bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of early breast cancer patient survival using ensembles of hypoxia signatures
Authors: Gong Inna Y. , Fox Natalie S. , Boutros Paul C.
Published: August 2017

Background

Biomarkers are a key component of precision medicine. However, full clinical integration of biomarkers has been met with challenges, partly attributed to analytical difficulties. It has been shown that biomarker reproducibility is susceptible to data preprocessing approaches. Here, we systematically evaluated machine-learning ensembles of preprocessing methods as a general strategy to improve biomarker performance for prediction of survival from early breast cancer.

Results

We risk stratified breast cancer patients into either low-risk or high-risk groups based on four published hypoxia signatures (Buffa, Winter, Hu, and Sorensen), using 24 different preprocessing approaches for microarray normalization. The 24 binary risk profiles determined for each hypoxia signature were combined using a random forest to evaluate the efficacy of a preprocessing ensemble classifier. We demonstrate that the best way of merging preprocessing methods varies from signature to signature, and that there is likely no ‘best’ preprocessing pipeline that is universal across datasets, highlighting the need to evaluate ensembles of preprocessing algorithms. Further, we developed novel signatures for each preprocessing method and the risk classifications from each were incorporated in a meta-random forest model. Interestingly, the classification of these biomarkers and its ensemble show striking consistency, demonstrating that similar intrinsic biological information are being faithfully represented. As such, these classification patterns further confirm that there is a subset of patients whose prognosis is consistently challenging to predict.

Conclusions

Performance of different prognostic signatures varies with pre-processing method. A simple classifier by unanimous voting of classifications is a reliable way of improving on single preprocessing methods. Future signatures will likely require integration of intrinsic and extrinsic clinico-pathological variables to better predict disease-related outcomes.

Abbreviations

AUC

area under the receiver operating characteristic curve

GCRMA

GeneChip Robust Multi-array Average

HG-U133A

Affymetrix Human Genome U133A

HG-U133 Plus 2.0

Affymetrix Human Genome Plus 2.0

HR

hazard ratio

MAS5

MicroArray Suite 5.0

MBEI

Model-base Expression Index

NSCLC

Non-small cell lung cancer

RF

Random forest

ROC

receiver operator characteristic

RMA

Robust Multi-array Average
Patterns of structural variation in human cancer
Authors: Li Yilong , Roberts Nicola D , Weischenfeldt Joachim , Wala Jeremiah A , Shapira Ofer , Schumacher Steven E. , Khurana Ekta , Korbel Jan , Imielinski Marcin , Beroukhim Rameen , Campbell Peter J ,   on behalf of the PCAWG-Structural Variation Working Group,   and the PCAWG Network
Published: August 2017

A key mutational process in cancer is structural variation, in which rearrangements delete, amplify or reorder genomic segments ranging in size from kilobases to whole chromosomes. We developed methods to group, classify and describe structural variants, applied to >2,500 cancer genomes. Nine signatures of structural variation emerged. Deletions have trimodal size distribution; assort unevenly across tumour types and patients; enrich in late-replicating regions; and correlate with inversions. Tandem duplications also have trimodal size distribution, but enrich in early-replicating regions, as do unbalanced translocations. Replication-based mechanisms of rearrangement generate varied chromosomal structures with low-level copy number gains and frequent inverted rearrangements. One prominent structure consists of 1-7 templates copied from distinct regions of the genome strung together within one locus. Such ‘cycles of templated insertions’ correlate with tandem duplications, frequently activating the telomerase gene,TERT,in liver cancer. Cancers access many rearrangement processes, flexibly sculpting the genome to maximise oncogenic potential.
A “Tug of War” maintains a dynamic protein-membrane complex as shown in all-atom simulations of C-Raf RBD-CRD bound to K-Ras4B at an anionic membrane
Authors: Li Zhen-Lu , Prakash Priyanka , Buck Matthias
Published: August 2017

Association of Raf kinase with activated Ras triggers downstream signaling cascades, towards regulating transcription in the cells’ nucleus. Dysregulation of Ras: Raf signaling stimulates cancers. We investigate the C-Raf RBD and CRD regions when bound to oncogenic K-Ras4B at the membrane. All-atom molecular dynamics simulations suggest that the membrane plays an integral role in regulating the configurational ensemble of the complex. Remarkably, the complex samples a few states dynamically, reflecting a competition between C-Raf CRD and K-Ras4B- membrane interactions. This competition arises because the interaction between the RBD and K-Ras is strong and the linker between the RBD and CRD is short. This study reveals a mechanism that maintains a modest binding for the overall complex at the membrane to facilitate fast signaling processes. It is likely a common mechanism for other multi-protein, if not multidomain proteins at membranes.
Novel application of explicit dynamics occupancy models to ongoing aquatic invasions
Authors: Sepulveda Adam J.
Published: August 2017

Identification of suitable habitats, where invasive species can establish, is an important step towards controlling their spread. Accurate identification is difficult for new or slow invaders because unoccupied habitats may be suitable, given enough time for dispersal, while occupied habitats may prove to be unsuitable for establishment.

To identify the suitable habitat of a recent invader, I used an explicit dynamics occupancy modelling framework to evaluate habitat covariates related to successful and failed establishments of American Bullfrogs (Lithobates catesbeianus) within the Yellowstone River floodplain of Montana, USA, from 2012 to 2016.

During this 5‐year period, bullfrogs failed to establish at most sites they colonized. Bullfrog establishment was most likely to occur and least likely to fail at sites closest to human‐modified ponds and lakes and those with emergent vegetation. These habitat covariates were generally associated with the presence of permanent water.

Suitable habitat for bullfrog establishment is abundant in the Yellowstone River floodplain, although many sites with suitable habitat remain uncolonized. Thus, the maximum distribution of bullfrogs is much greater than their current distribution.

Synthesis and applications. Focused control efforts on habitats with or proximate to permanent waters are most likely to reduce the potential for invasive bullfrog establishment and spread in the Yellowstone River. The novel application of explicit dynamics occupancy models is a useful and widely applicable tool for guiding management efforts towards those habitats where new or slow invaders are most likely to establish and persist.
Alcohol‐related presentations to the Royal Perth Hospital Emergency Department: A prospective study
Authors: McLay Stuart VB , MacDonald Ellen , Fatovich Daniel M ,   on behalf of the Alcohol Harm in Emergency Departments (AHED) Investigators
Published: August 2017

Objective

To quantify and describe alcohol‐related presentations to our ED, as part of the binational Alcohol Harm in Emergency Departments study.

Methods

A prospective observational study at Royal Perth Hospital of every patient attending ED for the 168‐h period commencing 08.00 hours Monday 1 December 2014. Patient presentations were classified as alcohol‐related (alcohol‐positive) using predefined criteria. These patients were compared to alcohol‐negative patients on a range of demographic and clinical descriptors.

Results

Two hundred and thirteen (15.2%) of 1403 patients screened were alcohol‐positive. Compared with alcohol‐negative patients, alcohol‐positive patients were more likely to be male (148/213, 69.5% vs 636/1190, 53.4%, P < 0.001) and younger (mean 38 years vs 48 years, P < 0.001). They were more likely to arrive in police custody (OR 3.7, 95% CI 1.3–9.5, P = 0.005), and be admitted to the State Adult Major Trauma Unit (OR 4.2, 95% CI 2.1–8.3, P < 0.001). Forty‐two (19.7%) of 213 patients had injuries suspected to be caused by an alcohol‐affected third party. The ED length of stay and admission rate were not significantly different between the groups.

Conclusions

15.2% of patient presentations over the study week were alcohol‐related. These patients were more likely to present with injury; one in five having injuries suspected to be caused by a third party affected by alcohol. This is a significant public health problem.
Ventilatory choices for intubated patients during helicopter stretcher winching
Authors: Hollott John
Published: August 2017

Introduction

The winching of intubated patients on a stretcher into a helicopter is a rare event. Intermittent positive pressure ventilation is mandatory, which can either be performed manually with a self‐inflating bag, or automatically using a portable ventilator. Theoretically automatic ventilation would provide improved oxygenation, more stable arterial carbon dioxide levels and a reduced risk of airway disconnection. Furthermore, the stretcher attendant may better perform winching procedures with higher situational awareness, contributing to crew and patient safety. However ventilator failure, and the diagnosis and management of such, is of concern.

Objective

The aim of this study is to compare automatic against manual ventilation during intubated helicopter stretcher winching.

Method

The trial had two phases. Initially a static winch on a hoist simulator was performed, followed by live winching into a helicopter. All stretcher attendants performed two winches with an intubated manikin. During one winch, the manikin was manually ventilated, and an automatic ventilator was used for the other. Airway pressures were measured.

Results

Automatic ventilation did not fail. Compared with automatic ventilation, manual ventilation displayed significant pauses, inconsistent rates and both high and low airway pressures. Automatic ventilation permitted better situational awareness and performance in winching manoeuvres. One airway disconnection occurred during manual ventilation.

Conclusions

During helicopter winching, automatic ventilation is superior in providing controlled, consistent and reliable ventilation for intubated patients. The stretcher attendant is also able to provide more attention to the winching manoeuvres with subsequent safety gains. The risk of automatic ventilator failure is low.
Water Quality Signals from Rural Land Use and Exurbanization in a Mountain Landscape: What's Clear and What's Confounded?
Authors: Jackson C. Rhett , Bahn Robert A. , Webster Jackson R.
Published: August 2017

In mountainous landscapes with high climatic and geomorphic variability, how do rural land uses and exurbanization alter hydrology and water quality? We evaluated effects of rural land use and exurbanization on streamflows, suspended sediment concentrations and loads, specific conductance, and summer water temperatures in 12 streams and rivers within the Upper Little Tennessee River basin in the southern Appalachian Mountains. Eleven streams featured low levels of development (>61% forest cover) but differed in land use patterning, basin size, annual precipitation, and watershed morphology. One urban stream, located within the largest town in the basin, provided the high development comparative endpoint. Even low levels of rural development and exurbanization were associated with substantial increases in suspended sediment concentrations, sediment loads, and summer stream temperature daily maxima and diurnal variation. Observed summer temperature increases were much larger than would be expected due to global climate change over the next century. Specific conductance was idiosyncratic among the smaller streams. These water quality changes were not accompanied by streamflow changes that were discernible amid the high natural variation in precipitation and geomorphology. The water quality findings suggest the need for applying the best management practices, including riparian buffers, to even low levels of rural development.
Patient harboring a novel PIK3CA point mutation after acquired resistance to crizotinib in an adenocarcinoma with ROS1 rearrangement: A case report and literature review
Authors: Xu Chun‐wei , Wang Wen‐xian , Huang Rong‐fang , He Cheng , Liao Xing‐hui , Zhu You‐cai , Du Kai‐qi , Zhuang Wu , Chen Yan‐ping , Chen Gang , Fang Mei‐yu
Published: August 2017

ROS1 rearrangement occurs in 1–2% of non‐small cell lung cancer (NSCLC) cases. These patients would benefit from treatment with the anaplastic lymphoma kinase inhibitor, crizotinib; however, resistance to crizotinib inevitably develops in such patients despite an initial response. The mechanism of acquired resistance to crizotinib in patients with NSCLC with ROS1 rearrangement has not yet been identified. Herein, we report a case of a 66‐year‐old woman diagnosed with adenocarcinoma. PCR revealed no EGFR or ALK mutations. After the patient underwent several rounds of chemotherapy, crizotinib was administered. The disease explosively progressed six months later. A novel PIK3CA gene point mutation (p.L531P) was detected by next generation sequencing. This case is the second report of bypass activation conferred crizotinib resistance in a patient with NSCLC with ROS1‐rearrangement, but is the first to confirm that activation of the mTOR signaling pathway leads to acquired crizotinib resistance.
Mannequin‐based Telesimulation: Increasing Access to Simulation‐based Education
Authors: Hayden Emily M. , Khatri Avni , Kelly Hillary R. , Yager Phoebe H. , Salazar Gloria M.
Published: August 2017

A telesimulation platform utilizes communications technology to provide mannequin‐based simulation education between learners and instructors located remotely from one another. Specifically, the instructor controls the mannequin and moderates the debriefing remotely. During these sessions, the instructor observes the learners in real time and provides immediate feedback during the debriefing. This platform obviates the need to have instructors, learners, and mannequins in the same place at the same time, potentially allowing simulation‐based educational sessions to occur with greater frequency for institutions not located proximate to formal simulation centers. Additionally, the telesimulation platform enables an experienced simulation instructor to observe and directly help new simulation instructors at remote simulation locations. Readily available Web‐conferencing, screen‐sharing software, microphones, and webcams makes telesimulation possible. Mannequin‐based telesimulation is relatively new and not well represented in the literature, but could facilitate systems changes, providing educational experiences to health care professionals in locations not currently benefiting from mannequin‐based simulation opportunities. Several research questions need to be addressed in future studies to better develop this educational approach, including technical feasibility, logistic issues, a comparison of telesimulation to other simulation approaches, and assessing limitations of the telesimulation platform.
“What Do People Do If They Don't Have Insurance?”: ED‐to‐ED Referrals
Authors: Medford‐Davis Laura N. , Prasad Siddharth , Rhodes Karin V.
Published: August 2017

Objective

Up to 20% of patients seen in public emergency departments (EDs) have already been seen for the same complaint at another ED, but little is known about the origin or impact of these duplicate ED visits. The goals of this investigation were to explore 1) whether patients making a repeat ED visit are self‐referred or indirectly referred from the other ED and 2) gather the perspective of affected patients on the health, social, and financial consequences of these duplicate ED visits.

Methods

This mixed‐methods study conducted over a 10‐week period during 2016 in a large public hospital ED in Texas prospectively surveyed patients seen in another ED for the same chief complaint. Selected patients presenting with fractures were then enrolled for semistructured qualitative interviews, which were audiotaped, transcribed, and independently coded by two team members until thematic saturation was reached.

Results

A total of 143 patients were identified as being recently seen at another local ED for the same chief complaint prior to presenting to the public hospital; 94% were uninsured and 61% presented with fractures. A total of 27% required admission at the public ED and 95% of those discharged required further outpatient follow‐up. Fifty‐one percent of patients completed a survey and qualitative interviews were conducted with 23 fracture patients. Fifty‐three percent of patients reported that staff at the first hospital told them to go the public hospital ED, and 23% reported referral from a follow‐up physician associated with the first hospital. Seventy‐three percent reported receiving the same tests at both EDs. Interview themes identified multiple health care visits for the same injury, concern about complications, disrespectful treatment at the first ED, delayed care, problems accessing needed follow‐up care without insurance, loss of work, and financial strain.

Conclusions

The majority of patients presenting to a public hospital ED after treatment for the same complaint in another local ED were indirectly referred to the public ED without transferring paperwork or records, incurring duplicate testing and patient anxiety.
Association between the antioxidant uric acid and depression and antidepressant medication use in 96 989 individuals
Authors: Wium‐Andersen M. K. , Kobylecki C. J. , Afzal S. , Nordestgaard B. G.
Published: August 2017

Objective

In the last decade, several studies have suggested that depression is accompanied by increased oxidative stress and decreased antioxidant defenses. We tested the hypothesis that high levels of the antioxidant uric acid are associated with lower risk of hospitalization with depression and use of prescription antidepressant medication.

Method

We examined plasma levels of the antioxidant uric acid in 96 989 individuals from two independent cohort studies. Logistic regression and Cox proportional hazards regression models were multivariable adjusted for age, gender, alcohol, smoking, income, body mass index, C‐reactive protein, hemoglobin, triglycerides, cardiovascular disease, diabetes, and intake of meat and vegetables. Results were performed separately in each study and combined in a meta‐analysis.

Results

In both studies, high uric acid was associated with lower risk of hospitalization as in‐patient or out‐patient with depression and antidepressant medication use. A doubling in uric acid was associated with an effect estimate of 0.57 (95% CI 0.49–0.65) and 0.77 (0.73–0.81) for hospitalization with depression and antidepressant medication use. The association was consistent across strata of all covariates. Results were attenuated in Cox regression analyses with less statistical power.

Conclusion

High plasma levels of uric acid were associated with low risk of depression hospitalization and antidepressant medication use.
Attraction of red turpentine beetle and otherScolytinae to ethanol, 3‐carene or ethanol + 3‐carene in anOregon pine forest
Authors: Kelsey Rick G. , Westlind Douglas J.
Published: August 2017

Red turpentine beetleDendroctonus valensLeConte is a non‐aggressive bark beetle inNorthAmerica that attacks weakened or recently dead pines, as well as their fresh logs or stumps. Fire‐injured ponderosa pines releasing stress‐induced ethanol are often attacked. The oleoresin from these trees frequently contains 3‐carene as a major component mixed with α‐ or β‐pinene. 3‐Carene lures usually attract moreD. valensthan α‐ or β‐pinene lures or 1 : 1 : 1 mixtures, whereas the attraction of ethanol + 3‐carene lures has never been tested.

Funnel traps with ethanol, 3‐carene or ethanol + 3‐carene lures, and a no lure blank, were set‐up as a randomized complete block design in a pine forest nearLaPine,Oregon,U.S.A.,from 23April until 11June 2015.

Dendroctonus valens,Hylastes nigrinus,Hylurgops reticulatus,Hylurgops porosusandHylastes gracilisexhibited similar responses, with highest numbers captured in traps with ethanol + 3‐carene. The response by the first three species was confirmed as synergistic.

Ipsspp.,Pityogenesspp.,Gnathotrichusspp.,Pachysquamus subcostulatusandHylastes macercomposed a second group whose numbers captured with ethanol lures were similar or greater than the 3‐carene or ethanol + 3‐carene lures. A reducedH. macerresponse to ethanol + 3‐carene was confirmed as an interruption.
Cortisol inhibits CSF2 and CSF3 via DNA methylation and inhibits invasion in first‐trimester trophoblast cells
Authors: Smith Arianna , Witte Elizabeth , McGee Devin , Knott Jason , Narang Kavita , Racicot Karen
Published: August 2017

Problem

Heightened maternal stress affects trophoblast function and increases risk for adverse pregnancy outcomes.

Methods of Study

Studies were performed using the first‐trimester trophoblast cell line, Sw.71. Cytokines were quantified using qPCR and ELISA. Epigenetic regulation of cytokines was characterized by inhibiting histone deacetylation (1 μmol/L suberoylanilide hydroxamic acid [SAHA]) or methylation (5 μmol/L 5‐azacytidine), or with chromatin immunoprecipitation (ChIP) with a pan‐acetyl histone‐3 antibody. Invasion assays used Matrigel chambers.

Results

Cortisol inhibited expression of CSF2 (GM‐CSF) and CSF3 (G‐CSF) in trophoblast cells. Cortisol‐associated inhibition was dependent on DNA methylation and was not affected by acetylation. There was also a modest decrease in trophoblast invasion, not dependent on loss of CSFs.

Conclusion

In first‐trimester trophoblast cells, the physiological glucocorticoid, cortisol, inhibited two cytokines with roles in placental development and decreased trophoblast invasion. Cortisol‐associated changes in trophoblast function could increase the risk for immune‐mediated abortion or other adverse pregnancy outcomes.
Source‐to‐sink analysis in an active extensional setting: Holocene erosion and deposition in the Sperchios rift, central Greece
Authors: Pechlivanidou Sofia , Cowie Patience A. , Hannisdal Bjarte , Whittaker Alexander C. , Gawthorpe Robert L. , Pennos Christos , Riiser Ole S.
Published: August 2017

We present a source‐to‐sink analysis to explain sediment supply variations and depositional patterns over the Holocene within an active rift setting. We integrate a range of modelling approaches and data types with field observations from the Sperchios rift basin, Central Greece that allow us to analyse and quantify (1) the size and characteristics of sediment source areas, (2) the dynamics of the sediment routing system from upstream fluvial processes to downstream deposition at the coastline, and (3) the depositional architecture and volumes of the Holocene basin fill. We demonstrate that the Sperchios rift comprises a ‘closed’ system over the Holocene and that erosional and depositional volumes are thus balanced. Furthermore, we evaluate key controls in the development of this source‐to‐sink system, including the role of pre‐existing topography, bedrock erodibility and lateral variations in the rate of tectonic uplift/subsidence. We show that tectonic subsidence alone can explain the observed grain size fining along the rift axis resulting in the downstream transition from a braided channel to an extensive meander belt (>15 km long) that feeds the fine‐grained Sperchios delta. Additionally, we quantify the ratios of sediment storage to bypass for the two main footwall‐sourced alluvial fan systems and relate the fan characteristics to the pattern and rates of fault slip. Finally, we show that ≥40% of the sediment that builds the Sperchios delta is supplied by ≤22% of the entire source area and that this can be primarily attributed to a longer‐term (~106 years) transient landscape response to fault segment linkage. Our multidisciplinary approach allows us to quantify the relative importance of multiple factors that control a complex source‐to‐sink system and thus improve our understanding of landscape evolution and stratigraphic development in active extensional tectonic settings.
Long‐term outcomes of narrow diameter implants in posterior jaws: A retrospective study with at least 8‐year follow‐up
Authors: Shi Jun‐Yu , Xu Feng‐Yuan , Zhuang Long‐Fei , Gu Ying‐Xin , Qiao Shi‐Chong , Lai Hong‐Chang
Published: August 2017

Objective

The aim of this study was to evaluate the long‐term survival, complications, peri‐implant conditions, marginal bone loss, and patient satisfaction of fixed dental prostheses supported by narrow diameter implants (NDIs) in the posterior jaws.

Materials and methods

This study was designed as a retrospective cohort study with a mean follow‐up time of 10.1 years (SD: 2.5 years). Patients receiving NDIs in posterior jaw were reviewed. Implant survival, hardware complication, modified plaque index (mPI), peri‐implant probing depth (PPD), percentage of bleeding on probing (BOP%), marginal bone loss (MBL), and patient satisfaction were evaluated. Log‐rank test and t test were used to detect the influence of implant location and restoration type.

Results

Sixty‐seven patients with 98 NDIs (Premolar site: 81, Molar site: 17, Single crowns: 33, Splinted restorations: 65) were included. The overall implant survival rates were 96.9% at implant level and 97.0% at patient level. Veneer chipping was the most common hardware complication. The veneer chipping rates were 19.4% at patient level and 18.4% at implant level. All patients showed acceptable oral hygiene. Thus, the average MBL was 1.19 mm at implant level and 1.15 mm at patient level. Eight implants (8.5%) and six patients (9.2%) were diagnosed with peri‐implantitis. Fifty‐eight patients (89.2%) were satisfied with the esthetics of the restorations, while 55 patients (84.6%) were satisfied with the function of the restorations.

Conclusion

Narrow diameter implants could be a predictable treatment option in the long term. High survival rates, high patient satisfaction, acceptable complication rates and marginal bone loss could be achieved. Further long‐term studies are needed to evaluate the predictability of NDIs in molar sites.
Recombinant Enaction: Manipulatives Generate New Procedures in the Imagination, by Extending and Recombining Action Spaces
Authors: Rahaman Jeenath , Agrawal Harshit , Srivastava Nisheeth , Chandrasekharan Sanjay
Published: August 2017

Manipulation of physical models such as tangrams and tiles is a popular approach to teaching early mathematics concepts. This pedagogical approach is extended by new computational media, where mathematical entities such as equations and vectors can be virtually manipulated. The cognitive and neural mechanisms supporting such manipulation‐based learning—particularly how actions generate new internal structures that support problem‐solving—are not understood. We develop a model of the way manipulations generate internal traces embedding actions, and how these action‐traces recombine during problem‐solving. This model is based on a study of two groups of sixth‐grade students solving area problems. Before problem‐solving, one group manipulated a tangram, the other group answered a descriptive test. Eye‐movement trajectories during problem‐solving were different between the groups. A second study showed that this difference required the tangram's geometrical structure, just manipulation was not enough. We propose a theoretical model accounting for these results, and discuss its implications.
Neurodevelopmental disorders in children with neurofibromatosis type 1
Authors: Vogel Alecia C , Gutmann David H , Morris Stephanie M
Published: August 2017

Over the past several decades, neurofibromatosis type 1 (NF1) has become increasingly recognized as a neurodevelopmental disorder conferring increased risk for several important neurodevelopmental problems. In this review, we summarize the specific neurodevelopmental problems encountered in the context of NF1. These include impairments in general cognitive function, deficits in specific cognitive domains such as executive function and visuospatial processing and risk for specific learning disorders, impairments in attention and social skills and the overlap with attention‐deficit–hyperactivity disorder and autism spectrum disorder, and the risk of developing other psychiatric conditions including anxiety and depression. Early recognition of these developmental impairments is important for the effective treatment of children with NF1, and further characterization is essential to improve our understanding of how mutations in the NF1 gene create the diversity of clinical neuropsychiatric symptomatology observed in this at‐risk population.
The value of space‐for‐time substitution for studying fine‐scale microevolutionary processes
Authors: Wogan Guinevere O.U. , Wang Ian J.
Published: August 2017

When the drivers of biological turnover in space are the same as those that drive turnover through time, space can be substituted for time to model how patterns of variation are predicted to change into the future. These space‐for‐time substitutions are widely used in ecological modeling but have only recently been applied to the study of microevolutionary processes, particularly over relatively fine spatial and temporal scales. Here, we review recent examples that have employed space‐for‐time substitution to study genetic patterns on stationary and non‐stationary landscapes and examine whether space can reliably substitute for time in studies of population divergence, genetic structure, and adaptive evolution. Although there are only a relatively few examples, several recent studies were excellently crafted to provide valuable insights into the conditions governing the validity of space‐for‐time substitutions applied to population genetic data. We found that, although caution should be taken, space‐for‐time substitutions appear valid for studying microevolutionary processes on both stationary and non‐stationary landscapes. Further studies can help to evaluate the conditions under which space‐for‐time substitutions are reliable. When these methods are reliable, they will play an important role in modeling genetic responses to environmental change, population viability on non‐stationary landscapes, and patterns of divergence and adaptation.
Recovery of a phytopathogenic bacterium Lonsdalea quercina from a lesser horseshoe bat in Moravian karst, Czech Republic
Authors: Kovacova V. , Kolarik M. , Bandouchova H. , Bartonicka T. , Berkova H. , Havelkova B. , Hrudova E. , Kohoutova L. , Martínková N. , Zukal J. , Pikula J.
Published: August 2017

While bats are important reservoirs and vectors of pathogenic agents with zoonotic potential, their skin‐associated microbial community could harbour organisms relevant to bat health as well as those associated with bat habitats in general. A total of 140 skin swabs collected from bats in the Czech Republic were cultured for bacteria from 2012 to 2013. A phytopathogen, isolated from a lesser horseshoe bat (Rhinolophus hipposideros), was identified as Lonsdalea quercina by MALDI‐TOF (matrix‐assisted laser desorption–ionization time‐of‐flight mass spectrometry) and characterized as Lonsdalea quercina subsp. britannica using phylogenetic analysis based on a 16S rRNA and two housekeeping (infB and atpD) genes. Lonsdalea quercina subsp. britannica is a gram‐negative facultative anaerobic bacterium reported to cause bark canker and drippy nut disease in oaks. Our finding provides evidence of Lonsdalea quercina in the Czech Republic (Moravian Karst). As the lesser horseshoe bat is a sedentary species, it may bio‐indicate the presence of the phytopathogenic bacterium in the broadleaved forests of the habitat of pathogen recovery. We therefore suggest active surveillance of the area of the Moravian Karst for signs of oak disease and/or decline.
Transmission mechanisms of fish electric signals
Authors: Fine Michael L , Kier Lemont B , Alvarez Julio C
Published: August 2017

Fishes utilize electric signals for passive and active electrolocation and communication at night in murky water. To our knowledge, the mechanism of transmission of fish electric signals through water has not been addressed. In such a medium, the transmission of electrical signals can occur by movement of ions (ion conduction) under the influence of a generated electric field, or through its perturbation by nearby objects that have electric permittivity different than water. This latter property refers to the ability of a medium to resist the formation of electric fields with no involvement of ion transport. In this study, we discuss the relevance of each mechanism in the context of previous reports on transmission of signals by electric fishes in water environments.
A micro‐computed tomographic study of band‐shaped root canal isthmuses, having their floor in the apical third of mesial roots of mandibular first molars
Authors: Keleş A. , Keskin C.
Published: August 2017

Aim

To conduct a quantitative and qualitative analysis of the band‐shaped isthmus area, the floor of which was in the apical third in the mesial roots of mandibular first molars using micro‐computed tomography (micro‐CT).

Methodology

Micro‐CT images of 269 mesial roots of mandibular first molars were evaluated, and 40 specimens with a band‐shaped isthmus, with a floor in the apical third, were selected. The major diameter, minor diameter, roundness, area and perimeter values for the most coronal and apical slices where the isthmus was visible were measured. The distances between these slices were measured as the isthmus length, and the total volume, structure model index and surface area of the isthmus were measured. The distances between the isthmus floor and two apical foramina and the number of root canal orifices were calculated. The dimensions of the isthmus roof and the floor were compared, and the data were analysed using descriptive statistics and Student's t‐tests with a significance threshold set at 5%.

Results

A total of 15% of the specimens had band‐shaped isthmuses with a floor in the apical third. The isthmus roof exhibited significantly greater major and minor diameter values compared to the isthmus floor (P < 0.05). No significant difference was detected between the isthmus roof and the floor with regard to roundness (P > 0.05).

Conclusion

Three‐ and two‐dimensional analyses of the mesial roots of mandibular molars revealed that band‐shaped isthmuses had complex shapes.
A multihesitant fuzzy linguistic multicriteria decision‐making approach for logistics outsourcing with incomplete weight information
Authors: Wang Jing , Wang Jian‐qiang , Tian Zhang‐peng , Zhao Dong‐yan
Published: August 2017

In selecting logistics service providers, the evaluation criteria can be easily prioritized and possibly interrelated with each other, and the assessment of alternatives under qualitative criteria is usually accomplished by more than one decision maker. A novel multicriteria decision‐making approach with multihesitant fuzzy linguistic term elements (MHFLTEs) based on the Heronian mean (HM) and prioritized average operators can effectively deal with the problems inherent in such a scenario. Multihesitant fuzzy linguistic term sets (MHFLTSs) were proposed on the basis of multihesitant fuzzy sets (MHFSs) and hesitant fuzzy linguistic sets (HFLSs), where each MHFLTE can contain nonconsecutive and repeated linguistic terms. Using MHFLTEs, one decision maker can provide one or several consecutive linguistic terms in evaluating an alternative under one specific criterion, different decision makers’ evaluation values can be collected, and the frequency of a linguistic term in the evaluation information can accord with reality. This paper revises the basic operations and comparison method for MHFLTEs on the basis of the originals and defines some multihesitant fuzzy linguistic HM operators for MHFLTEs to deal with problems in which weight information cannot be accurately established for criteria, but their priorities can be provided in groups or without groups. Finally, the validity and effectiveness of the proposed approach are demonstrated through an illustration of a logistics outsourcing problem and a comparison analysis.
The importance of temporal resolution for niche modelling in dynamic marine environments
Authors: Fernandez Marc , Yesson Chris , Gannier Alexandre , Miller Peter I , Azevedo José MN
Published: August 2017

Aim

Highly dynamic ocean environments can experience dramatic changes over relatively short timeframes, affecting the spatial distribution of resources and therefore the presence or absence of highly mobile species. We use simulation studies to investigate how different temporal resolutions might affect the results of species distribution models for highly mobile species (e.g. cetaceans) in marine environments.

Location

Azores archipelago, Portugal.

Methods

We developed three virtual species with different habitat preferences influenced by (1) only static (topographic), (2) only dynamic (oceanographic), and (3) both dynamic and static variables. Assuming that species would reposition themselves daily according to these preferences (as has been observed for large marine foragers such as cetaceans), we used two different approaches (generalized linear model and generalized boosted model) to test the effect of using daily, weekly and monthly environmental datasets to model distributions.

Results

The results showed that the selection of different temporal scales has a very important effect on model predictions. When dynamic variables are important components of habitat preference, models based on daily or weekly timeframes performed best at reconstructing the known niche.

Main conclusion

It is important that we consider temporal resolution when applying species distribution models. Several factors (e.g. species ecology and oceanographic characteristics of the ecosystem) should be taken into consideration when selecting an adequate temporal scale for niche modelling. For fine scale applications (e.g. dynamic ocean management), highly dynamic ecosystems, and highly mobile species, our results suggest exploring temporal resolution of 7–8 days rather than coarser temporal scales. For some applications annual, seasonal or even monthly averages may produce inferior or inaccurate models.
Chronic urticaria and the metabolic syndrome: a cross‐sectional community‐based study of 11 261 patients
Authors: Shalom G. , Magen E. , Babaev M. , Tiosano S. , Vardy D.A. , Linder D. , Horev A. , Saadia A. , Comaneshter D. , Agmon‐Levin N. , Cohen A.D.
Published: August 2017

Background

Emerging evidence suggests that chronic urticaria (CU) is associated with chronic, low‐grade, inflammatory process.

Objective

To evaluate the association between CU and metabolic syndrome and its components in a large community‐based medical database.

Methods

A cross‐sectional study of CU patients and matched controls was performed. CU was defined as eight urticaria diagnoses (with each two diagnoses registered within a period of 6 weeks) from 2002 to 2012. Data regarding the prevalence of metabolic syndrome, its components and possible complications were collected.

Results

The study included 11 261 patients with CU and 67 216 controls. In a univariate analysis, CU was significantly associated with higher body mass index (BMI) and a higher prevalence of obesity, diabetes, hyperlipidaemia, hypertension, metabolic syndrome, chronic renal failure and gout. Multivariate analysis demonstrated a significant association between CU and metabolic syndrome (OR = 1.12, 95% CI 1.1–1.2, P < 0.001) and its components – obesity (OR = 1.2, 95% CI 1.1–1.3, P < 0.001), diabetes (OR = 1.08, 95% CI 1.01–1.15, P = 0.001), hyperlipidaemia (OR = 1.2, 95% CI 1.1–1.2, P < 0.001) and hypertension (OR = 1.1, 95% CI 1.1–1.2, P < 0.001).

Conclusions

CU patients may have one or more undiagnosed components of metabolic syndrome despite their young age. Thus, appropriate targeted screening is advised.
Stalk size and altruism investment within and among populations of the social amoeba
Authors: Votaw H. R. , Ostrowski E. A.
Published: August 2017

Reproductive division of labour is common in many societies, including those of eusocial insects, cooperatively breeding vertebrates, and most forms of multicellularity. However, conflict over what is best for the individual vs. the group can prevent an optimal division of labour from being achieved. In the social amoeba Dictyostelium discoideum, cells aggregate to become multicellular and a fraction behaves altruistically, forming a dead stalk that supports the rest. Theory suggests that intra‐organismal conflict over spore–stalk cell fate can drive rapid evolutionary change in allocation traits, leading to polymorphisms within populations or rapid divergence between them. Here, we assess several proxies for stalk size and spore–stalk allocation as metrics of altruism investment among strains and across geographic regions. We observe geographic divergence in stalk height that can be partly explained by differences in multicellular size, as well as variation among strains in clonal spore–stalk allocation, suggesting within‐population variation in altruism investment. Analyses of chimeras comprised of strains from the same vs. different populations indicated genotype‐by‐genotype epistasis, where the morphology of the chimeras deviated significantly from the average morphology of the strains developed clonally. The significantly negative epistasis observed for allopatric pairings suggests that populations are diverging in their spore–stalk allocation behaviours, generating incompatibilities when they encounter one another. Our results demonstrate divergence in microbial social traits across geographically separated populations and demonstrate how quantification of genotype‐by‐genotype interactions can elucidate the trajectory of social trait evolution in nature.
Puccinia coronata f. sp. avenae: a threat to global oat production
Authors: Nazareno Eric S. , Li Feng , Smith Madeleine , Park Robert F. , Kianian Shahryar F. , Figueroa Melania
Published: August 2017

Puccinia coronata f. sp. avenae (Pca) causes crown rust disease in cultivated and wild oat (Avena spp.). The significant yield losses inflicted by this pathogen make crown rust the most devastating disease in the oat industry. Pca is a basidiomycete fungus with an obligate biotrophic lifestyle, and is classified as a typical macrocyclic and heteroecious fungus. The asexual phase in the life cycle of Pca occurs in oat, whereas the sexual phase takes place primarily in Rhamnus species as the alternative host. Epidemics of crown rust happens in areas with warm temperatures (20–25 °C) and high humidity. Infection by the pathogen leads to plant lodging and shrivelled grain of poor quality.

Disease symptoms: Infection of susceptible oat varieties gives rise to orange–yellow round to oblong uredinia (pustules) containing newly formed urediniospores. Pustules vary in size and can be larger than 5 mm in length. Infection occurs primarily on the surfaces of leaves, although occasional symptoms develop in the oat leaf sheaths and/or floral structures, such as awns. Symptoms in resistant oat varieties vary from flecks to small pustules, typically accompanied by chlorotic halos and/or necrosis. The pycnial and aecial stages are mostly present in the leaves of Rhamnus species, but occasionally symptoms can also be observed in petioles, young stems and floral structures. Aecial structures display a characteristic hypertrophy and can differ in size, occasionally reaching more than 5 mm in diameter.

Taxonomy: Pca belongs to the kingdom Fungi, phylum Basidiomycota, class Pucciniomycetes, order Pucciniales and family Pucciniaceae.

Host range: Puccinia coronata sensu lato can infect 290 species of grass hosts. Pca is prevalent in all oat‐growing regions and, compared with other cereal rusts, displays a broad telial host range. The most common grass hosts of Pca include cultivated hexaploid oat (Avena sativa) and wild relatives, such as bluejoint grass, perennial ryegrass and fescue. Alternative hosts include several species of Rhamnus, with R. cathartica (common buckthorn) as the most important alternative host in Europe and North America.

Control: Most crown rust management strategies involve the use of rust‐resistant crop varieties and the application of fungicides. The attainment of the durability of resistance against Pca is difficult as it is a highly variable pathogen with a great propensity to overcome the genetic resistance of varieties. Thus, adult plant resistance is often exploited in oat breeding programmes to develop new crown rust‐resistant varieties.

Useful website: https://www.ars.usda.gov/midwest-area/st-paul-mn/cereal-disease-lab/docs/cereal-rusts/race-surveys/.
Development of a genetic sexing strain of Anopheles arabiensis for KwaZulu‐Natal, South Africa
Authors: DANDALO L. C. , MUNHENGA G. , KAISER M. L. , KOEKEMOER L. L.
Published: August 2017

An efficient sexing system is important for the release of sterile males for any control programme using the sterile insect technique. This study describes the development and characterization of a new genetic sexing strain from South Africa (GMK), needed for the planned implementation of such a programme in northern KwaZulu‐Natal Province. The base colony used was a locally modified laboratory strain of Anopheles arabiensis containing a sex‐linked gene conferring dieldrin resistance to male mosquitoes. Female A. arabiensis mosquitoes from northern KwaZulu‐Natal were mated with these males and backcrossed to introduce the dieldrin resistance gene to the Y chromosome. The resulting strain therefore had an overall genotype representing the local population but with the Y chromosome containing the dieldrin resistance gene. Life‐history characteristics, stability of the sex‐linked resistance marker, and reduction in dieldrin waste were investigated. The strain showed semi‐sterility exhibited by low egg hatch rates, faster development in the immature stages and longer adult survivorship compared with the parental strains. While the GMK strain carrying the dieldrin‐resistant gene was successfully established, the stability of the gene is limited, requiring periodic purification. Dieldrin waste can be limited by treating many more eggs than currently recommended.
Endothelial glycocalyx in health and kidney disease: Rising star or false Dawn?
Authors: Liew Hui , Roberts Matthew A , MacGinley Robert , McMahon Lawrence P
Published: August 2017

Summary at a Glance

The endothelial glycocalyx on the surface of vascular endothelial cells, an early indicator of endothelial injury and a potential marker of vascular injury, could be demonstrated by a variety of methods of assessment, including novel optical approaches and might be a potential therapeutic target.