bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low-cost analog fiber optic links for in-house distribution of millimeter-wave signals
Authors: Brendel Friederike , Poëtte Julien , Cabon Béatrice , van Dijk Frédéric 
Published: February 2011

In this article, analog fiber optic links (radio-over-fiber, RoF, links) are presented as a flexible, low-cost solution for in-house distribution of millimeter-wave (mmw) signals. Mode-locked laser diodes (MLLD) serve as inexpensive mmw sources for the downlink distribution of mmw signals across an optical fiber link. We compare the robustness of direct and external RF modulation for such MLLD-based RoF systems, whereas the error vector magnitude (EVM) of the received symbols serves as a figure of merit. On the eve of 60 GHz WLAN standardization, we experimentally investigate the transmission of narrowband WLAN (IEEE 802.11a) signals in the millimetric range at moderate data rates. We also demonstrate broadband transmission of multi-band orthogonal frequency-division multiplexing (MB-OFDM) ultra-wideband (UWB) european computer manufacturers association (ECMA 368) signals in the 60 GHz band for data rates of up to 480 Mbps.
Localization of Label-Retaining Cells in Murine Vocal Fold Epithelium
Authors: Leydon Ciara , Bartlett Rebecca S. , Roenneburg Drew A. , Thibeault Susan L. 
Published: February 2011

Purpose
Epithelial homeostasis is critical for vocal fold health, yet little is known about the cells that support epithelial self-renewal. As a known characteristic of stem cells is that they are slow-cycling in vivo, the purpose of this prospective controlled study was to identify and quantify slow-cycling cells or putative stem cells in murine vocal fold epithelium.

Method
Twelve mice were administered daily intraperitoneal injections of a nucleotide dye, bromodeoxyuridine (BrdU), over 7 consecutive days. Under this pulse-chase paradigm, slow-cycling cells retain the dye (label-retaining cells; LRCs) while more rapidly cycling cells lose dye to dilution during multiple cell divisions. The percentage of label-retaining cells (%LRCs) was calculated following a chase period of 2, 4, and 8 weeks postinjections.

Results

The %LRCs decreased significantly from 9.4% at 2 weeks to 3.1% at 8 weeks following injections (
p
< .05). No statistically significant differences in the quantity of BrdU-positive cells were measured between the anterior, mid-membranous, or cartilaginous regions of the vocal fold (
p
> .05).

Conclusion
These findings are consistent with the presence and first report of a small population of putative stem cells along the length of murine vocal fold epithelium.
High efficiency multichannel collimator for structural studies of liquids and low-Z materials at high pressures and temperatures
Authors: Morard G. , Mezouar M. , Bauchau S. , Álvarez-Murga M. , Hodeau J.-L. , Garbarino G. 
Published: February 2011

A high efficiency multichannel collimator (MCC) device has been developed at the high pressure beamline ID27 of the European Synchrotron Radiation Facility to drastically reduce the x-ray background from the sample environment in the Paris-Edinburgh press. The main technical difficulty, which resides in the minimum slits size achievable using the classical mono-bloc design, has been resolved using an original concept based on a set of independent slits. Then, a very small slit size of 50 μm was manufactured resulting in a great improvement of the signal to background ratio. In addition, the transfer function of the MCC has been measured using the x-ray diffusion signal of a metal doped glass and efficiently applied to correct the raw data. The potential of this new device is illustrated in two challenging examples: iron–sulfur liquid structures and C60 polymerization process at high pressure and high temperature.
FIMO: scanning for occurrences of a given motif
Authors: Grant Charles E. , Bailey Timothy L. , Noble William Stafford 
Published: February 2011

AbstractSummary: A motif is a short DNA or protein sequence that contributes to the biological function of the sequence in which it resides. Over the past several decades, many computational methods have been described for identifying, characterizing and searching with sequence motifs. Critical to nearly any motif-based sequence analysis pipeline is the ability to scan a sequence database for occurrences of a given motif described by a position-specific frequency matrix.Results: We describe Find Individual Motif Occurrences (FIMO), a software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices. The program computes a log-likelihood ratio score for each position in a given sequence database, uses established dynamic programming methods to convert this score to a P-value and then applies false discovery rate analysis to estimate a q-value for each position in the given sequence. FIMO provides output in a variety of formats, including HTML, XML and several Santa Cruz Genome Browser formats. The program is efficient, allowing for the scanning of DNA sequences at a rate of 3.5 Mb/s on a single CPU.Availability and Implementation: FIMO is part of the MEME Suite software toolkit. A web server and source code are available at http://meme.sdsc.edu.Contact: t.bailey@imb.uq.edu.au; t.bailey@imb.uq.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.
Defining an informativeness metric for clustering gene expression data
Authors: Mar Jessica C. , Wells Christine A. , Quackenbush John 
Published: February 2011

Abstract
Motivation: Unsupervised ‘cluster’ analysis is an invaluable tool for exploratory microarray data analysis, as it organizes the data into groups of genes or samples in which the elements share common patterns. Once the data are clustered, finding the optimal number of informative subgroups within a dataset is a problem that, while important for understanding the underlying phenotypes, is one for which there is no robust, widely accepted solution.
Results: To address this problem we developed an ‘informativeness metric’ based on a simple analysis of variance statistic that identifies the number of clusters which best separate phenotypic groups. The performance of the informativeness metric has been tested on both experimental and simulated datasets, and we contrast these results with those obtained using alternative methods such as the gap statistic.
Availability: The method has been implemented in the Bioconductor R package attract; it is also freely available from http://compbio.dfci.harvard.edu/pubs/attract_1.0.1.zip.
Contact: jess@jimmy.harvard.edu; johnq@jimmy.harvard.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Analysis of Dynamic Intratidal Compliance in a Lung Collapse Model
Authors: Schumann Stefan , Vimlati László , Kawati Rafael , Guttmann Josef , Lichtwarck-Aschoff Michael 
Published: February 2011

Background
For mechanical ventilation to be lung-protective, an accepted suggestion is to place the tidal volume (V(T)) between the lower and upper inflection point of the airway pressure-volume relation. The drawback of this approach is, however, that the pressure-volume relation is assessed under quasistatic, no-flow conditions, which the lungs never experience during ventilation. Intratidal nonlinearity must be assessed under real (i.e., dynamic) conditions. With the dynamic gliding-SLICE technique that generates a high-resolution description of intratidal mechanics, the current study analyzed the profile of the compliance of the respiratory system (C(RS)).

Methods
In 12 anesthetized piglets with lung collapse, the pressure-volume relation was acquired at different levels of positive end-expiratory pressure (PEEP: 0, 5, 10, and 15 cm H(2)O). Lung collapse was assessed by computed tomography and the intratidal course of C(RS) using the gliding-SLICE method.

Results
Depending on PEEP, C(RS) showed characteristic profiles. With low PEEP, C(RS) increased up to 20% above the compliance at early inspiration, suggesting intratidal recruitment; whereas a profile of decreasing C(RS), signaling overdistension, occurred with V(T) > 5 ml/kg and high PEEP levels. At the highest volume range, C(RS) was up to 60% less than the maximum. With PEEP 10 cm H(2)O, C(RS) was high and did not decrease before 5 ml/kg V(T) was delivered.

Conclusions
The profile of dynamic C(RS) reflects nonlinear intratidal mechanics of the respiratory system. The SLICE analysis has the potential to detect intratidal recruitment and overdistension. This might help in finding a combination of PEEP and V(T) level that is protective from a lung-mechanics perspective.
MicroRNAs Regulate the Timing of Embryo Maturation in Arabidopsis
Authors: Willmann Matthew R. , Mehalick Andrew J. , Packer Rachel L. , Jenik Pablo D. 
Published: February 2011

AbstractThe seed is a key evolutionary adaptation of land plants that facilitates dispersal and allows for germination when the environmental conditions are adequate. Mature seeds are dormant and desiccated, with accumulated storage products that are to be used by the seedling after germination. These properties are imposed on the developing embryo by a maturation program, which operates during the later part of embryogenesis. A number of “master regulators” (the “LEC genes”) required for the induction of the maturation program have been described, but it is not known what prevents this program from being expressed during early embryogenesis. Here, we report that Arabidopsis (Arabidopsis thaliana) embryos mutant for strong alleles of DICER-LIKE1, the enzyme responsible for the biosynthesis of microRNAs (miRNAs), mature earlier than their wild-type counterparts. This heterochronic phenotype indicates that miRNAs are key regulators of the timing of the maturation program. We demonstrate that miRNAs operate in part by repressing the master regulators LEAFY COTYLEDON2 and FUSCA3 and identify the trihelix transcription factors ARABIDOPSIS 6B-INTERACTING PROTEIN1-LIKE1 (ASIL1) and ASIL2 and the histone deacetylase HDA6/SIL1 as components that act downstream of miRNAs to repress the maturation program early in embryogenesis. Both ASIL1 and HDA6/SIL1 are known to act to prevent the expression of embryonic maturation genes after germination, but to our knowledge, this is the first time they have been shown to have a role during embryogenesis. Our data point to a common negative regulatory module of maturation during early embryogenesis and seedling development.
RNAi‐mediated resistance to Cassava brown streak Uganda virus in transgenic cassava
Authors: YADAV JITENDER S. , OGWOK EMMANUEL , WAGABA HENRY , PATIL BASAVAPRABHU L. , BAGEWADI BASAVARAJ , ALICAI TITUS , GAITAN‐SOLIS ELIANA , TAYLOR NIGEL J. , FAUQUET CLAUDE M. 
Published: February 2011

SUMMARYCassava brown streak disease (CBSD), caused by Cassava brown streak Uganda virus (CBSUV) and Cassava brown streak virus (CBSV), is of new epidemic importance to cassava (Manihot esculenta Crantz) production in East Africa, and an emerging threat to the crop in Central and West Africa. This study demonstrates that at least one of these two ipomoviruses, CBSUV, can be efficiently controlled using RNA interference (RNAi) technology in cassava. An RNAi construct targeting the near full‐length coat protein (FL‐CP) of CBSUV was expressed constitutively as a hairpin construct in cassava. Transgenic cassava lines expressing small interfering RNAs (siRNAs) against this sequence showed 100% resistance to CBSUV across replicated graft inoculation experiments. Reverse transcriptase‐polymerase chain reaction (RT‐PCR) analysis showed the presence of CBSUV in leaves and some tuberous roots from challenged controls, but not in the same tissues from transgenic plants. This is the first demonstration of RNAi‐mediated resistance to the ipomovirus CBSUV in cassava.
The SLT2 mitogen‐activated protein kinase‐mediated signalling pathway governs conidiation, morphogenesis, fungal virulence and production of toxin and melanin in the tangerine pathotype of Alternaria alternata
Authors: YAGO JONAR INGAN , LIN CHING‐HSUAN , CHUNG KUANG‐REN 
Published: February 2011

SUMMARYFungi respond and adapt to different environmental stimuli via signal transduction systems. We determined the function of a yeast SLT2 mitogen‐activated protein (MAP) kinase homologue (AaSLT2) in Alternaria alternata, the fungal pathogen of citrus. Analysis of the loss‐of‐function mutant indicated that AaSLT2 is required for the production of a host‐selective toxin, and is crucial for fungal pathogenicity. Moreover, the A. alternata slt2 mutants displayed hypersensitivity to cell wall‐degrading enzymes and chemicals such as Calcofluor white and Congo red. This implicates an important role of AaSLT2 in the maintenance of cell wall integrity in A. alternata. The A. alternata slt2 mutants were also hypersensitive to a heteroaromatic compound, 2‐chloro‐5‐hydroxypyridine, and a plant growth regulator, 2,3,5‐triiodobenzoic acid. Developmentally, the AaSLT2 gene product was shown to be critical for conidial formation and hyphal elongation. Compared with the wild‐type, the mutants produced fewer but slightly larger conidia with less transverse septae. The mutants also accumulated lower levels of melanin and chitin. Unlike the wild‐type progenitor, the A. alternata slt2 mutants produced globose, swollen hyphae that did not elongate in a straight radial direction. All defective phenotypes in the mutant were restored by transformation and expression of a wild‐type copy of AaSLT2 under the control of its endogenous promoter. This study highlights an important role of the AaSLT2 MAP kinase‐mediated signalling pathway, regulating diverse physiological, developmental and pathological functions, in the tangerine pathotype of A. alternata.
Mapping studies of the Peach latent mosaic viroid reveal novel structural features
Authors: DUBÉ AUDREY , BOLDUC FRANÇOIS , BISAILLON MARTIN , PERREAULT JEAN‐PIERRE 
Published: February 2011

SUMMARYKnowledge of the structure of a viroid is critically important to elucidate the roles played by the various RNA motifs in the steps of the viroid's life cycle. A new technique, RNA‐selective 2′‐hydroxyl acylation analysed by primer extension (SHAPE), has recently been shown to be fast, reliable and applicable to the study of various RNA molecules. Consequently, this method was used to probe sequence variants of Peach latent mosaic viroid (PLMVd). Initially, probing data from RNA strands of both polarities of the Siberian C variant confirmed the secondary structures previously determined using both conventional and fastidious approaches. Subsequently, analysis of an Alberta variant showed an identical structure for the strand of (−) polarity, but the (+) polarity strand exhibited two differences from the Siberian C variant: the P11–L11 stem–loop domain formed a cruciform structure, and nucleotides from loops L1 and L11 were involved in the formation of a pseudoknot. The existence of both of these motifs was confirmed by site‐directed mutagenesis. The subsequent probing of 12 natural sequence variants led to the elucidation of the criteria governing the formation of this novel pseudoknot. Importantly, this study revealed that the heterogeneity of a viroid is not limited to its nucleotide sequence, but may also occur at the structural level.
Everyday clinical experience of alitretinoin in the treatment of severe chronic hand eczema: seven case studies
Authors: English J. , Graham-Brown R. , de Sica Chapman A. , Alexandroff A. B. 
Published: February 2011

Summary
Chronic hand eczema (CHE) is a debilitating and distressing disease for patients, the physical symptoms of which are compounded by psychosocial problems. Alitretinoin is an endogenously occurring physiological vitamin A derivative (retinoid) that possesses strong anti-inflammatory and immunomodulatory activity. It is currently the only licensed product for severe CHE unresponsive to treatment with potent topical corticosteroids, and has been proven to be highly effective in clinical trials with two-thirds of patients who responded to treatment remaining in remission at 6 months. For those that did relapse, a second study showed they could be successfully retreated with a further 3–6 month course of alitretinoin. Seven case studies of alitretinoin have been provided by consultant dermatologists showing its use in normal UK clinical practice. The cases chosen demonstrate the efficacy of alitretinoin across several different subtypes of CHE, and the positive effects the treatment brought to patients’ quality of life.
Investigating the contribution of community nurses to anticipatory care: a qualitative exploratory study
Authors: Kennedy Catriona , Harbison Jean , Mahoney Catherine , Jarvis Alison , Veitch Linda 
Published: February 2011

kennedy c., harbison j., mahoney c., jarvis a. & veitch l. (2011) Investigating the contribution of community nurses to anticipatory care: a qualitative exploratory study. Journal of Advanced Nursing67(7), 1558–1567.AbstractAims.  To investigate how one aspect of anticipatory care is understood and delivered in practice. ‘Anticipatory care’ in this context can be understood as proactive care, which is oriented towards prevention of adverse events.Background.  Scotland has identified the intention to move away from a preoccupation with acute care and invest in health improvement and anticipatory care. Community nurses are the key, yet little is known about how they understand and deliver anticipatory care.Methods.  A qualitative case study design using individual in‐depth interviews (n = 10), observation (n = 9) and focus groups (n = 5) was selected. Five focus group interviews were carried out with district nurses, practice nurses and health visitors. Subsequently, nine observation events took place, each focused on a single nurse/client encounter. Data were collected during 2008 and 2009 in one Community Health Partnership in Scotland.Findings.  Two approaches to anticipatory care emerged; these were influenced by participants’ roles and responsibilities. Approach 1 derives from Government policy agenda and is focused on protocol‐focused management of long‐term illness. Approach 2 is synonymous with long‐standing nursing activity focused on holistic care of individual patients. Both approaches are proactive in nature.Conclusions.  There is scope to develop a more conceptually complex model of anticipatory care, building on this initial exploration, within which all aims, roles, practices and methods of evaluation can be located and clearly visible. This offers the potential to enable practitioners to interpret and apply policy – otherwise change may be limited and result in service gaps.
Exploring and comparing the experience and coping behaviour of men and women with colorectal cancer at diagnosis and during surgery
Authors: McCaughan Eilis , Prue Gillian , Parahoo Kader , McIlfatrick Sonja , McKenna Hugh 
Published: February 2011

mccaughan e., prue g., parahoo k., mcilfatrick s. & mckenna h. (2011) Exploring and comparing the experience and coping behaviour of men and women with colorectal cancer at diagnosis and during surgery. Journal of Advanced Nursing67(7), 1591–1600.AbstractAim.  This paper is a report of a study exploring and comparing the experience of men and women with colorectal cancer at diagnosis and during surgery.Background.  Men have higher incidence and mortality rates for nearly all cancers and frequently use health behaviours that reflect their masculinity. There has been minimal investigation into the influence of gender on the experience of a ‘shared’ cancer.Methods.  From November 2006 to November 2008, a qualitative study was conducted involving 38 individuals (24 men, 14 women) with colorectal cancer. Data were generated using semi‐structured interviews at four time points over an 18‐month period. This paper reports the participants’ experience at diagnosis and during surgery (time point 1) with the purpose of examining the impact of gender on this experience.Findings.  In general, men appeared more accepting of their diagnosis. The majority of females seemed more emotional and more affected by the physical side effects. However, there was variation in both gender groups, with some men and women portraying both ‘masculine’ and ‘feminine’ traits. There was also individual variation in relation to context.Conclusions.  It appears that many men may have been experiencing side effects and/or psychological distress that they were reluctant to discuss, particularly as some men portrayed typical ‘masculine’ traits in public, but felt able to open up in private. Nurses should not make assumptions based on the traditional view of masculinity, and should determine how each man wants to deal with their diagnosis and not presume that all men need to ‘open up’ about their illness.
The accuracy of using integrated electronic health care data to identify patients with undiagnosed diabetes mellitus
Authors: Ho Michael L. , Lawrence Nadine , van Walraven Carl , Manuel Doug , Keely Erin , Malcolm Janine , Reid Robert D. , Forster Alan J. 
Published: February 2011

AbstractRationale, aims and objectives  Diabetes mellitus is a growing health and economic burden. Identification of patients with unrecognized diabetes, or those at high risk for diabetes, provides an opportunity for timely intervention. This study assessed the accuracy of using electronic health care data to identify patients with undiagnosed diabetes.Methods  The study was conducted at a tertiary‐care teaching facility in Ottawa, Canada. The study cohort was a stratified random sample of hospitalizations between 1 January 2003 and 31 December 2008. We used diagnostic codes, pharmacy orders and serum glucose tests to classify patients into six groups: ‘recognized diabetes’ (a diabetes diagnostic code or any diabetes medication), ‘probable diabetes’ (maximum glucose ≥ 11.1 mmol L−1), ‘possible diabetes’ (maximum glucose between 7.8 and 11.1 mmol L−1), ‘unlikely diabetes’ (maximum glucose between 6.0 and 7.8 mmol L−1), ‘no diabetes’ (maximum glucose < 6.0 mmol L−1) and ‘unknown diabetes status’ (no glucose test). We compared this electronic classification to a reference standard chart review performed by a blinded abstractor.Results  A total of 500 hospitalizations were included. The prevalence of each diabetes group was: recognized – 17%; probable – 4%; possible – 15%; unlikely – 20%; none – 15%; and unknown – 29%. Our electronic algorithm correctly classified 88.8% (95% confidence interval 85.7–91.3) of hospitalizations (weighted‐Kappa = 0.885; 95% confidence interval 0.851–0.919). The sensitivity, specificity and positive predictive values of our algorithm for ‘known diabetes’ was 0.842, 0.988 and 0.941, respectively. For patients at a ‘high risk for diabetes’ (maximum glucose > 7.8 mmol L−1), the corresponding values were 0.921, 0.971 and 0.872.Conclusions  Patients with diagnosed and undiagnosed diabetes can be accurately identified using electronic health care data.
Thinking without knowing – Child psychoanalytic psychotherapy in the UK and evidence‐based practice
Authors: Rous Elizabeth , Clark Andrew 
Published: February 2011

AbstractBackground  Child psychoanalytic psychotherapy has been criticized for its reluctance to embrace evidence‐based practice. This study aims to explore the historical narrative of a sample of child psychoanalytic psychotherapists about progress in developing the evidence base.Methods  Fourteen psychotherapists were interviewed and the transcripts analysed for common themes about evidence‐based practice.Results  Child psychoanalytic psychotherapists were generally positive about developing evidence‐based practice but had reservations about the narrowness of hierarchies used by commissioners to assess evidence.Conclusion  The child psychoanalytical psychotherapists interviewed for this study recognized the need to promote evidence‐based practice, in particular, to inform commissioners of Child Mental Health Services.