bluuebunny/crossref_metadata_2025 huggingface dataset:
Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees
Authors: Solomon Brad , Kingsford Carleton
Published: March 2015

Enormous databases of short-read RNA-seq sequencing experiments such as the NIH Sequence Read Archive (SRA) are now available. However, these collections remain difficult to use due to the inability to search for a particular expressed sequence. A natural question is which of these experiments contain sequences that indicate the expression of a particular sequence such as a gene isoform, lncRNA, or uORF. However, at present this is a computationally demanding question at the scale of these databases.

We introduce an indexing scheme, the Sequence Bloom Tree (SBT), to support sequence-based querying of terabase-scale collections of thousands of short-read sequencing experiments. We apply SBT to the problem of finding conditions under which query transcripts are expressed. Our experiments are conducted on a set of 2652 publicly available RNA-seq experiments contained in the NIH for the breast, blood, and brain tissues, comprising 5 terabytes of sequence. SBTs of this size can be queried for a 1000 nt sequence in 19 minutes using less than 300 MB of RAM, over 100 times faster than standard usage of SRA-BLAST and 119 times faster than STAR. SBTs allow for fast identification of experiments with expressed novel isoforms, even if these isoforms were unknown at the time the SBT was built. We also provide some theoretical guidance about appropriate parameter selection in SBT and propose a sampling-based scheme for potentially scaling SBT to even larger collections of files. While SBT can handle any set of reads, we demonstrate the effectiveness of SBT by searching a large collection of blood, brain, and breast RNA-seq files for all 214,293 known human transcripts to identify tissue-specific transcripts.

The implementation used in the experiments below is in C++ and is available as open source athttp://www.cs.cmu.edu/∼ckingsf/software/bloomtree.
MMR: A Tool for Read Multi-Mapper Resolution
Authors: Kahles Andre , Behr Jonas , Rätsch Gunnar
Published: March 2015

Motivation: Mapping high throughput sequencing data to a reference genome is an essential step for most analysis pipelines aiming at the computational analysis of genome and transcriptome sequencing data. Breaking ties between equally well mapping locations poses a severe problem not only during the alignment phase, but also has significant impact on the results of downstream analyses. We present the multimapper resolution (MMR) tool that infers optimal mapping locations from the coverage density of other mapped reads. Results: Filtering alignments with MMR can significantly improve the performance of downstream analyses like transcript quantitation and differential testing. We illustrate that the accuracy (Spearman correlation) of transcript quantification increases by 17% when using reads of length 51. In addition, MMR decreases the alignment file sizes by more than 50% and this leads to a reduced running time of the quantification tool. Our efficient implementation of the MMR algorithm is easily applicable as a post-processing step to existing alignment files in BAM format. Its complexity scales linearly with the number of alignments and requires no further inputs. Supplementary Material: Source code and documentation are available for download at http://github.com/ratschlab/mmr. Supplementary text and figures, comprehensive testing results and further information can be found at http://bioweb.me/mmr.
Burn or rot: leaf traits explain why flammability and decomposability are decoupled across species
Authors: Grootemaat Saskia , Wright Ian J. , van Bodegom Peter M. , Cornelissen Johannes H. C. , Cornwell William K.
Published: March 2015

In fireprone ecosystems, two important alternative fates for leaves are burning in a wildfire (when alive or as litter) or they get consumed (as litter) by decomposers. The influence of leaf traits on litter decomposition rate is reasonably well understood. In contrast, less is known about the influence of leaf traits on leaf and litter flammability. The aim of this study was twofold: (i) to determine which morphological and chemical leaf traits drive flammability and (ii) to determine whether different (combinations of) morphological and chemical leaf traits drive interspecific variation in decomposition and litter flammability and, in turn, help us understand the relationship between decomposability and flammability.

To explore the relationships between leaf traits and flammability of individual leaves, we used 32 evergreen perennial plant species from eastern Australia in standardized experimental burns on three types of leaf material (i.e. fresh, dried and senesced). Next, we compared these trait–flammability relationships to trait–decomposability relationships as obtained from a previous decomposition experiment (focusing on senesced leaves only).

Within the three parameters of leaf flammability that we measured, interspecific variation in time to ignition was mainly explained by specific leaf area and moisture content. Flame duration and smoulder duration were mostly explained by leaf dry mass and to a lesser degree by leaf chemistry, namely, nitrogen, phosphorus and tannin concentrations.

The variation in the decomposition constant across species was unrelated to our measures of flammability. Moreover, different combinations of morphological and chemical leaf properties underpinned the interspecific variation in decomposability and flammability. In contrast to litter flammability, decomposability was driven by lignin and phosphorus concentrations.

The decoupling of flammability and decomposability leads to three possible scenarios for species’ influence on litter fates: (i) fast‐decomposing species for which flammability is irrelevant because there will not be enough litter to support a fire; (ii) species with slow‐decomposing leaves and a high flammability; and (iii) species with slow‐decomposing leaves and a low flammability. We see potential for making use of the decoupled trait–decomposition–flammability relationships when modelling carbon and nutrient fluxes. Including information on leaf traits in models can improve the prediction of fire behaviour. We note that herbivory is another key fate for leaves, but this study was focused on fire and decomposition.
Utilizing spectral decomposition to determine the distribution of injected CO2 at the Snøhvit Field
Authors: White James C. , Williams Gareth A. , Grude Sissel , Chadwick R. Andrew
Published: March 2015

Time‐lapse 3D seismic reflection data, covering the CO2 storage operation at the Snøhvit gas field in the Barents Sea, show clear amplitude and time‐delay differences following injection. The nature and extent of these changes suggest that increased pore fluid pressure contributes to the observed seismic response, in addition to a saturation effect.

Spectral decomposition using the smoothed pseudo‐Wigner–Ville distribution has been used to derive discrete‐frequency reflection amplitudes from around the base of the CO2 storage reservoir. These are utilized to determine the lateral variation in peak tuning frequency across the seismic anomaly as this provides a direct proxy for the thickness of the causative feature.

Under the assumption that the lateral and vertical extents of the respective saturation and pressure changes following CO2 injection will be significantly different, discrete spectral amplitudes are used to distinguish between the two effects. A clear spatial separation is observed in the distribution of low‐ and high‐frequency tuning. This is used to discriminate between direct fluid substitution of CO2, as a thin layer, and pressure changes that are distributed across a greater thickness of the storage reservoir. The results reveal a striking correlation with findings derived from pressure and saturation discrimination algorithms based on amplitude versus offset analysis.
Imaging pre‐existing natural fractures using microseismic data
Authors: Kim Myungsun , Tak Heewon , Byun Joongmoo
Published: March 2015

In hydraulic fracturing treatments, locating not only hydraulic fractures but also any pre‐existing natural fractures and faults in a subsurface reservoir is very important. Hydraulic fractures can be tracked by locating microseismic events, but to identify the locations of natural fractures, an additional technique is required. In this paper, we present a method to image pre‐existing fractures and faults near a borehole with virtual reverse vertical seismic profiling data or virtual single‐well profiling data (limited to seismic reflection data) created from microseismic monitoring using seismic interferometry. The virtual source data contain reflections from natural fractures and faults, and these features can be imaged by applying migration to the virtual source data. However, the imaging zone of fractures in the proposed method is strongly dependent on the geographic extent of the microseismic events and the location and direction of the fracture. To verify our method, we produced virtual reverse vertical seismic profiling and single‐well profiling data from synthetic microseismic data and compared them with data from real sources in the same relative position as the virtual sources. The results show that the reflection travel times from the fractures in the virtual source data agree well with travel times in the real‐source data. By applying pre‐stack depth migration to the virtual source data, images of the natural fractures were obtained with accurate locations. However, the migrated section of the single‐well profiling data with both real and virtual sources contained spurious fracture images on the opposite side of the borehole. In the case of virtual single‐well profiling data, we could produce correct migration images of fractures by adopting directional redatuming for which the occurrence region of microseismic events is divided into several subdivisions, and fractures located only on the opposite side of the borehole are imaged for each subdivision.
Business Growth, Size and Age: Evidence from the Business Longitudinal Survey (BLS) Data in Australia
Authors: Bhattacharya Mita
Published: March 2015

Despite the important role small and medium‐sized enterprises (SMEs) play in the Australian economy, little is known from empirical literature on the formation, growth and frequent dissolution of these businesses. Considering the dynamics of business behaviour, this article analyses the performance, business formation (or dissolution) and variability of growth. Using only available Business Longitudinal Survey (BLS) data from the Australian Bureau of Statistics (ABS), manufacturing businesses are considered for the analysis. Firm growth, the variability of firm growth and the probability that a firm will fail (or survive) depend on firm age. Incorporating the age for Australian businesses, we are able to explain the importance of maturity in analysing growth and survival process of SMEs.
Patent Protection, Innovation and Technology Licensing
Authors: Wang Leonard F.S. , Mukherjee Arijit
Published: March 2015

We show that the common wisdom suggesting higher investment in innovation under a stronger patent protection may not be true if the innovator can license its technology ex‐post innovation. If the initial cost of production is high and the slope of the marginal cost of undertaking innovation is moderate, investment in innovation is maximised at a patent protection that is weaker than the strongest patent protection. Otherwise, strongest patent protection maximises investment in innovation. We also show that welfare is maximised neither at the strongest patent protection nor at the weakest patent protection but at an intermediate patent protection. Our results are important for patent policies.
When Second‐Best is Still a No‐Brainer: Why Labour Should Shoot for a Majority Coalition in May 2015
Authors: Yong Ben , Bale Tim
Published: March 2015

The chances of Labour winning the 2015 general election with a comfortable overall majority are vanishingly small. It could, however, emerge as the largest party or finish just a handful of seats behind the Conservatives. Either scenario would give it at least a chance—and a bigger chance than many realise, we argue—of forming a government. In that event, Labour may be faced with a choice between getting together with another party (or parties) to form a majority coalition or else forming a minority government (either on its own or with one or more partners), which could assemble different majorities for different pieces of legislation or try to negotiate a ‘confidence and supply’ agreement. Given the precedents from the UK and overseas, we argue that, faced with this dilemma, Labour should do all it can to form a majority coalition. We also argue that Labour can learn some useful lessons from the Cameron–Clegg coalition.
It matters whether reading comprehension is conceptualised as rate or accuracy
Authors: Rønberg Louise Flensted , Petersen Dorthe Klint
Published: March 2015

This study shows that it makes a difference whether accuracy measures or rate measures are used when assessing reading comprehension. When the outcome is reading comprehension accuracy (i.e., the number of correct responses), word reading skills (measured as access to orthographic representations) account for a modest amount of the variance in the reading comprehension of 10‐year old children. However, this changes when reading comprehension is conceptualised as rate (i.e., number of correct responses per minute); when this is done, the correlation with word reading increases. The result was validated in two different reading comprehension tests. Moreover, this study indicates that it is not merely efficient word reading that influences the process of comprehending at a fast rate. When word reading and receptive vocabulary are controlled, a written measure of the ability to access and connect similar word meanings (synonym judgement) explains additional variance in reading comprehension rate.
Gardening the Wild: Change in the Flora and Vegetation of a Suburban Coastal Reserve 1911–2013
Authors: IVEY‐LAW MEGAN , KIRKPATRICK JAMIE B.
Published: March 2015

Intensively used and managed remnants of native vegetation in cities can have characteristics that result as much from ecological gardening as processes independent of humans. We test the degree to which the changes in vegetation of the Bayside Reserve, Melbourne, are consistent with the outcome we would expect from an ecologically gardened nature and to what degree they reflect ongoing processes of exotic invasion and synthetic vegetation dynamics. We compared species lists from 1911, 1971 and 2013 and sample area data from 1971 and 2013. The flora became richer and more exotic, although some native plant species lost in 1971 had been reintroduced to the reserve in 2013. Between 1971 and 2013, the vegetation increased in cover, shrub and tree density, sample areas species richness, and nativeness, the latter two results being inconsistent with the usual patterns of increasing exoticness and decline in species richness with shrub and tree encroachment. These variations from normality were likely to have resulted from the impacts of planting of natives and weeding of exotics, activity that has created combinations of species that probably never occurred in pre‐European vegetation. Although it might not be possible to return to pre‐European ecosystems within this vegetation remnant, the gardened approximation helps some locally uncommon species survive and may make people more sympathetic to nature conservation as a whole.
Feasibility of Including Green Tea Products for an Analytically Verified Dietary Supplement Database
Authors: Saldanha Leila , Dwyer Johanna , Andrews Karen , Betz Joseph , Harnly James , Pehrsson Pamela , Rimmer Catherine , Savarala Sushma
Published: March 2015

The Dietary Supplement Ingredient Database (DSID) is a federally funded, publicly accessible dietary supplement database that currently contains analytically derived information on micronutrients in selected adult and children's multivitamin and mineral (MVM) supplements. Other constituents in dietary supplement products such as botanicals are also of interest and thus are being considered for inclusion in the DSID. Thirty‐eight constituents, mainly botanicals were identified and prioritized by a federal interagency committee. Green tea was selected from this list as the botanical for expansion of the DSID. This article describes the process for prioritizing dietary ingredients in the DSID. It also discusses the criteria for inclusion of these ingredients, and the approach for selecting and testing products for the green tea pilot study.
What Shapes Abortion Law? – A Global Perspective
Authors: Hildebrandt Achim
Published: March 2015

This article analyses a correlate of abortion law that has not been addressed in previous research: the effects of past or present communist rule. As communists reject any moral standards that were based on religious beliefs, they liberalized abortion law after they gained power. A quantitative analysis of 170 nations shows that countries with a communist past or present have more liberal abortion laws.

Moreover, abortion law tends to be more liberal, the more modern and globalized a country is and the more women are represented in the workforce and in parliament. A larger percentage of Catholics in the population, in contrast, correlates with more restrictive legislation. Some countries do not fit this general pattern and the article discusses the reasons. Based on the empirical results it goes on to present the implications of the findings for public policy: in many countries strong and persistent socioeconomic and cultural forces stand in the way of further abortion law liberalization. Under these conditions, proponents of liberalization have greater chances of success if they take a moderate stance and focus on women's health instead of women's rights.
Referral patterns for oral squamous cell carcinoma in Australia: 20 years progress
Authors: Kaing L , Manchella S , Love C , Nastri A , Wiesenfeld D
Published: March 2015

Background

The aim of this study was to identify changes in referral patterns and delays in diagnosis and treatment of oral squamous cell carcinoma (OSCC), managed at a tertiary institution in Victoria, Australia.

Methods

The hospital records of all patients with newly diagnosed OSCC, managed by The Royal Melbourne Hospital (RMH) Head and Neck Tumour Stream between January 2008 and December 2010, were retrospectively reviewed.

Results

Of the 101 patients, 52% first sought help from general medical practitioners (GMP) while 43% initially attended a general dental practitioner (GDP). The most common site of OSCC was oral tongue (42%). The most common presentation was ulceration (31%). Seventy per cent of patients presented with T1 (39%) or T2 (31%) tumours. The diagnostic delay ranged from 0 to 8 years with an average of 4.5 months. Patient delay ranged from 0 to 1.4 years with an average of 1.8 months. Professional delay ranged from 0 to 8 years with an average of 2 months.

Conclusions

Delays in patients seeking advice have decreased compared to previous studies, while delays in professionals making a diagnosis have not improved considerably. There has been a significant shift towards initial presentation to GMP rather than GDP. Further decrease in delays is possible by improving both population awareness and clinician education.
Phosphorus conservation during post‐fire regeneration in a Chilean temperate rainforest
Authors: Seaman B. J. , Albornoz F. E. , Armesto J. J. , Gaxiola A.
Published: March 2015

Nitrogen and phosphorus are the main elements limiting net primary production in terrestrial ecosystems. When growing in nutrient‐poor soils, plants develop physiological mechanisms to conserve nutrients, such as reabsorbing elements from senescing foliage (i.e. nutrient retranslocation). We investigated the changes in soil N and P in post‐fire succession in temperate rainforests of southern Chile. In this area, forest recovery often leads to spatially scattered, discrete regeneration with patches varying in age, area, species richness and tree cover, representing different degrees of recovery from disturbance. We hypothesized that soil nutrient concentrations should differ among tree regenerating patches depending on the progress of forest regeneration and that nutrient resorption should increase over time as colonizing trees respond to limited soil nutrients. To evaluate these hypotheses, we sampled 40 regeneration patches in an area of 5 ha, spanning a broad range of vegetation complexity, and collected soil, tree foliage and litter samples to determine N and P concentrations. Nutrient concentrations in leaf litter were interpreted as nutrient resorption proficiency. We found that soil P was negatively correlated with all the indicators of successional progress, whereas total soil N was independent of the successional progress. Foliar N and P were unrelated to soil nutrient concentrations; however, litter N was negatively related to soil N, and litter P was positively related with soil P. Finally, foliar N:P ratios ranged from 16 to 25, which suggests that P limitation can hamper post‐fire regeneration. We provide evidence that after human‐induced fires, succession in temperate forests of Chile can become nutrient limited and that high nutrient retranslocation is a key nutrient conservation strategy for regenerating tree communities.
Investigation of Recessive Effects in Schizophrenia Using Next‐Generation Exome Sequence Data
Authors: Curtis David
Published: March 2015

A number of gene‐wise approaches to analysis were applied to whole exome sequence data from 2545 Swedish schizophrenia cases with 2545 matched controls. A weighted burden test was used to detect dominant and additive effects. Recessive effects were investigated by testing whether there was an excess of cases bearing two or more rare, functional variants or whether there was an excess of cases in which both phased haplotypes carried at least one rare, functional variant. Counts for cases were compared with controls and also with the expectation under Hardy‐Weinberg equilibrium. Analyses were performed using the SCOREASSOC program. No gene produced statistically significant results although COMT was highly ranked by the weighted burden test and within it the Ala72Ser polymorphism rs6267 had an uncorrected p value of 0.00003. A number of spurious results were generated, some apparently due to miscalling of homozygotes and others due to a failure to eradicate the effects of linkage disequilibrium between variants. These problems were not marked when using phased haplotypes but this method failed to produce any significant or suggestive findings. If there are exonic variants with recessive effects on the risk of schizophrenia, then the methods used were unable to detect them.
Ventricular Conduction Defects After Transcatheter Aortic Valve Implantation: A Single‐Institute Analysis
Authors: Kawaguchi Akira T. , D'Allessandro Cosimo , Collet Jean Philippe , Cluzel Philippe , Makri Ralouka , Leprince Pascal
Published: March 2015

Patients with aortic stenosis tend to develop ventricular conduction problems, which are known adverse events following transcatheter aortic valve implantation (TAVI). Changes in ventricular conduction status after TAVI were analyzed in 195 consecutive patients from a single institute registered in FRANCE2 between February 2010 and June 2012. Among the 195 patients, 29 had a prior pacemaker implantation (+PM) and 6 had acute catastrophic hemodynamics that made a full electrocardiogram (ECG) unavailable. Among the remaining 160, PM was newly required in 28 (17.5%, PM+) but not in 132 (PM−), which included 21 (13.1%) who developed new left bundle branch block (BBB), 12 (7.5%) had right BBB, and 99 (61.9%) had no change. While PM requirement had no correlation with preoperative factors, there was significant association with the development of right BBB with Edwards Sapien/XT (P = 0.003), and new left BBB (P = 0.012) and complete heart block requiring PM with CoreValve (22.6% vs. Edwards Sapien/XT, 7.4%, P = 0.016). Whereas postoperative survival regarding PM status (+PM, PM+, PM–), vascular access, valve size or type showed no difference, delayed heart block (n = 12, Day 2 or later) was associated with poor survival (P = 0.038) compared with the remaining PM+ patients with earlier onset (n = 16, Day 0 or 1). As a result, PM+ patients (n = 28) had significantly longer intensive care unit (ICU) stay and hospitalization than PM− or +PM patients. The results suggest that ventricular conduction problems requiring PM occurred more frequently after TAVI (17.5%) than with usual surgical replacement. Nonetheless, conduction problems failed to influence postoperative survival for up to 3 years on average with use of PM, but therefore did increase medical costs.
Acetylcholine contributes to control the physiological inflammatory response during the peri‐implantation period
Authors: Paparini D. , Gori S. , Grasso E. , Scordo W. , Calo G. , Pérez Leirós C. , Ramhorst R. , Salamone G.
Published: March 2015

Background

Maternal antigen‐presenting cells attracted to the pregnant uterus interact with trophoblast cells and modulate their functional profile to favour immunosuppressant responses. Non‐neuronal cholinergic system is expressed in human cytotrophoblast cells and in immune cells with homeostatic regulatory functions.

Aim

The aim of this work was to evaluate whether non‐neuronal acetylcholine conditions maternal monocyte and DC migration and activation profiles.

Methods

We used an in vitro model resembling maternal–placental interface represented by the co‐culture of human trophoblast cells (Swan‐71 cell line) and monocytes or DC.

Results

When cytotrophoblast cells were treated with neostigmine (Neo) to concentrate endogenous acetylcholine levels, monocyte migration was increased. In parallel, high levels of IL‐10 and decreased levels of TNF‐α were observed upon interaction of maternal monocytes with trophoblast cells. This effect was synergized by Neo and was prevented by atropine, a muscarinic acetylcholine receptor antagonist. Similarly, trophoblast cells increased the migration of DC independently of Neo treatment; however, enhanced IL‐10 and MCP‐1 synthesis in trophoblast–DC co‐cultures with no changes in TNF‐α and IL‐6 was observed. In fact, there were no changes in HLA‐DR, CD86 or CD83 expression. Finally, trophoblast cells treated with Neo increased the expression of two antigen‐presenting cells attracting chemokines, MCP‐1, MIP‐1α and RANTES through muscarinic receptors, and it was prevented by atropine.

Conclusions

Our present results support a novel role of acetylcholine synthesized by trophoblast cells to modulate antigen‐presenting cell migration and activation favouring an immunosuppressant profile that contributes to immune homeostasis maintenance at the maternal–foetal interface.
Appraisals to affect: Testing the integrative cognitive model of bipolar disorder
Authors: Palmier‐Claus Jasper E. , Dodd Alyson , Tai Sara , Emsley Richard , Mansell Warren
Published: March 2015

Objective

Cognitive models have suggested that extreme appraisals of affective states and maladaptive affect regulation strategies are important in the development of bipolar symptomatology. Little is known about the pathway by which these appraisals and behaviours interact in the formation of activated and depressed affective states. This study tested the predictions that (1) ascent behaviours mediate the relationship between positive appraisals of activated mood and activation; and (2) descent behaviours mediate the relationship between negative appraisals of activated mood and depression.

Method

A total of 52 individuals with a DSM‐IV diagnosis of bipolar I or II disorder (confirmed by structured interview) completed biweekly assessments of affect regulation behaviours and mood for 4 weeks. Positive and negative appraisals of affective states were assessed at baseline through the Hypomanic Attitudes and Positive Prediction Inventory. Multilevel mediation analysis was used to explore the data.

Results

Ascent behaviours partially mediated the relationship between positive appraisals of activated mood and activation. Descent behaviours, but not negative appraisals of activated mood, predicted levels of depression indicating the absence of a mediation effect.

Conclusion

The results suggest that positive appraisals of activated mood can escalate activation in individuals with bipolar disorder. Such appraisals may be inherently rewarding and reinforcing directly elevating levels of activation, whilst increasing individuals' use of ascent behaviours. The results are consistent with the view that appraisals and behaviours should be targeted during cognitive behavioural therapy for bipolar disorder.

Practitioner points

It may be beneficial to target positive appraisals of activated mood in cognitive behavioural therapy for mania.

Cognitive behavioural therapists may also wish to focus on identifying and targeting individuals' use of ascent behaviours to reduce highly activated states.
Second malignancies following treatment of chronic myeloid leukaemia in the tyrosine kinase inhibitor era
Authors: Gunnarsson Niklas , Stenke Leif , Höglund Martin , Sandin Fredrik , Björkholm Magnus , Dreimane Arta , Lambe Mats , Markevärn Berit , Olsson‐Strömberg Ulla , Richter Johan , Wadenvik Hans , Wallvik Jonas , Själander Anders
Published: March 2015

Given that tyrosine kinase inhibitors (TKIs) have dramatically improved the survival of patients with chronic myeloid leukaemia (CML), we were interested in examining the possible risk of long‐term adverse events, such as the emergence of other neoplasms. Therefore, we studied the development of second malignancies in 868 patients diagnosed with CML between 2002 and 2011 using the Swedish CML register, cross‐linked to the Swedish Cancer register. With a median follow‐up of 3·7 (range 0–9·9) years, 65 (7·5%) patients developed 75 second malignancies (non‐haematological), 52 of which were of the invasive type. Compared to expected rates in the background population, the risk of second malignancies was higher in the CML cohort, with a standardized incidence ratio (SIR) of 1·52 (95% CI 1·13–1·99). The SIR before and after the second year following diagnosis of CML was 1·58 and 1·47, respectively. Among specific cancer types, gastrointestinal and nose and throat cancer were significantly increased. Founded on a population‐based material, our results indicate that CML patients treated in the TKI era are at an increased risk of developing a second malignancy, with indications that this risk may more likely be linked to CML itself rather than to the TKI treatment.
Risk factors for pericardial effusion in adult patients receiving allogeneic haematopoietic stem cell transplantation
Authors: Liu Yao‐Chung , Chien Sheng‐Hsuan , Fan Nai‐Wen , Hu Ming‐Hung , Gau Jyh‐Pyng , Liu Chia‐Jen , Yu Yuan‐Bin , Liu Chun‐Yu , Hsiao Liang‐Tsai , Liu Jin‐Hwang , Chiou Tzeon‐Jye , Tzeng Cheng‐Hwai
Published: March 2015

Pericardial effusion (PE) is a rare but potentially life‐threatening complication for allogeneic haematopoietic stem cell transplantation (HSCT) recipients. The risk factors, aetiology, incidence and therapy are largely unclear. To investigate this issue, we reviewed 391 adult patients undergoing allogeneic HSCT between January 2003 and December 2013. Twelve out of 391 patients (3·1%) developed PE of moderate to large amounts, including 9 out of 12 patients (75%) identified as late‐onset PE. Two out of the nine patients with late‐onset PE experienced recurrent effusion. The median age at HSCT was 44·5 years (range: 22–63 years) among the 12 patients with PE and 47 years in the late‐onset patients. Multivariate analysis revealed that multiple transplant procedures was a significant risk factor for PE (P = 0·036) and a trend as risk factor in patients aged>50 years (P = 0·066). For late‐onset PE, pre‐transplant age>50 years (P = 0·032) and extensive chronic graft‐versus‐host disease (cGVHD) (P = 0·006) remained statistically significant on multivariate analysis. Currently, there are no published data exploring the risk factors for post‐transplant PE in adult patients of allogeneic HSCT. Our study determined the risk factors and incidence for the post‐transplant PE, especially in the late‐onset group.
Fabry disease and enzyme replacement therapy in classic patients with same mutation: different formulations – different outcome?
Authors: Politei J. , Schenone A.B. , Cabrera G. , Heguilen R. , Szlago M.
Published: March 2015

We describe the results of the multidisciplinary evaluation in patients with Fabry disease and the same genetic mutation and their outcomes using different approved enzyme replacement therapy (ERT). We measured baseline data and serial results of neuropathic pain assessment and renal, cardiac and cerebrovascular functioning. Pain scale showed improvement in all male cases treated with agalsidasa beta. A mild improvement was detected in agalsidasa alfa‐treated patients after 1 year with posterior increase. During the agalsidase beta shortage, two male patients were switched to agalsidasa alfa, after 1 year both cases presented an increase in scale values. Renal evolution showed a tendency toward a decrease in proteinuria in patients using agalsidase beta and worsening with agalsidase alfa. We found improvement in two females using agalsidase beta and no changes in the other cases regarding cardiac functioning. Brain magnetic resonance imaging (MRI) showed increase of white matter lesions in four patients. Improvement and stabilization in neuropathic pain, renal and cardiac functioning and brain MRI were found mainly in patients treated with agalsidase beta. Following the reported recommendations on reintroduction of agalsidase beta after the enzyme shortage, we decided to switch all patients to agalsidase beta.
Genetic risk factors affecting mitochondrial function are associated with kidney disease in people with Type 1 diabetes
Authors: Swan E. J. , Salem R. M. , Sandholm N. , Tarnow L. , Rossing P. , Lajer M. , Groop P. H. , Maxwell A. P. , McKnight A. J. ,   the GENIE Consortium
Published: March 2015

Aim

To evaluate the association with diabetic kidney disease of single nucleotide polymorphisms (SNPs) that may contribute to mitochondrial dysfunction.

Methods

The mitochondrial genome and 1039 nuclear genes that are integral to mitochondrial function were investigated using a case (n = 823 individuals with diabetic kidney disease) vs. control (n = 903 individuals with diabetes and no renal disease) approach. All people included in the analysis were of white European origin and were diagnosed with Type 1 diabetes before the age of 31 years. Replication was conducted in 5093 people with similar phenotypes to those of the discovery collection. Association analyses were performed using the plink genetic analysis toolset, with adjustment for relevant covariates.

Results

A total of 25 SNPs were evaluated in the mitochondrial genome, but none were significantly associated with diabetic kidney disease or end‐stage renal disease. A total of 38 SNPs in nuclear genes influencing mitochondrial function were nominally associated with diabetic kidney disease and 16 SNPS were associated with end‐stage renal disease, secondary to diabetic kidney disease, with meta‐analyses confirming the same direction of effect. Three independent signals (seven SNPs) were common to the replication data for both phenotypes with Type 1 diabetes and persistent proteinuria or end‐stage renal disease.

Conclusions

Our results suggest that SNPs in nuclear genes that influence mitochondrial function are significantly associated with diabetic kidney disease in a white European population.
Intensive multifactorial treatment modifies the effect of family history of diabetes on glycaemic control in people with Type 2 diabetes: a post hoc analysis of the ADDITION‐Denmark randomized controlled trial
Authors: Eliraqi G. M. , Vistisen D. , Lauritzen T. , Sandbæk A. , Jørgensen M. E. , Færch K.
Published: March 2015

Aim

To investigate whether intensive multifactorial treatment can reverse the predisposed adverse phenotype of people with Type 2 diabetes who have a family history of diabetes.

Methods

Data from the randomized controlled trial ADDITION‐Denmark were used. A total of 1441 newly diagnosed patients with diabetes (598 with family history of diabetes) were randomized to intensive treatment or routine care. Family history of diabetes was defined as having one parent and/or sibling with diabetes. Linear mixed‐effects models were used to assess the changes in risk factors (BMI, waist circumference, blood pressure, lipids and HbA1c) after 5 years of follow‐up in participants with and without a family history of diabetes. An interaction term between family history of diabetes and treatment group was included in the models to test for a modifying effect of the intervention. All analyses were adjusted for age, sex, baseline value of the risk factor and general practice (random effect).

Results

At baseline, participants with a family history of diabetes were younger and had a 1.1 mmol/mol (0.1%) higher HbA1c concentration at the time of diagnosis than those without a family history of diabetes. Family history of diabetes modified the effect of the intervention on changes in HbA1c levels. In the group receiving routine care, participants with a family history of diabetes experienced an improvement in HbA1c concentration that was 3.3 mmol/mol (0.3%) lower than the improvement found in those without a family history of diabetes after 5 years of follow‐up. In the intensive treatment group, however, there was no difference in HbA1c concentrations between participants with and without a family history of diabetes after 5 years of treatment.

Conclusions

Intensive treatment of diabetes may partly remove the adverse effects of family history of diabetes on glycaemic control. The effect of this improvement on long‐term diabetic complications warrants further investigation.
Impact of the Diabetes Inpatient Care and Education (DICE) project and the DICE Care Pathway on patient outcomes and trainee doctor's knowledge and confidence
Authors: Rajendran R. , Kerry C. , Round R.‐M. , Barker S. , Scott A. , Rayman G.
Published: March 2015

Aim

To evaluate the impact of the Diabetes Inpatient Care and Education project and a comprehensive diabetes care pathway, the Diabetes Inpatient Care and Education Care Pathway, on patient outcomes and on the knowledge and confidence of trainee doctors.

Methods

The effect on patient outcomes was evaluated by comparing the National Diabetes Inpatient Audit data before (2012) and after (2013) implementing the Diabetes Inpatient Care and Education project. The impact on trainee doctors was evaluated using the Modified Kirkpatrick model. Just before the project began and again 3 months later, trainee doctors were surveyed to assess their knowledge and confidence in inpatient diabetes care.

Results

Patient harm was found to have been reduced significantly when National Diabetes Inpatient Audit data for 2012 and 2013 were compared. Severe hypoglycaemia decreased from 15.4 to 9.7%, medication errors from 56.9 to 21.1% and insulin errors from 31 to 7%. Across the 96 trainee doctors surveyed, the mean (sd) knowledge and confidence scores increased significantly (P < 0.001 for both) from 57.1 (16.8) and 61.8 (14.9) to 68.4 (13.3) and 74.3 (11.7), respectively.

Conclusion

The Diabetes Inpatient Care and Education project and the Diabetes Inpatient Care and Education Care Pathway improved patient outcomes and the knowledge and confidence of trainee doctors in this hospital. The impact of a similar project in other hospitals needs to be evaluated.
Greater consumption of protein‐poor anthropogenic food by urban relative to rural coyotes increases diet breadth and potential for human–wildlife conflict
Authors: Murray M. , Cembrowski A. , Latham A. D. M. , Lukasik V. M. , Pruss S. , St Clair C. C.
Published: March 2015

Reports of encounters between people and generalist urban‐adapted carnivores are increasing around the world. In North America, coyotes Canis latrans are among the carnivores that appear to be especially capable of incorporating novel anthropogenic food types, including those found in cities. Consuming anthropogenic food may benefit coyotes by increasing their dietary diversity, but it may also lead to increased interactions and conflicts with humans. To test these hypotheses, we compared the diets of urban and rural coyotes from two urban and three rural sites spanning 32 200 km2 in Alberta, Canada. We analyzed scat samples to calculate diet diversity at the level of both individuals (species per scat) and populations (Shannon index) and to determine the frequency of anthropogenic food consumption. We complemented this comparison with stable isotope analyses of hair samples taken from individual urban and rural coyotes that were or were not reported by the public for repeatedly visiting backyards and schoolyards during the day. Relative to rural coyotes, urban coyotes had more diverse diets at the level of both individuals and populations, consumed anthropogenic food more often, and animals less often, than rural coyotes. Although urban coyotes assimilated more anthropogenic food than the rural coyotes overall, the urban coyotes reported for conflict assimilated less protein and were more likely to be diseased. Our results suggest that processed anthropogenic food may contribute to the success of urban coyotes, but does not entirely correlate with conflict. Instead, some seemingly innocuous, but low‐protein food sources such as bird feeders, compost, and cultivated fruit trees may contribute disproportionately to encounters with people for coyotes and other urban‐adapted opportunistic carnivores.
Multicentered patient‐based evidence of the role of free light chain ratio normalization in multiple myeloma disease relapse
Authors: Radocha Jakub , Pour Luděk , Pika Tomáš , Maisnar Vladimír , Špička Ivan , Gregora Evžen , Krejčí Marta , Minařík Jiří , Machálková Kateřina , Straub Jan , Pavlíček Petr , Hájek Roman , Žák Pavel
Published: March 2015

Introduction

The normalization of free light chain ratio (FLCr) has been introduced as a marker of stringent complete remission (CR) of multiple myeloma (MM). There is currently a lack of literature assessing the role of FLCr on MM disease progression and remission status.

Patients and methods

A multicentered retrospective review of 125 patients with MM in CR and various FLCr values was completed. Parameters of interest included patient demographics, FLCr values, complete remission (CR)/relapse status, and time to progression (TTP). The FLCr values were recorded to provide time‐dependent findings on the role of FLCr on progression‐free survival and overall survival (OS).

Results

The mean follow‐up time of 125 patients from five hospitals in the Czech Republic was 31 months. A total of 47.2% of patients relapsed (54 of 125) during the follow‐up period. The median TTP of patients with normal FLCr (n = 66) was 54.4 and 40.2 months for patients with abnormal FLCr (n = 59) (P = 0.217). None of the patients reached median overall survival regardless of FLCr values (P = 0.821). In the subgroup of newly diagnosed patients after upfront autologous stem cell transplantation (ASCT), there were 55.6% of patients (35 of 63) with normal FLCr and 44.4% (28 of 64) with abnormal FLCr. A total of 34.9% of patients (22 of 63) relapsed in this subgroup. Within the abnormal FLCr patients, a median TTP was 56.3 months, but no median TTP was reached among the normal FLCr patients (P = 0.746). Median OS in patients with normal (nFLCr) and abnormal FLCr (aFLCr) was not reached (P = 0.787).

Conclusion

We did not observe any benefit from FLCr normalization in CR in myeloma patients in terms of progression‐free survival or overall survival.
Unifying ecology and macroevolution with individual‐based theory
Authors: Rosindell James , Harmon Luke J. , Etienne Rampal S.
Published: March 2015

A contemporary goal in both ecology and evolutionary biology is to develop theory that transcends the boundary between the two disciplines, to understand phenomena that cannot be explained by either field in isolation. This is challenging because macroevolution typically uses lineage‐based models, whereas ecology often focuses on individual organisms. Here, we develop a new parsimonious individual‐based theory by adding mild selection to the neutral theory of biodiversity. We show that this model generates realistic phylogenies showing a slowdown in diversification and also improves on the ecological predictions of neutral theory by explaining the occurrence of very common species. Moreover, we find the distribution of individual fitness changes over time, with average fitness increasing at a pace that depends positively on community size. Consequently, large communities tend to produce fitter species than smaller communities. These findings have broad implications beyond biodiversity theory, potentially impacting, for example, invasion biology and paleontology.
Aphis (Toxoptera) citricidus (Kirkaldy) [Hemiptera: Aphididae] and Chile
Authors: Nieto Nafría J. M. , Fuentes‐Contreras E. , Pérez Hidalgo N.
Published: March 2015

As there was no consensus on the presence or absence of Aphis (Toxoptera) citricidus (Kirkaldy) in Chile, a meticulous literature survey has been carried out to clarify the issue. From this survey, it can be concluded that A. (T.) citricidus is not present in Chile, that it has never been cited as present from first‐hand information/observations in this country, and that all available Chilean records of this species are due to old (and now abandoned) taxonomic interpretations or poor transmission of information.
Première observation du puceron brun Pterochloroides persicae (Cholodkovsky) (Homoptera, Aphididae, Lachninae) sur pêcher en Algérie
Authors: Laamari M. , Cœur d'Acier A. , Jousselin E.
Published: March 2015

Le puceron brun Pterochloroides persicae a été observé pour la première fois sur pêcher (Prunus persica) en Algérie (localités de Batna et Arris ; Nord‐est algérien) en septembre 2013. Au cours du mois de décembre de la même année, d'autres colonies se sont installées sur Prunus armeniaca, Salix pedicellata et Salix babylonica. Sur le même arbre et durant la journée, les colonies se déplacent continuellement à la recherche des endroits les moins exposés au soleil.
Data on ecology of the purple scale Lepidosaphes beckii (Newman) on citrus in Greece
Authors: Stathas G. J. , Skouras P. J. , Kontodimas D. C.
Published: March 2015

The ecology of the purple scale Lepidosaphes beckii (Newman) (Hemiptera: Diaspididae) was studied on citrus, in the area of Kalamata (Messinia ‐ Peloponnese) from May 2009 to May 2011. Observations on infested citrus branches were conducted to study the phenology of the scale. Yellow sticky traps were hung in infested trees and examined to monitor the flights of male L. beckii as well as the flights of adults of parasitoids and predators of this pest. Lepidosaphes beckii mainly infested the leaves and fruits and to a lesser extent the shoots and stems. During the period of the study all developmental stages of L. beckii were found. Sticky transparent band traps were also placed on shoots and were examined to monitor the fluctuation in the population of crawlers. From the crawlers caught in the traps three population peaks were recorded in June, August and October. Natural enemies of the scale consisted of the parasitoids Aphytis lepidosaphes Compère and Encarsia sp. (Hymenoptera: Aphelinidae), which together parasitized up to 32% of L. beckii as well as the predators Chilocorus bipustulatus (L.) and Rhyzobius lophanthae Blaisdell (Coleoptera: Coccinellidae).