bluuebunny/crossref_metadata_2025_split huggingface dataset:
The first reported treatment of Nager syndrome associated hearing loss with bone-anchored hearing aids: case report
Authors: Davies G P , Johnson I J M 
Published: October 2011

AbstractObjective:To report the first case of treatment of Nager syndrome associated conductive hearing loss with bone-anchored hearing aids, in a three-year-old boy.Method:Clinical case report and current literature review regarding the use of bone-anchored hearing aids in the treatment of conductive hearing loss in children.Results:A three year eight month old boy with Nager syndrome was successfully treated for conductive hearing loss using bilateral bone-anchored hearing aids.Conclusion:This is the first case report of the use of bone-anchored hearing aids to treat Nager syndrome associated conductive hearing loss. Treatment was safe and successful in this case.
FromScotiato ‘Operation Tabarin’: developing British policy for Antarctica
Authors: Dudeney John R. , Walton David W.H. 
Published: October 2011

ABSTRACTThe roots of a British Antarctic policy can be traced, paradoxically, back to the establishment of a meteorological station by the Scottish Antarctic Expedition in the South Orkneys, in 1903, and the indifference of the British Government to its almost immediate transfer to the Argentine Government. It was from that modest physical presence upon Laurie Island that Argentina came increasingly to challenge British claims to the sovereignty of the Falkland Islands Dependencies (FID), first in the late 1920s and then more extensively in the second world war. This challenge shaped British policy for the next forty years, with further complications caused by overlapping territorial claims made by Chile and the possible territorial ambitions of the USA. Britain's eventual response, at the height of World War II, was to establish permanent occupation of Antarctica from the southern summer of 1943–1944. This occupation was given the military codename Operation Tabarin. However, it was never a military operation as such, although monitoring the activities of enemy surface raiders and submarines provided a convenient cover story, as did scientific research once the operation became public. Whilst successive parties, rich in professional scientists, considerably expanded the pre-war survey and research of the Discovery Investigations Committee, their physical occupancy of the Antarctic islands and Peninsula was essentially a political statement, whereby the Admiralty and Colonial Office (CO) strove to protect British territorial rights, whilst the Foreign Office (FO) endeavoured to minimise disruption to Britain's long-standing economic and cultural ties with Argentina, and most critically, the shipment of war-time meat supplies. In meeting that immediate need, Tabarin also provided the basis from which Britain's subsequent post-war leadership in Antarctic affairs developed.
Sorted
Authors: SWIERSTRA WOUTER 
Published: October 2011

The problem of the Dutch national flag was formulated by Dijkstra (1976) as follows:
There is a row of buckets numbered from 1 to n. It is given that:
P1:each bucket contains one pebbleP2:each pebble is either red, white, or blue.A minicomputer is placed in front of this row of buckets and has to be programmed in such a way that it will rearrange (if necessary) the pebbles in the order of the Dutch national flag.The minicomputer in question should perform this rearrangement using two commands:
•swapi j for 1≤i≤n and 1≤j≤n exchanges the pebbles stored in the buckets numbered i and j;•read (i) for 1≤i≤n returns the colour of the pebble currently lying in bucket number i. Dijkstra originally named this operation buck.
Role of Frontotemporal Fiber Tract Integrity in Task-Switching Performance of Healthy Controls and Patients with Temporal Lobe Epilepsy
Authors: Kucukboyaci N. Erkut , Girard H.M. , Hagler D.J. , Kuperman J. , Tecoma E.S. , Iragui V.J. , Halgren E. , McDonald C.R. 
Published: October 2011

AbstractThe objective of this study is to investigate the relationships among frontotemporal fiber tract compromise and task-switching performance in healthy controls and patients with temporal lobe epilepsy (TLE). We performed diffusion tensor imaging (DTI) on 30 controls and 32 patients with TLE (15 left TLE). Fractional anisotropy (FA) was calculated for four fiber tracts [uncinate fasciculus (UncF), arcuate fasciculus (ArcF), dorsal cingulum (CING), and inferior fronto-occipital fasciculus (IFOF)]. Participants completed the Trail Making Test-B (TMT-B) and Verbal Fluency Category Switching (VFCS) test. Multivariate analyses of variances (MANOVAs) were performed to investigate group differences in fiber FA and set-shifting performances. Canonical correlations were used to examine the overall patterns of structural-cognitive relationships and were followed by within-group bivariate correlations. We found a significant canonical correlation between fiber FA and task-switching performance. In controls, TMT-B correlated with left IFOF, whereas VFCS correlated with FA of left ArcF and left UncF. These correlations were not significant in patients with TLE. We report significant correlations between frontotemporal fiber tract integrity and set-shifting performance in healthy controls that appear to be absent or attenuated in patients with TLE. These findings suggest a breakdown of typical structure-function relationships in TLE that may reflect aberrant developmental or degenerative processes. (JINS, 2012,18, 57–67)
Cunningham: a BLAST Runtime Estimator
Authors: White James , Matalka Malcolm , Fricke W. Florian , Angiuoli Samuel 
Published: October 2011

AbstractBLAST is arguably the single most important piece of software ever written for the biological sciences. It is the core of most bioinformatics workflows, being a critical component of genome homology searches and annotation. It has influenced the landscape of biology by aiding in everything from functional characterization of genes to pathogen detection to the development of novel vaccines. While BLAST is very popular, it is also often one of the most computationally intensive parts of bioinformatics analysis. In our workflows, BLAST typically takes the majority of cpu time, and we need to parallelize to finish in a reasonable time frame. Waiting for BLAST to finish without having any clue of how long it’s going to take is kind of depressing, and you could waste a day of work trying to run a job that would never finish. If you feel the same way we do, then check out Cunningham, a tool we designed to estimate BLAST runtimes for shotgun sequence datasets using sequence composition statistics. We’ve trained its models on real metagenomic sequence data using the Amazon EC2 cloud, and it will provide a relatively quick estimate for datasets with up to tens of millions of sequences. It’s not perfect, but it’ll give you at least some idea of expected runtime, how large a cluster you’re going to need, how much you’ll need to partition your data, etc. We use it all the time now, so we hope it’ll be useful to someone else out there. Cunningham has been implemented in CloVR for efficient autoscaling in the cloud and is freely available at http://clovr.org.
CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version 1.0
Authors: Fricke W. Florian , White James , Arze Cesar , Matalka Malcolm , Team The CloVR , White Owen , Angiuoli Samuel 
Published: October 2011

AbstractThe CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:A) Mothur – a C++-based software package used for clustering 16S rRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha diversity);B) The Ribosomal Database (RDP) naïve Bayesian classifier assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;C) Qiime – a python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including phylogenetic distance (UniFrac) for within-(alpha diversity) and between-(beta diversity) sample analysis;D) Metastats and custom R scripts used to generate additional statistical and graphical evaluations.Though some of the different protocols used in CloVR-16S overlap in purpose (e.g. OTU clustering), the end-user benefits from their overall complementary nature as they focus on different aspects of the phylogenetic analysis. CloVR-16S accepts as input raw multiplex 454-pyrosequencer output, i.e. pooled pyro-tagged sequences from multiple samples, or alternatively, pre-processed sequences from multiple samples in separate files. This protocol is available in CloVR beta versions 0.5 and 0.6.
Conversion of the enzyme guanylate kinase into a mitotic-spindle orienting protein by a single mutation that inhibits GMP-induced closing
Authors: Johnston Christopher A. , Whitney Dustin S. , Volkman Brian F. , Doe Chris Q. , Prehoda Kenneth E. 
Published: October 2011

New protein functions can require complex sequence changes, but the minimal path is not well understood. The guanylate kinase enzyme (GK
enz
), which catalyzes phosphotransfer from ATP to GMP, evolved into the GK domain (GK
dom
), a protein-binding domain found in membrane associate guanylate kinases that function in mitotic spindle orientation and cell adhesion. Using an induced polarity assay for GK
dom
function, we show that a single serine to proline mutation is sufficient to switch extant GK
enz
into a functional GK
dom
. The mutation blocks catalysis (GK
enz
function) but allows protein binding and spindle orientation (GK
dom
function). Furthermore, whereas the GK
enz
undergoes a large closing motion upon GMP binding, fluorescence quenching and NMR demonstrate that the S → P mutation inhibits GMP-induced GK movements. Disrupting GK closing with a mutation at a different position also leads to GK
dom
function, suggesting that blocking the GK
enz
closing motion is sufficient for functional conversion of GK
enz
to GK
dom
. Although subtle changes in protein function can require complex sequence paths, our work shows that entirely new functions can arise from single mutations that alter protein dynamics.
Altitudinal and Climatic Adaptation Is Mediated by Flowering Traits andFRI,FLC, andPHYCGenes in Arabidopsis
Authors: Méndez-Vigo Belén , Picó F. Xavier , Ramiro Mercedes , Martínez-Zapater José M. , Alonso-Blanco Carlos 
Published: October 2011

AbstractExtensive natural variation has been described for the timing of flowering initiation in many annual plants, including the model wild species Arabidopsis (Arabidopsis thaliana), which is presumed to be involved in adaptation to different climates. However, the environmental factors that might shape this genetic variation, as well as the molecular bases of climatic adaptation by modifications of flowering time, remain mostly unknown. To approach both goals, we characterized the flowering behavior in relation to vernalization of 182 Arabidopsis wild genotypes collected in a native region spanning a broad climatic range. Phenotype-environment association analyses identified strong altitudinal clines (0–2600 m) in seven out of nine flowering-related traits. Altitudinal clines were dissected in terms of minimum winter temperature and precipitation, indicating that these are the main climatic factors that might act as selective pressures on flowering traits. In addition, we used an association analysis approach with four candidate genes, FRIGIDA (FRI), FLOWERING LOCUS C (FLC), PHYTOCHROME C (PHYC), and CRYPTOCHROME2, to decipher the genetic bases of this variation. Eleven different loss-of-function FRI alleles of low frequency accounted for up to 16% of the variation for most traits. Furthermore, an FLC allelic series of six novel putative loss- and change-of-function alleles, with low to moderate frequency, revealed that a broader FLC functional diversification might contribute to flowering variation. Finally, environment-genotype association analyses showed that the spatial patterns of FRI, FLC, and PHYC polymorphisms are significantly associated with winter temperatures and spring and winter precipitations, respectively. These results support that allelic variation in these genes is involved in climatic adaptation.
Modulation of Phototropic Responsiveness in Arabidopsis through Ubiquitination of Phototropin 1 by the CUL3-Ring E3 Ubiquitin Ligase CRL3NPH3
Authors: Roberts Diana , Pedmale Ullas V. , Morrow Johanna , Sachdev Shrikesh , Lechner Esther , Tang Xiaobo , Zheng Ning , Hannink Mark , Genschik Pascal , Liscum Emmanuel 
Published: October 2011

Abstract
Plant phototropism is an adaptive response to changes in light direction, quantity, and quality that results in optimization of photosynthetic light harvesting, as well as water and nutrient acquisition. Though several components of the phototropic signal response pathway have been identified in recent years, including the blue light (BL) receptors phototropin1 (phot1) and phot2, much remains unknown. Here, we show that the phot1-interacting protein NONPHOTOTROPIC HYPOCOTYL3 (NPH3) functions as a substrate adapter in a CULLIN3-based E3 ubiquitin ligase, CRL3NPH3. Under low-intensity BL, CRL3NPH3 mediates the mono/multiubiquitination of phot1, likely marking it for clathrin-dependent internalization from the plasma membrane. In high-intensity BL, phot1 is both mono/multi- and polyubiquitinated by CRL3NPH3, with the latter event targeting phot1 for 26S proteasome-mediated degradation. Polyubiquitination and subsequent degradation of phot1 under high-intensity BL likely represent means of receptor desensitization, while mono/multiubiquitination-stimulated internalization of phot1 may be coupled to BL-induced relocalization of hormone (auxin) transporters.
How much unsuccessful quitting activity is going on among adult smokers? Data from the International Tobacco Control Four Country cohort survey
Authors: Borland Ron , Partos Timea R. , Yong Hua‐Hie , Cummings K. Michael , Hyland Andrew 
Published: October 2011

ABSTRACTAims  To document accurately the amount of quitting, length of quit attempts and prevalence of plans and serious thought about quitting among smokers.Design  We used longitudinal data from 7 waves of the International Tobacco Control Policy Evaluation Four Country Survey (ITC‐4). We considered point‐prevalence data and cumulative prevalence over the 7 years of the study. We also derived annual estimates of quit activity from reports of quit attempts starting only within more recent time‐frames, to control for biased recall.Setting  Australia, Canada, the United Kingdom and the United States.Participants  A total of 21 613 smokers recruited across seven waves.Measurements  Reported life‐time quit attempts, annual quit attempts, length of attempts, time since last attempt started, frequency of aborted attempts, plans to quit and serious thought about quitting.Findings  Around 40.1% (95% CI: 39.6–40.6) of smokers report attempts to quit in a given year and report an average of 2.1 attempts. Based on free recall, this translates to an average annual quit attempt rate of 0.82 attempts per smoker. Estimates derived only from the preceding month to adjust for recall bias indicate an annual rate of approximately one attempt per smoker. There is a high prevalence of quit‐related activity, with more than a third of smokers reporting thoughts or actions related to quitting in a given month. More than half the surveyed smokers eventually succeeded in quitting for at least 1 month, and a majority of these for over 6 months.Conclusions  Smokers think a great deal about stopping and make many unsuccessful quit attempts. Many have been able to last for extended periods and yet they still relapsed. More attention needs to be focused on translating quit‐related activity into long‐term abstinence.
What is the difference between dependence and withdrawal reactions? A comparison of benzodiazepines and selective serotonin re‐uptake inhibitors
Authors: Nielsen Margrethe , Hansen Ebba Holme , Gøtzsche Peter C. 
Published: October 2011

ABSTRACTAims  To explore the rationale for claiming that benzodiazepines cause dependence while selective serotonin re‐uptake inhibitors (SSRIs) do not.Methods  We analysed the definitions of dependence and withdrawal reactions as they had appeared over time in the Diagnostic Statistical Manual of Mental Diseases (DSM) and the International Classification of Diseases (ICD). We also compared the discontinuation symptoms described for the two drug groups in a systematic review.Results  The definition of substance dependence has changed over time in both the DSM and ICD. In the most recent classifications several criteria, including behavioural, physiological and cognitive manifestations, must be fulfilled. This change was published with the revision of the DSM‐III revision in 1987 (DSM‐IIIR), after the recognition of benzodiazepine dependence and just before the SSRIs were marketed in 1987–88. We found that discontinuation symptoms were described with similar terms for benzodiazepines and SSRIs and were very similar for 37 of 42 identified symptoms described as withdrawal reactions.Conclusions  Withdrawal reactions to selective serotonin re‐uptake inhibitors appear to be similar to those for benzodiazepines; referring to these reactions as part of a dependence syndrome in the case of benzodiazepines, but not selective serotonin re‐uptake inhibitors, does not seem rational.
Expression of natural killer cell activating receptors in patients with chronic lymphocytic leukaemia
Authors: Costello Régis T. , Knoblauch Benjamin , Sanchez Carole , Mercier Delphine , Le Treut Thérèse , Sébahoun Gérard 
Published: October 2011

SummaryRecent advances in chronic lymphocytic leukaemia (CLL) treatment, more particularly through upfront use of anti‐CD20 monoclonal antibodies, have prolonged patient progression‐free survival. Nonetheless, apart from allogeneic stem cell transplantation, no curative treatment is available. One possible explanation for the lack of cure in CLL could be a defective immune anti‐tumour response. As the result of abnormal HLA class I molecule expression, CLL cells escape from specific T‐lymphocyte immunity but should be the target for the innate natural killer (NK) cell‐mediated immune response. Defective NK cytotoxicity as the result of decreased expression of the natural cytotoxicity receptors (NCRs) NKp30/NCR3, NKp44/NCR2 and NKp46/NCR1 has been described in haematological malignancies such as acute myeloid leukaemia. This prompted us to focus our attention on NCR expression on NK cells from patients with CLL. Although we failed to detect any difference between CLL patients and healthy age‐matched controls, a precise analysis of clinical data showed a correlation between decreased NCR expression and poor prognosis factors such as low haemoglobin level, high (> 30 × 109 per litre) lymphocyte count or elevated C‐reactive protein. Together, these observations support the rationale for restoration of normal NK cell functions in patients with CLL, putatively through the use of immune therapy protocols that already have demonstrated some benefit in acute myeloid leukaemia such as interleukin‐2 plus histamine dihydrochloride.
p38a MAPK is involved in BMP‐2‐induced odontoblastic differentiation of human dental pulp cells
Authors: Qin W. , Lin Z. M. , Deng R. , Li D. D. , Song Z. , Tian Y. G. , Wang R. F. , Ling J. Q. , Zhu X. F. 
Published: October 2011

Qin W, Lin ZM, Deng R, Li DD, Song Z, Tian YG, Wang RF, Ling JQ, Zhu XF. p38a MAPK is involved in BMP‐2‐induced odontoblastic differentiation of human dental pulp cells. International Endodontic Journal, 45, 224–233, 2012.AbstractAim  To investigate whether the p38α mitogen‐activated protein kinases (MAPK) is involved in bone morphogenetic protein (BMP)‐2‐induced odontoblastic differentiation of human dental pulp cells (HDPCs).Methodology  Recombinant retrovirus encoding shRNA against p38α MAPK was constructed to investigate the role of p38α MAPK on BMP‐2‐induced odontoblastic differentiation of HDPCs. HDPCs were transfected with retrovirus expressing sh‐p38α. Activation of p38α MAPK was detected by Western blot. The effects of p38α MAPK on BMP‐2‐induced odontoblastic differentiation of HDPCs were measured by alkaline phosphatase (ALP) activity, and the expression of odontoblastic markers was identified by quantitative real‐time polymerase chain reaction analysis. The effect of SD‐282, a p38a‐specific inhibitor, on BMP‐2‐induced odontoblastic differentiation was also investigated.Results  BMP‐2 dose‐ and time‐dependently upregulated phosphorylation of p38α of HDPCs. Compared with BMP‐2‐treatment group, gene knock‐down of p38α MAPK significantly inhibited ALP activity and the formation of mineralized nodules in HDPCs. Moreover, suppression of p38α MAPK repressed the odontoblastic differentiation in HDPCs. Consistently, inhibition of p38α by SD‐282 also decreased odontoblastic differentiation.Conclusions  p38α MAPK is involved in BMP‐2‐induced odontoblastic differentiation of HDPCs.
A meta‐analysis of the traits affecting dispersal ability in butterflies: can wingspan be used as a proxy?
Authors: Sekar Sandhya 
Published: October 2011

Summary1. Dispersal ability of a species is a key ecological characteristic, affecting a range of processes from adaptation, community dynamics and genetic structure, to distribution and range size. It is determined by both intrinsic species traits and extrinsic landscape‐related properties.2. Using butterflies as a model system, the following questions were addressed: (i) given similar extrinsic factors, which intrinsic species trait(s) explain dispersal ability? (ii) can one of these traits be used as a proxy for dispersal ability? (iii) the effect of interactions between the traits, and phylogenetic relatedness, on dispersal ability.3. Four data sets, using different measures of dispersal, were compiled from published literature. The first data set uses mean dispersal distances from capture–mark–recapture studies, and the other three use mobility indices. Data for six traits that can potentially affect dispersal ability were collected: wingspan, larval host plant specificity, adult habitat specificity, mate location strategy, voltinism and flight period duration. Each data set was subjected to both unifactorial, and multifactorial, phylogenetically controlled analyses.4. Among the factors considered, wingspan was the most important determinant of dispersal ability, although the predictive powers of regression models were low. Voltinism and flight period duration also affect dispersal ability, especially in case of temperate species. Interactions between the factors did not affect dispersal ability, and phylogenetic relatedness was significant in one data set.5. While using wingspan as the only proxy for dispersal ability maybe problematic, it is usually the only easily accessible species‐specific trait for a large number of species. It can thus be a satisfactory proxy when carefully interpreted, especially for analyses involving many species from all across the world.