part-time chair that I now hold in Aberdeen. I hope it may encourage and help tomorrow's scientists on whom the Earth's future very much depends.
Amorphus suaedae sp. nov., isolated from the root of a tidal flat plant, Suaeda maritima
Authors: Hwang Jung Moon , Chung Eu Jin , Park Jeong Ae , Jeong Jae Heon , Jeon Che Ok , Chung Young Ryun
Published: May 2013

A novel bacterial strain, YC6899T, was isolated from the root ofSuaedae maritimagrowing on a tidal flat of Namhae Island, Korea. Cells were Gram-reaction-negative, rod-shaped, non-motile, slightly halophilic and heterotrophic. Strain YC6899Tgrew optimally at a salinity of 2–4 %, at 25–37 °C and at pH 6.5–8.0. Phylogenetic analysis of 16S rRNA gene sequences demonstrated that strain YC6899Twas closely related toAmorphus orientalisYIM D10T(96.1 % similarity) andAmorphus coralliRS.Sph.026T(95.9 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown aminolipids, an unknown aminophospholipid, an unknown aminoglycolipid, unknown glycolipids and unknown lipids. The major fatty acids of strain YC6899Twere C19 : 0cyclo ω8cand C18 : 1ω7c. The G+C content of the genomic DNA was 61.3 mol%. Strain YC6899Tcontained ubiquinone-10 (Q-10) as the major respiratory quinone system. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YC6899Trepresents a novel species within the genusAmorphus, for which the nameAmorphus suaedaesp. nov. is proposed. The type strain is YC6899T( = KACC 14912T = NBRC 107845T).
Falsochrobactrum ovis gen. nov., sp. nov., isolated from a sheep
Authors: Kämpfer Peter , Glaeser Stefanie , Busse Hans-Jürgen , Eisenberg Tobias , Scholz Holger
Published: May 2013

A Gram-stain-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (B1315T) was isolated from the placenta of a sheep with abortion. On the basis of 16S rRNA gene sequence analyses the strain was assigned to the

Brucella

–

Ochrobactrum

–

Paenochrobactrum

–

Pseudochrobactrum

group with 94.5–94.8 %, 94.3–96.1 %, 95.0–95.1 %, and 95.9–96.1 % sequence similarities to type strains of species of the four genera, respectively. Phylogenetic trees indicated a close relationship to the type strains of

Ochrobactrum gallinifaecis

and

Ochrobactrum oryzae

(95.9 and 96.1 % sequence similarity, respectively). Chemotaxonomic data confirmed the allocation of strain B1315T to the family

Brucellaceae

(quinone system: ubiquinone Q-10 and major fatty acids: C18 : 1ω7c and C19 : 0 cyclo ω8c). The polar lipid profile contained the major lipids diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and the unidentified but unique phospholipid PL7. The polyamine pattern of strain B1315T contained the major polyamines spermidine and putrescine. On the basis of the 16S rRNA gene and recA sequence phylogeny and chemotaxonomic data strain B1315T was clearly different from the genera

Brucella

,

Ochrobactrum

,

Paenochrobactrum

and

Pseudochrobactrum

. On the basis of these data we propose the novel genus Falsochrobactrum gen. nov. with the type species Falsochrobactrum ovis sp. nov. with the type strain B1315T ( = CCM 8460T = LMG 27356T.) The taxonomic allocation of

O. gallinifaecis

, which grouped inconsistently together with strain B1315T on the basis of 16S rRNA gene sequence data, but shows the chemotaxonomic features of the genus

Ochrobactrum

, remains to be clarified.
Description of

Lactobacillus

iwatensis sp. nov., isolated from orchardgrass (Dactylis glomerata L.) silage, and

Lactobacillus

backii sp. nov.
Authors: Tohno Masanori , Kitahara Maki , Irisawa Tomohiro , Masuda Takaharu , Uegaki Ryuichi , Ohkuma Moriya , Tajima Kiyoshi
Published: May 2013

Two bacterial strains, designated IWT246T and IWT248, were isolated from orchardgrass (Dactylis glomerata L.) silage from Iwate prefecture, Japan, and examined for a taxonomic study. Both organisms were rod-shaped, Gram-stain-positive, catalase-negative, facultatively anaerobic and homofermentative. The cell wall did not contain meso-diaminopimelic acid and the major fatty acids were C18 : 1ω9c and C19 cyclo 9,10/:1. Comparative analyses of 16S rRNA, pheS and rpoA gene sequences revealed that these strains were novel and belonged to the genus

Lactobacillus

. Based on 16S rRNA gene sequence similarity, the isolates were most closely related to the type strains of the following members of the genus

Lactobacillus

:

Lactobacillus coryniformis subsp. coryniformis

(96.7 % similarity),

L. coryniformis subsp. torquens

(96.6 %),

L. bifermentans

(95.5 %) and

L. rennini

(94.1 %). However, the 16S rRNA gene sequences of both IWT246T and IWT248 were 99.7 % similar to that of ‘

Lactobacillus

backi’ JCM 18665; this name has not been validly published. Genotypic, phenotypic and chemotaxonomic analyses confirmed that these novel strains occupy a unique taxonomic position. DNA–DNA hybridization experiments demonstrated genotypic separation of the novel isolates from related

Lactobacillus

species. The name

Lactobacillus

iwatensis sp. nov. is proposed for the novel isolates, with strain IWT246T ( = JCM 18838T = DSM 26942T) as the type strain. Our results also suggest that ‘L. backi’ does represent a novel

Lactobacillus

species. The cells did not contain meso-diaminopimelic acid in their cell-wall peptidoglycan and the major fatty acids were C16 : 0, C19 cyclo 9,10/:1 and summed feature 10 (one or more of C18 : 1ω11c, C18 : 1ω9t, C18 : 1ω6t and unknown ECL 17.834). We therefore propose the corrected name

Lactobacillus

backii sp. nov., with the type strain JCM 18665T ( = LMG 23555T = DSM 18080T = L1062T).
The beneficial effects of leptin on REM sleep deprivation-induced cognitive deficits in mice
Authors: Chang Hsiao-Fu , Su Chun-Lin , Chang Chih-Hua , Chen Yu-Wen , Gean Po-Wu
Published: May 2013

Leptin, a 167 amino acid peptide, is synthesized predominantly in the adipose tissues and plays a key role in the regulation of food intake and body weight. Recent studies indicate that leptin receptor is expressed with high levels in many brain regions that may regulate synaptic plasticity. Here we show that deprivation of rapid eye movement (REMD) sleep resulted in impairment of both cue and contextual fear memory. In parallel, surface expression of GluR1 was reduced in the amygdala. Intraperitoneal injection of leptin to the REMD mice rescued memory impairment and reversed surface GluR1 reduction. Using whole-cell recording to evaluate the synaptic function of the thalamus–lateral amygdala (LA) pathway, we found a decrease in frequency and amplitude of miniature excitatory postsynaptic currents (mEPSCs) concomitant with reduced AMPA/NMDA ratios in the REMD mice. By contrast, paired-pulse facilitation (PPF) was increased. The effects of REMD on mEPSCs and AMPA/NMDA ratio could be reversed by leptin treatment, whereas on PPR it could not. Phosphatase and tensin homolog (PTEN), a dual protein/lipid phosphatase, down-regulates the effect of the PI-3 kinase pathway. Fear conditioning increased whereas REMD led to a decrease in the phosphorylated states of PTEN, Akt, and glycogen synthase kinase-3β (GSK3β), and the effects of REMD were reversed by leptin. These results suggest that both pre- and postsynaptic functions of the thalamus–LA pathway were altered by fear conditioning and REMD in opposite directions. Leptin treatment reversed REMD-induced memory deficits primarily by a postsynaptic action by restoring surface expression of GluR1 without affecting PPR.
Hippocampus and medial prefrontal cortex contributions to trace and contextual fear memory expression over time
Authors: Beeman Christopher L. , Bauer Philip S. , Pierson Jamie L. , Quinn Jennifer J.
Published: May 2013

Previous work has shown that damage to the dorsal hippocampus (DH) occurring at recent, but not remote, timepoints following acquisition produces a deficit in trace conditioned fear memory expression. The opposite pattern has been observed with lesions to the medial prefrontal cortex (mPFC). The present studies address: (1) whether these lesion effects are observable within 30 d of training; (2) whether lesions of the ventral hippocampus (VH) produce temporally graded retrograde amnesia similar to DH lesions; and (3) whether the lesion-to-test interval critically contributes to these lesion deficits. In Experiment 1, excitotoxic lesions of the DH, VH, or mPFC were made at 1 or 30 d following trace fear conditioning. DH and VH lesioned animals showed a deficit in freezing to the tone at the recent, but not remote, timepoint. Medial PFC lesioned animals showed the opposite pattern. In Experiment 2, lesions to DH, VH, or mPFC were made 1 d following training, while testing occurred 30 d later. There were no deficits in freezing to the tone in any lesion condition compared to controls. These results suggest that systems consolidation of trace fear memory occurs within 30 d of acquisition, but does not depend on hippocampus–mPFC interactions during this period.