bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying similarity in animal vocal sequences: which metric performs best?
Authors: Kershenbaum Arik , Garland Ellen C. 
Published: July 2015

SummaryMany animals communicate using sequences of discrete acoustic elements which can be complex, vary in their degree of stereotypy, and are potentially open‐ended. Variation in sequences can provide important ecological, behavioural or evolutionary information about the structure and connectivity of populations, mechanisms for vocal cultural evolution and the underlying drivers responsible for these processes. Various mathematical techniques have been used to form a realistic approximation of sequence similarity for such tasks.Here, we use both simulated and empirical data sets from animal vocal sequences (rock hyrax,Procavia capensis; humpback whale,Megaptera novaeangliae; bottlenose dolphin,Tursiops truncatus; andCarolina chickadee,Poecile carolinensis) to test which of eight sequence analysis metrics are more likely to reconstruct the information encoded in the sequences, and to test the fidelity of estimation of model parameters, when the sequences are assumed to conform to particular statistical models.Results from the simulated data indicated that multiple metrics were equally successful in reconstructing the information encoded in the sequences of simulated individuals (Markov chains,n‐gram models, repeat distribution and edit distance) and data generated by different stochastic processes (entropy rate andn‐grams). However, the string edit (Levenshtein) distance performed consistently and significantly better than all other tested metrics (including entropy,Markov chains,n‐grams, mutual information) for all empirical data sets, despite being less commonly used in the field of animal acoustic communication.TheLevenshtein distance metric provides a robust analytical approach that should be considered in the comparison of animal acoustic sequences in preference to other commonly employed techniques (such asMarkov chains, hiddenMarkov models orShannon entropy). The recent discovery that non‐Markovian vocal sequences may be more common in animal communication than previously thought provides a rich area for future research that requires non‐Markovian‐based analysis techniques to investigate animal grammars and potentially the origin of human language.
Impact of segmentation errors and retinal blood vessels on retinal nerve fibre layer measurements using spectral‐domain optical coherence tomography
Authors: Ye Cong , Yu Marco , Leung Christopher Kai‐shun 
Published: July 2015

AbstractPurposeTo investigate the impact of retinal blood vessels and retinal nerve fibre layer (RNFL) segmentation errors on RNFL measurement.MethodsOne eye of 180 subjects (60 normal, 66 mild‐to‐moderate and 54 advanced glaucoma subjects) was randomly selected for RNFL imaging with a spectral‐domain OCT. The boundaries of the RNFL detected by the instrument software were checked, and the segmentation errors were corrected by a customized computer program. The differences in average and regional RNFL thicknesses (RNFLT) before and after the correction were analysed to determine the frequency of segmentation error (defined as an absolute difference in average RNFLT >5.0 μm). The ratio of retinal blood vessel cross‐sectional area to RNFL cross‐sectional area was calculated.ResultsThe difference in average RNFLT (postsegmentation minus presegmentation refinement) ranged from −3.0 to 2.5 μm (mean ± standard deviation: 0.83 ± 0.86 μm) in the normal, −2.5 to 5.0 μm (0.56 ± 1.08 μm) in the mild‐to‐moderate glaucoma and −11.0 to 9.5 μm (0.05 ± 3.49 μm) in the advanced glaucoma groups (p = 0.003). A total of 15% of eyes had average RNFLT measurement error >5.0 μm in the advanced glaucoma group. The proportion of retinal blood vessels in the RNFL also increased with the severity of glaucoma (p < 0.001) with 4.2 ± 1.0% in the normal group, 4.9 ± 1.5% in the mild‐to‐moderate and 8.5 ± 3.5% in the advanced glaucoma groups.ConclusionsInclusion of retinal blood vessels and RNFL segmentation error could adversely affect RNFL measurement, particularly in advanced glaucoma when the RNFL was thin.
The Effect of Alpinia zerumbet Essential Oil on Post‐Stroke Muscle Spasticity
Authors: Maia Maurício Oliva Nascimento , Dantas Camila Gomes , Xavier Filho Lauro , Cândido Edna Aragão Farias , Gomes Margarete Zanardo 
Published: July 2015

AbstractThe essential oil of Alpinia zerumbet (EOAz) presents myorelaxant and antispasmodic actions on cardiac and smooth muscles. The aim of this study was to investigate the effect of EOAz on the skeletal muscle contraction in post‐stroke spasticity. Fifteen adults with unilateral hemiparesis and spasticity resulting from stroke were submitted to surface electromyography readings of the gastrocnemius muscle, before and after 10 daily applications (dermal 0.05 mL per muscle belly) of EOAz. The healthy contralateral muscles without applying the oil were used as controls. The analysis showed that, in both lateral and medial gastrocnemius, the values of all studied variables (root mean square, maximum amplitude and median power frequency) were significantly decreased in pathological legs during muscle contraction (Wilcoxon test, p < 0.05). Moreover, spastic muscles presented different results before and after dermal application of EOAz: The mean values of root mean square and median power frequency were significantly increased in lateral and medial gastrocnemius, and also, the maximum amplitude increased in medial gastrocnemius (Mann–Whitney test, p < 0.05). The results suggest that EOAz acts in the skeletal spastic muscle contraction by promoting relaxation and improvement of the muscular performance. Thus, the EOAz can be useful for the clinical management of secondary effects in patients with cerebral vascular disease.
Should We Reject Donated Organs on Moral Grounds or Permit Allocation Using Non‐Medical Criteria?: A Qualitative Study
Authors: Moorlock Greg , Ives Jonathan , Bramhall Simon , Draper Heather 
Published: July 2015

AbstractConditional and directed deceased organ donations occur when donors (or often their next of kin) attempt to influence the allocation of their donated organs. This can include asking that the organs are given to or withheld from certain types of people, or that they are given to specified individuals. Donations of these types have raised ethical concerns, and have been prohibited in many countries, including the UK. In this article we report the findings from a qualitative study involving interviews with potential donors (n = 20), potential recipients (n = 9) and transplant staff (n = 11), and use these results as a springboard for further ethical commentary.We argue that although participants favoured unconditional donation, this preference was grounded in a false distinction between ‘medical’ and ‘non‐medical’ allocation criteria. Although there are good reasons to maintain organ allocation based primarily upon the existing ‘medical’ criteria, it may be premature to reject all other potential criteria as being unacceptable. Part of participants' justification for allocating organs using ‘medical’ criteria was to make the best use of available organs and avoid wasting their potential benefit, but this can also justify accepting conditional donations in some circumstances. We draw a distinction between two types of waste – absolute and relative – and argue that accepting conditional donations may offer a balance between these forms of waste.
Against ‘Saving Lives’: Equal Concern and Differential Impact
Authors: Chappell Richard Yetter 
Published: July 2015

AbstractBioethicists often present ‘saving lives’ as a goal distinct from, and competing with, that of extending lives by as much as possible. I argue that this usage of the term is misleading, and provides unwarranted rhetorical support for neglecting the magnitudes of the harms and benefits at stake in medical allocation decisions, often to the detriment of the young. Equal concern for all persons requires weighting equal interests equally, but not all individuals have an equal interest in ‘life‐saving’ treatment.
Mixtures of Multivariate Power Exponential Distributions
Authors: Dang Utkarsh J. , Browne Ryan P. , McNicholas Paul D. 
Published: July 2015

SummaryAn expanded family of mixtures of multivariate power exponential distributions is introduced. While fitting heavy-tails and skewness have received much attention in the model-based clustering literature recently, we investigate the use of a distribution that can deal with both varying tail-weight and peakedness of data. A family of parsimonious models is proposed using an eigen-decomposition of the scale matrix. A generalized expectation–maximization algorithm is presented that combines convex optimization via a minorization–maximization approach and optimization based on accelerated line search algorithms on the Stiefel manifold. Lastly, the utility of this family of models is illustrated using both toy and benchmark data.
Comparison of robot‐assisted and laparoscopic partial nephrectomy for complex renal tumours with a RENAL nephrometry score ≥7: peri‐operative and oncological outcomes
Authors: Wang Yubin , Ma Xin , Huang Qingbo , Du Qingshan , Gong Huijie , Shang Jiwen , Zhang Xu 
Published: July 2015

ObjectiveTo evaluate the peri‐operative, functional and oncological outcomes of robot‐assisted partial nephrectomy (RAPN) and laparoscopic partial nephrectomy (LPN) for moderately or highly complex tumours (defined as RENAL nephrometry score ≥7).Patients and MethodsWe retrospectively analysed the medical charts of 216 patients with complex tumours who underwent LPN (n = 135) or RAPN (n = 81) between 2008 and 2014. Peri‐operative data, pathological variables, complications, functional and oncological outcomes were reviewed.ResultsDemographic characteristics were similar in the two groups. LPN was associated with a longer operating time (149.6 vs 135.6 min; P = 0.017) and greater estimated blood loss (220.8 vs 196.5 mL; P = 0.013). RAPN was associated with a higher direct cost. There were no differences in warm ischaemia time, transfusion rate, conversion rate, hospital stay, operative complications and estimated glomerular filtration rate change at 6 months after surgery. The mean follow‐ups for LPN and RAPN were 31.4 and 16.5 months, respectively. The 3‐year recurrence‐free survival rate was 95.2% for LPN and 97.1% for RAPN (P = 0.71).ConclusionIn patients with complex tumours, RAPN and LPN provided acceptable and similar results in terms of peri‐operative, functional and oncological outcomes. RAPN was superior to LPN in terms of estimated blood loss and operating time, and LPN was the more cost‐effective approach. Both surgery techniques remain viable options in the management of complex tumours with RENAL scores ≥7.
Potential clinical application of interleukin‐27 as an antitumor agent
Authors: Yoshimoto Takayuki , Chiba Yukino , Furusawa Jun‐Ichi , Xu Mingli , Tsunoda Ren , Higuchi Kaname , Mizoguchi Izuru 
Published: July 2015

Cancer immunotherapies such as sipuleucel‐T and ipilimumab are promising new treatments that harness the power of the immune system to fight cancer and achieve long‐lasting remission. Interleukin (IL)‐27, a member of the IL‐12 heterodimeric cytokine family, has pleiotropic functions in the regulation of immune responses with both pro‐inflammatory and anti‐inflammatory properties. Evidence obtained using a variety of preclinical mouse models indicates that IL‐27 possesses potent antitumor activity against various types of tumors through multiple mechanisms without apparent adverse effects. These mechanisms include those mediated not only by CD8+ T cells, natural killer cells and macrophages, but also by antibody‐dependent cell‐mediated cytotoxicity, antiangiogenesis, direct antiproliferative effects, inhibition of expression of cyclooxygenase‐2 and prostaglandin E2, and suppression of epithelial–mesenchymal transition, depending on the characteristics of individual tumors. However, the endogenous role of IL‐27 subunits and one of its receptor subunits, WSX‐1, in the susceptibility to tumor development after transplantation of tumor cell lines or endogenously arising tumors seems to be more complicated. IL‐27 functions as a double‐edged sword: IL‐27 increases IL‐10 production and the expression of programmed death ligand 1 and T‐cell immunoglobulin and mucin domain‐3, and promotes the generation of regulatory T cells, and IL‐27 receptor α singling enhances transformation; IL‐27 may augment protumor effects as well. Here, we review both facets of IL‐27, antitumor effects and protumor effects, and discuss the potential clinical application of IL‐27 as an antitumor agent.
Platelet‐Rich Plasma: A Study of the Variables that May Influence Its Effect on Bone Regeneration
Authors: Jovani‐Sancho Mª del Mar , Sheth Chirag C , Marqués‐Mateo Mariano , Puche‐Torres Miguel 
Published: July 2015

AbstractBackgroundCurrently, the use of platelet‐rich plasma in bone regeneration is a real option, although more than one opinion has alerted us to the absence of clinical benefits.PurposeAnalysis of the factors able to modify the characteristics of the platelet preparation obtained by Curasan, Plasma Rich in Growth Factors (PRGF), Platelet Concentrate Collection System (PCCS) and SmartPrep systems, relating them to the type of clinical application and the final bone regeneration achieved.Materials and MethodsA search was conducted in PubMed using the keywords “platelet‐rich plasma,” “PRP,” “platelet rich growth factors,” and “oral bone regeneration.” Four widely accepted protocols for the obtention of PRP (above) were analyzed. Any clinical studies with controls, using the four preparation protocols and with a 4 to 6 weeks follow‐up period were compared. The protocols were also grouped according to the type of PRP application: PRP‐alone, with bone, or with bone substitutes.ResultsBone regeneration was not achieved in any of the cases using PRP obtained by Curasan and PCCS systems, whereas PRP obtained by SmartPrep achieved it only in one in three published cases and PRGF in one in six.ConclusionBased on the poor results observed in current literature, the use of PRP in oral surgery cannot be recommended.
Patient satisfaction and prosthetic aspects with mini‐implants retained mandibular overdentures. A 5‐year prospective study
Authors: Elsyad Moustafa Abdou 
Published: July 2015

AbstractPurposeThis study aimed to evaluate patient satisfaction and prosthetic aspects during a 5‐year prospective clinical study of mini dental implants (MDIs) retaining mandibular overdentures.Materials and methodsThis observational prospective clinical study was conducted on a group of completely edentulous patients (n = 28) with retention problems of conventional mandibular dentures. All patients received new maxillary and mandibular conventional dentures. A total of 112 MDIs (four per patient) were inserted using the flapless surgical approach and immediately loaded by the new mandibular dentures (overdentures). Patients indicated satisfaction with their prosthesis using a questionnaire and a visual analogue scale (VAS). Patient satisfaction and prosthetic complications were recorded 6 months (T6 m), 1 (T1), 3 (T3), and 5 (T5) years after overdenture insertion.ResultsThe patient satisfaction with eating (hard/soft) food (P < 0.001), talking (P < 0.001), appearance (P = 0.001), comfort (P < 0.001), healing process (P = 0.013), socialization (P < 0.001), stability/retention of mandibular dentures (P = 0.001), ease of oral hygiene (P = 0.008), and ease of handling the dentures (P < 0.001) increased significantly with time. After 5 years, the most common complication was wear/damage of O/rings (n = 235), O/ring replacement (n = 125), maxillary denture relining times (n = 13), worn teeth (n = 10), overdentures relines (n = 10), detachment of the metal housings (n = 9), and fracture of mandibular overdentures (n = 8). Mucositis, soreness, and decubitis ulcer under overdenture occurred most often at T6 m and decreased significantly with time (P = 0.002, 0.005, and 0.024, respectively).ConclusionWithin the limitations of this clinical study, patient satisfaction with mini‐implant retained mandibular overdentures increased significantly with time. However, this treatment required a considerable amount of prosthetic maintenance and repair after 5 years of service.
Effects of reduced water quality on coral reefs in and out of no‐take marine reserves
Authors: Wenger Amelia S. , Williamson David H. , da Silva Eduardo T. , Ceccarelli Daniela M. , Browne Nicola K. , Petus Caroline , Devlin Michelle J. 
Published: July 2015

AbstractNear‐shore marine environments are increasingly subjected to reduced water quality, and their ability to withstand it is critical to their persistence. The potential role marine reserves may play in mitigating the effects of reduced water quality has received little attention. We investigated the spatial and temporal variability in live coral and macro‐algal cover and water quality during moderate and major flooding events of the Fitzroy River within the Keppel Bay region of the Great Barrier Reef Marine Park from 2007 to 2013. We used 7 years of remote sensing data on water quality and data from long‐term monitoring of coral reefs to quantify exposure of coral reefs to flood plumes. We used a distance linear model to partition the contribution of abiotic and biotic factors, including zoning, as drivers of the observed changes in coral and macro‐algae cover. Moderate flood plumes from 2007 to 2009 did not affect coral cover on reefs in the Keppel Islands, suggesting the reef has intrinsic resistance against short‐term exposure to reduced water quality. However, from 2009 to 2013, live coral cover declined by ∼50% following several weeks of exposure to turbid, low salinity water from major flood plume events in 2011 and subsequent moderate events in 2012 and 2013. Although the flooding events in 2012 and 2013 were smaller than the flooding events between 2007 to 2009, the ability of the reefs to withstand these moderate floods was lost, as evidenced by a ∼20% decline in coral cover between 2011 to 2013. Although zoning (no‐take reserve or fished) was identified a significant driver of coral cover, we recorded consistently lower coral cover on reserve reefs than on fished reefs throughout the study period and significantly lower cover in 2011. Our findings suggest that even reefs with an inherent resistance to reduced water quality are not able to withstand repeated disturbance events. The limitations of reserves in mitigating the effects of reduced water quality on near‐shore coral reefs underscores the importance of integrated management approaches that combine effective land‐based management with networks of no‐take reserves.
Reconstruction and validation of a constraint‐based metabolic network model for bone marrow‐derived mesenchymal stem cells
Authors: Fouladiha H. , Marashi S.‐A. , Shokrgozar M. A. 
Published: July 2015

AbstractObjectivesOver recent years, constraint‐based modelling of metabolic networks has become increasingly popular; the models are suitable for system‐level modelling of cell physiology. The goal of the present work was to reconstruct a constraint‐based metabolic network model of bone marrow‐derived mesenchymal stem cells (BMMSCs).Materials and methodsTo reconstruct aBMMSC‐specific metabolic model, transcriptomic data ofBMMSCs, and additionally, the human generic metabolic network model (Recon1) were used. Then, using themCADREalgorithm, a draft metabolic network was reconstructed. Literature and proteomic data were subsequently used to refine and improve the draft. From this,iMSC1255 was derived to be the metabolic network model ofBMMSCs.ResultsiMSC1255 has 1255 genes, 1850 metabolites and 2288 reactions. After including additional constraints based on previously reported experimental results, our model successfully predictedBMMSCgrowth rate and metabolic phenotypes.ConclusionsHere,iMSC1255 is introduced to be the metabolic network model of bone marrow‐derived mesenchymal stem cells. Based on current knowledge, this is the first report on genome‐scale reconstruction and validation of a stem cell metabolic network model.
Using citizen science to monitor pollination services
Authors: BIRKIN LINDA , GOULSON DAVE 
Published: July 2015

1. Pollination by insects is a vital ecosystem service and the need for its assessment is increasing in recognition and political pressure, but there are currently no large‐scale systematic monitoring schemes in place to measure the direct provision of this service.2. This study tested a protocol for using a citizen science approach to quantify pollination service provision in gardens and allotments, requiring participants to grow Vica faba L. plants and carry out some simple manipulations of the pollination environment (flowers with bees excluded, flowers hand‐pollinated, or flowers left for local pollinators to visit). Volunteers assessed yield in the three treatments.3. Eighty participants from across the U.K. successfully completed all parts of the protocol; a further 93 participants were unsuccessful but actively engaged with the project.4. Overall, the present results suggest that pollination services for V. faba are currently not limiting in gardens or allotments in the U.K. It is possible and cost‐effective to recruit volunteers to collect data on pollination deficits using this protocol.5. The approach used in this paper, which could readily be extended to incorporate other plant species reliant on different guilds of pollinators, is feasible for adoption as a national monitoring scheme for pollination services.
Pathogenicity ofHeterobasidion annosum(Fr.)Bref.sensu strictoon coniferous tree species inTurkey
Authors: Doğmuş‐Lehtijärvi H. T. , Erdoğan R. C. , Lehtijärvi A. , Woodward S. , Aday Kaya A. G. 
Published: July 2015

SummaryTwo‐year‐old seedlings ofPinus brutia,P. brutiavar.eldarica,Pinus pineaand 3‐year‐old seedlings ofPinus radiata,Pinus sylvestris,Pinus nigraandCedrus libaniwere inoculated on the lower stem with isolates ofHeterobasidion annosums.s. collected from theBlackSea andMediterranean regions ofTurkey. In total, 315 seedlings were inoculated inApril 2014 and incubated in a growth chamber for 7 weeks at 18–20°C. All isolates were pathogenic on the seven different hosts and had the ability to grow in living sapwood. The isolates had a greater growth onC. libani,P. sylvestrisandP. radiataseedlings compared to plants of the other species tested. The least affected species wereP. brutiaandP. nigra. The isolates originating from theBlackSea region caused longer lesions on the hosts. Overall mortality during 7 weeks of incubation was 4%.