bluuebunny/crossref_metadata_2025 huggingface dataset:
Lemon: a framework for rapidly mining structural information from the Protein Data Bank
Authors: Fine Jonathan , Chopra Gaurav
Published: March 2019

Motivation

The Protein Data Bank (PDB) currently holds over 140 000 biomolecular structures and continues to release new structures on a weekly basis. The PDB is an essential resource to the structural bioinformatics community to develop software that mine, use, categorize and analyze such data. New computational biology methods are evaluated using custom benchmarking sets derived as subsets of 3D experimentally determined structures and structural features from the PDB. Currently, such benchmarking features are manually curated with custom scripts in a non-standardized manner that results in slow distribution and updates with new experimental structures. Finally, there is a scarcity of standardized tools to rapidly query 3D descriptors of the entire PDB.

Results

Our solution is the Lemon framework, a C++11 library with Python bindings, which provides a consistent workflow methodology for selecting biomolecular interactions based on user criterion and computing desired 3D structural features. This framework can parse and characterize the entire PDB in <10 min on modern, multithreaded hardware. The speed in parsing is obtained by using the recently developed MacroMolecule Transmission Format to reduce the computational cost of reading text-based PDB files. The use of C++ lambda functions and Python bindings provide extensive flexibility for analysis and categorization of the PDB by allowing the user to write custom functions to suite their objective. We think Lemon will become a one-stop-shop to quickly mine the entire PDB to generate desired structural biology features.

Availability and implementation

The Lemon software is available as a C++ header library along with a PyPI package and example functions at https://github.com/chopralab/lemon.

Supplementary information

Supplementary data are available at Bioinformatics online.
ECOGEMS: efficient compression and retrieve of SNP data of 2058 rice accessions with integer sparse matrices
Authors: Yao Wen , Huang Fangfang , Zhang Xuehai , Tang Jihua
Published: March 2019

We proposed to store large-scale genotype data as integer sparse matrices, which consumed much fewer computing resources for storage and analysis than traditional approaches. In addition, the raw genotype data could be readily recovered from integer sparse matrices. Utilizing this approach, we stored the genotype data of 1612 Asian cultivated rice accessions and 446 Asian wild rice accessions across 8 584 244 SNP sites in the ECOGEMS database with 310 MB of disk usage. Graphical interface for visualization, analysis and download of SNP data were implemented in ECOGEMS, which made it a valuable resource for rice functional genomic studies.

Availability and implementation

The code and data of ECOGEMS are freely available at https://github.com/venyao/ECOGEMS. ECOGEMS is deployed at http://ecogems.ncpgr.cn and http://150.109.59.144: 3838/ECOGEMS/ for online use.

Supplementary information

Supplementary data are available at Bioinformatics online.
In utero Exposure to Anesthetics Alters Neuronal Migration Pattern in Developing Cerebral Cortex and Causes Postnatal Behavioral Deficits in Rats
Authors: Gluncic V , Moric M , Chu Y , Hanko V , Li J , Lukić I K , Lukić A , Edassery S L , Kroin J S , Persons A L , Perry P , Kelly L , Shiveley T J , Nice K , Napier C T , Kordower J H , Tuman K J
Published: March 2019

During fetal development, cerebral cortical neurons are generated in the proliferative zone along the ventricles and then migrate to their final positions. To examine the impact of in utero exposure to anesthetics on neuronal migration, we injected pregnant rats with bromodeoxyuridine to label fetal neurons generated at embryonic Day (E) 17 and then randomized these rats to 9 different groups receiving 3 different means of anesthesia (oxygen/control, propofol, isoflurane) for 3 exposure durations (20, 50, 120 min). Histological analysis of brains from 54 pups revealed that significant number of neurons in anesthetized animals failed to acquire their correct cortical position and remained dispersed within inappropriate cortical layers and/or adjacent white matter. Behavioral testing of 86 littermates pointed to abnormalities that correspond to the aberrations in the brain areas that are specifically developing during the E17. In the second set of experiments, fetal brains exposed to isoflurane at E16 had diminished expression of the reelin and glutamic acid decarboxylase 67, proteins critical for neuronal migration. Together, these results call for cautious use of anesthetics during the neuronal migration period in pregnancy and more comprehensive investigation of neurodevelopmental consequences for the fetus and possible consequences later in life.
Successful Treatment of Antibiotic-resistant, Poly-microbial Bone Infection With Bacteriophages and Antibiotics Combination
Authors: Nir-Paz Ran , Gelman Daniel , Khouri Ayman , Sisson Brittany M , Fackler Joseph , Alkalay-Oren Sivan , Khalifa Leron , Rimon Amit , Yerushalmy Ortal , Bader Reem , Amit Sharon , Coppenhagen-Glazer Shunit , Henry Matthew , Quinones Javier , Malagon Francisco , Biswas Biswajit , Moses Allon E , Merril Greg , Schooley Robert T , Brownstein Michael J , Weil Yoram A , Hazan Ronen
Published: March 2019

A patient with a trauma-related left tibial infection associated with extensively drug-resistant Acinetobacter baumannii and multidrug-resistant Klebsiella pneumoniae was treated with bacteriophages and antibiotics. There was rapid tissue healing and positive culture eradication. As a result, the patient’s leg did not have to be amputated and he is undergoing rehabilitation.
Dynamic-SoS: An Approach for the Simulation of Systems-of-Systems Dynamic Architectures
Authors: Manzano Wallace , Graciano Neto Valdemar Vicente , Nakagawa Elisa Yumi
Published: March 2019

Systems-of-Systems (SoS) combine heterogeneous, independent systems to offer complex functionalities for highly dynamic smart applications. Besides their dynamic architecture with continuous changes at runtime, SoS should be reliable and work without interrupting their operation and with no failures that could cause accidents or losses. SoS architectural design should facilitate the prediction of the impact of architectural changes and potential failures due to SoS behavior. However, existing approaches do not support such evaluation. Hence, these systems have been usually built without a proper evaluation of their architecture. This article presents Dynamic-SoS, an approach to predict/anticipate at design time the SoS architectural behavior at runtime to evaluate whether the SoS can sustain their operation. The main contributions of this approach comprise: (i) characterization of the dynamic architecture changes via a set of well-defined operators; (ii) a strategy to automatically include a reconfiguration controller for SoS simulation; and (iii) a means to evaluate architectural configurations that an SoS could assume at runtime, assessing their impact on the viability of the SoS operation. Results of our case study reveal Dynamic-SoS is a promising approach that could contribute to the quality of SoS by enabling prior assessment of its dynamic architecture.
Brain Protein Synthesis Rates in the UM-HET3 Mouse Following Treatment With Rapamycin or Rapamycin With Metformin
Authors: Reid Justin J , Linden Melissa A , Peelor Frederick F , Miller Richard A , Hamilton Karyn L , Miller Benjamin F
Published: March 2019

Treatment with the mechanistic target of rapamycin (mTOR) inhibitor, rapamycin (RAP), alone and in combination with the antidiabetic drug, metformin (RAP+MET), extends lifespan in mice. The mechanisms underlying lifespan extension are unclear. One possibility is improved capacity for proteostatic maintenance. We have previously characterized peripheral protein synthesis rates following treatment with RAP. However, it is unknown if RAP+MET elicits similar changes, or if either treatment affects protein synthesis in the brain. We hypothesized that 8 weeks of treatment with RAP and RAP+MET would alter brain protein synthesis rates to reflect proteostatic processes. Using the stable isotopic tracer, deuterium oxide (D2O), we demonstrate in UM-HET3 mice that protein synthesis rates measured in whole brain were unaffected by treatment in young male mice, whereas RAP+MET decreased mitochondrial protein synthesis in young females. Conversely, RAP increased mitochondrial protein synthesis rates in older females. Activity through the AMPK/mTOR pathway was affected in a sex-specific manner in young mice, and minimal changes were observed in the older cohort. Thus, we establish D2O for measurements of biogenesis in the brain. These results provide initial insights into the effects of RAP and RAP+MET on brain protein synthesis. Additionally, these data emphasize that responses to slowed aging treatments vary with sex and age.
Interface-targeted seismic velocity estimation using machine learning
Authors: Schuba C Nur , Schuba Jonathan P , Gray Gary G , Davy Richard G
Published: March 2019

We present a new approach to estimate 3-D seismic velocities along a target interface. This approach uses an artificial neural network trained with user-supplied geological and geophysical input features derived from both a 3-D seismic reflection volume and a 2-D wide-angle seismic profile that were acquired from the Galicia margin, offshore Spain. The S-reflector detachment fault was selected as the interface of interest. The neural network in the form of a multilayer perceptron was employed with an autoencoder and a regression layer. The autoencoder was trained using a set of input features from the 3-D reflection volume. This set of features included the reflection amplitude and instantaneous frequency at the interface of interest, time-thicknesses of overlying major layers and ratios of major layer time-thicknesses to the total time-depth of the interface. The regression model was trained to estimate the seismic velocities of the crystalline basement and mantle from these features. The ‘true’ velocities were obtained from an independent full-waveform inversion along a 2-D wide-angle seismic profile, contained within the 3-D data set. The autoencoder compressed the vector of inputs into a lower dimensional space, then the regression layer was trained in the lower dimensional space to estimate velocities above and below the targeted interface. This model was trained on 50 networks with different initializations. A total of 37 networks reached minimum achievable error of 2 per cent. The low standard deviation (<300  m s−1) between different networks and low errors on velocity estimations demonstrate that the input features were sufficient to capture variations in the velocity above and below the targeted S-reflector. This regression model was then applied to the 3-D reflection volume where velocities were predicted over an area of ∼400 km2. This approach provides an alternative way to obtain velocities across a 3-D seismic survey from a deep non-reflective lithology (e.g. upper mantle) , where conventional reflection velocity estimations can be unreliable.
Volunteerism as adolescent health promotion asset: a scoping review
Authors: Hernantes Naia , Pumar-Méndez María J , López-Dicastillo Olga , Iriarte Andrea , Mujika Agurtzane
Published: March 2019

The Aim of this scoping review was to explore the available literature on volunteerism in adolescence and the benefits that this activity may report in their healthy development, from a salutogenic perspective. Searches were conducted in Pubmed, Cinahl, PsycINFO and Cochrane Library home databases; 15 articles were selected. Almost all of the studies were conducted in the United States between 1990 and 2000, primarily developed by psychologists and sociologists. The impact of volunteering was reflected in aspects that can be classified based on Lerner's dimensions of the PYD model. Volunteer activities promote an Improved academic, social, cognitive, and vocational competence in adolescents. An increase in conflict resolution capacity, leadership and personal agency, as well as improved pro-social attitudes and relationships with adults and peers, all of which contributed to their self-identification with the community. Moreover, increased positive development of adolescents reduces the rates of risky behaviors. Volunteerism may represent an opportunity for health promotion in adolescence. The concept of volunteering as an asset for health promotion during adolescence evokes the need to adopt and favor this view with regard to key areas of study associated with this stage such as education and health. Teams that work in community health, especially those in primary care, should recognize and value existing volunteer groups as an asset to promote the healthy development of adolescents. Friendlier health services should be encouraged that include comprehensive services from within educational institutions to community actions.
The impact of gardening on nutrition and physical health outcomes: a systematic review and meta-analysis
Authors: Kunpeuk Watinee , Spence William , Phulkerd Sirinya , Suphanchaimat Rapeepong , Pitayarangsarit Siriwan
Published: March 2019

Community gardening has been widely recognized as a multicomponent approach that has affected a broad range of health and well-being outcomes. The objective of this study was to investigate the association between community gardening and nutrition and physical health among adults. A systematic review and meta-analysis were conducted. Five electronic databases were searched systematically. Quality of included studies was appraised by several quality assessment tools related to the study design of each included article. Evidence from 19 articles was included (14 cross-sectional studies, 4 quasi-experimental studies and 1 case–control study). Although the majority of included studies appeared to have moderate quality, there existed weaknesses in the methods used, including low response rate and lack of confounder controls. Due to diversity in the measurement units, only body mass index (BMI) data could be pooled to perform meta-analysis. The results suggest that gardening had a significantly positive effect on BMI reduction. Subgroup analysis showed that quasi-experimental and case–control studies produced greater pooled effect size than those of cross-sectional design. Funnel plot and Egger’s test showed no significant evidence of publication bias. As robust evidence for the effect of community gardening on BMI reduction was found, this intervention should be integrated in health promoting policy to improve population health.
Leukocyte Profiles Reflect Geographic Range Limits in a Widespread Neotropical Bat
Authors: Becker Daniel J , Nachtmann Cecilia , Argibay Hernan D , Botto Germán , Escalera-Zamudio Marina , Carrera Jorge E , Tello Carlos , Winiarski Erik , Greenwood Alex D , Méndez-Ojeda Maria L , Loza-Rubio Elizabeth , Lavergne Anne , de Thoisy Benoit , Czirják Gábor Á , Plowright Raina K , Altizer Sonia , Streicker Daniel G
Published: March 2019

Quantifying how the environment shapes host immune defense is important for understanding which wild populations may be more susceptible or resistant to pathogens. Spatial variation in parasite risk, food and predator abundance, and abiotic conditions can each affect immunity, and these factors can also manifest at both local and biogeographic scales. Yet identifying predictors and the spatial scale of their effects is limited by the rarity of studies that measure immunity across many populations of broadly distributed species. We analyzed leukocyte profiles from 39 wild populations of the common vampire bat (Desmodus rotundus) across its wide geographic range throughout the Neotropics. White blood cell differentials varied spatially, with proportions of neutrophils and lymphocytes varying up to six-fold across sites. Leukocyte profiles were spatially autocorrelated at small and very large distances, suggesting that local environment and large-scale biogeographic factors influence cellular immunity. Generalized additive models showed that bat populations closer to the northern and southern limits of the species range had more neutrophils, monocytes, and basophils, but fewer lymphocytes and eosinophils, than bats sampled at the core of their distribution. Habitats with access to more livestock also showed similar patterns in leukocyte profiles, but large-scale patterns were partly confounded by time between capture and sampling across sites. Our findings suggest that populations at the edge of their range experience physiologically limiting conditions that predict higher chronic stress and greater investment in cellular innate immunity. High food abundance in livestock-dense habitats may exacerbate such conditions by increasing bat density or diet homogenization, although future spatially and temporally coordinated field studies with common protocols are needed to limit sampling artifacts. Systematically assessing immune function and response over space will elucidate how environmental conditions influence traits relevant to epidemiology and help predict disease risks with anthropogenic disturbance, land conversion, and climate change.
Acute impacts of bottom trawl gears on benthic metabolism and nutrient cycling
Authors: Tiano Justin C , Witbaard Rob , Bergman Magda J N , van Rijswijk Pieter , Tramper Anton , van Oevelen Dick , Soetaert Karline
Published: March 2019

Research on the environmental impacts of bottom fishing gears has focused mainly on structural characteristics of benthic habitats such as faunal composition and the physical features of the seafloor. This study focuses more on functional characteristics by addressing the biogeochemical consequences associated with tickler chain beam trawl and electric PulseWing trawl gears. In June 2017, professional fishermen trawled experimental transects with both types of gears in the Frisian Front area of the North Sea. Box core sediment samples and in situ landers were used to evaluate biogeochemical fluxes and sediment characteristics in untrawled and trawled areas (samples taken 3.5–70 h after fishing). A reduction of sedimentary chlorophyll a was observed, which was larger following tickler chain (83%) compared to PulseWing trawling (43%). This displacement of surface material caused significant decreases in the sediment oxygen consumption in tickler chain (41%) and PulseWing trawled samples (33%) along with a deeper penetration of oxygen in the sediment (tickler chain: 3.78 mm, PulseWing: 3.17 mm) compared to untrawled areas (2.27 mm). Our research implies that bottom trawl disturbance can lead to immediate declines in benthic community metabolism, with tickler chain trawling exhibiting more prominent alterations than PulseWing trawling on benthic biogeochemical processes.
Frailty, disability and comorbidity: different domains lead to different effects after surgical aortic valve replacement in elderly patients
Authors: Piñón Miguel , Paredes Emilio , Acuña Beatriz , Raposeiras Sergio , Casquero Elena , Ferrero Ana , Torres Ivett , Legarra Juan José , Pradas Gonzalo , Barreiro-Morandeira Francisco , Rodriguez-Pascual Carlos
Published: March 2019

OBJECTIVES

Frailty syndrome predicts adverse outcomes after surgical aortic valve replacement. However, disability or comorbidity is frequently associated with preoperative frailty evaluation. The effects of these domains on early and late outcomes were analysed.

METHODS

A prospective study including patients aged ≥75 years with symptomatic severe aortic stenosis who received aortic valve replacement with or without coronary artery bypass grafting was conducted. We used the Cardiovascular Health Study Frailty Phenotype to assess frailty, the Lawton–Brody index to define disability and the Charlson comorbidity index (CCI) to evaluate comorbidity.

RESULTS

Frailty was identified in 57 (31%), dependence in 18 (9.9%) and advanced comorbidity (CCI ≥ 4) in 67 (36.6%) of the 183 enrolled patients. Operative mortality (1.6%), transfusion rate and duration of stay increased in patients with CCI ≥4 (P < 0.005). There was a non-significant trend for these adverse outcomes among the frail patients. Follow-up was achieved in all patients (median/interquartile range 869/699–1099 days). Kaplan–Meier univariable analysis showed a reduced survival rate for frail and dependent patients and for those with multiple comorbidities (P < 0.05). According to multivariable analysis, frailty and comorbidity were independent risk factors for 1-year mortality, while disability and comorbidity, but not frailty, were risk factors for 3-year mortality (P < 0.05).

CONCLUSIONS

Surgical aortic valve replacement in patients aged ≥75 years is a safe procedure with low mortality rates. Operative outcomes are mainly affected by comorbidities. The main influence of survival occurs throughout the first year, and an improved functional status prevents any progression towards disabilities, which could potentially benefit long-term outcomes.

Clinical trial registration number

NCT02745314
Design Nationalism, Technological Pragmatism and the Performance of Canadian-ness: The Case of the Contempra Telephone
Authors: Hadlaw Jan
Published: March 2019

The Contempra is widely considered to be the first telephone designed and manufactured in Canada. Designed in 1967, Canada’s centennial year, it was a conspicuous departure from prevailing conventions of North American telephone styling in both its conception and design. It was designated as an icon of Canadian modern design and became a symbol of Canada’s identity as a modern nation at home and abroad. Its popularity in domestic and international markets set the stage for the transformation of its developer, Northern Electric, into a global telecommunication leader and Canada’s most valuable corporation, eventually renamed Nortel Networks. The history of the Contempra’s design and development offers an opportunity to consider how designed technological artefacts take on cultural and ideological meaning. Most accounts celebrate the Contempra as a distinctly Canadian design story, but do not elaborate on or question its ‘Canadian-ness’, and they are silent on the circumstances and events that culminated in the telephone’s development. This article examines the historical events, ideological discourses, human relationships, design values and material constraints that set the stage for what can be best described as the Contempra telephone’s performance of modern Canadian nationalism.
Categories of Resistance to Sugarcane Aphid (Hemiptera: Aphididae) Among Sorghum Genotypes
Authors: Paudyal Sulochana , Armstrong John Scott , Giles Kristopher L , Payton Mark E , Opit George P , Limaje Ankur
Published: March 2019

The sugarcane aphid Melanaphis sacchari (Zehnter) (Hemiptera: Aphididae) has emerged as a potential threat to sorghum (Sorghum bicolor (L.) Moench) production in the United States. Since the late summer of 2013, finding and advancing M. sacchari-resistant germplasm has been a priority for all stakeholders involved. We evaluated 23 sorghum genotypes for resistance to the sugarcane aphid by testing for tolerance, and antixenosis. In addition, nine sorghum germplasm were evaluated for the expression of antibiosis. Free-choice and no-choice tests were conducted to explore the functional categories of resistance. Levels of resistance to M. sacchari were compared with the known resistant ‘TX 2783’ and the susceptible ‘KS 585’. Sorghum entries AG1201, AG1301, W844-E, and DKS 37-07 were identified as expressing tolerance, antibiosis, and antixenosis, while H13073 expressed antibiosis and GW1489 expressed both tolerance and antibiosis. These resistant sorghums identified during this study will have a significant impact on reducing economic damage from the sugarcane aphid infestations.
STOP1 regulates the expression of HsfA2 and GDHs that are critical for low-oxygen tolerance in Arabidopsis
Authors: Enomoto Takuo , Tokizawa Mutsutomo , Ito Hiroki , Iuchi Satoshi , Kobayashi Masatomo , Yamamoto Yoshiharu Y , Kobayashi Yuriko , Koyama Hiroyuki
Published: March 2019

The SENSITIVE TO PROTON RHIZOTOXICITY 1 (STOP1) transcription factor regulates gene expression associated with multiple stress tolerances in plant roots. In this study, we investigated the mechanism responsible for the sensitivity of the stop1 mutant to low-oxygen stress in Arabidopsis. Transcriptomic analyses revealed that two genes involved in low-oxygen tolerance, namely GLUTAMATE DEHYDROGENASE 1 (GDH1) and GDH2, showed lower expression levels in the stop1 mutant than in the wild-type. Sensitivity of the gdh1gdh2 double-mutant to low-oxygen conditions was partly attributable to the low-oxygen sensitivity of the stop1 mutant. Two transcription factors, STOP2 and HEAT SHOCK FACTOR A2 (HsfA2), were expressed at lower levels in the stop1 mutant. An in planta complementation assay indicated that CaMV35S::STOP2 or CaMV35S::HsfA2 partially rescued the low-oxygen tolerance of the stop1 mutant, which was concomitant with recovered expression of genes regulating low-pH tolerance and genes encoding molecular chaperones. Prediction of cis-elements and in planta promoter assays revealed that STOP1 directly activated the expression of HsfA2. Similar STOP1-dependent low-oxygen sensitivity was detected in tobacco. Suppression of NtSTOP1 induced low-oxygen sensitivity, which was associated with lower expression levels of NtHsfA2 and NtGDHs compared with the wild-type. Our results indicated that STOP1 pleiotropically regulates low-oxygen tolerance by transcriptional regulation.
Single photoionization of the Kr-like Rb ii ion in the photon energy range 22–46.0 eV
Authors: McLaughlin Brendan M , Babb James F
Published: March 2019

Single photoionization cross-sections for Kr-like Rb+ ions are reported in the energy (wavelength) range from 22 (564 Å) to 46 eV (270 Å). Theoretical cross-section calculations for this trans-Fe element are compared with measurements from the ASTRID radiation facility in Aarhus, Denmark and from the dual laser plasma technique, at respectively 40 and 35 meV FWHM energy resolution. In the photon energy region 22–32 eV the spectrum is dominated by excitation auto-ionizing resonance states. Above 32 eV the cross-section exhibits classic Fano window resonances features, which are analysed and discussed. Large-scale theoretical photoionization cross-section calculations, performed using a Dirac Coulomb R-matrix approximation are benchmarked against these high-resolution experimental results. Comparison of the theoretical work with the experimental studies allowed the identification of resonance features and their parameters in the spectra in addition to contributions from excited metastable states of the Rb+ ions.
Mock galaxy shape catalogues in the Subaru Hyper Suprime-Cam Survey
Authors: Shirasaki Masato , Hamana Takashi , Takada Masahiro , Takahashi Ryuichi , Miyatake Hironao
Published: March 2019

We use the full-sky ray-tracing weak lensing simulations to generate 2268 mock catalogues for the Subaru Hyper Suprime-Cam (HSC) survey first-year shear catalogue. Our mock catalogues take into account various effects as in the real data: the survey footprints, inhomogeneous angular distribution of source galaxies, statistical uncertainties in photometric redshift (photo-z) estimate, variations in the lensing weight, and the statistical noise in galaxy shape measurements including both intrinsic shapes and the measurement errors. We then utilize our mock catalogues to evaluate statistical uncertainties expected in measurements of cosmic shear two-point correlations ξ± with tomographic redshift information for the HSC survey. We develop a quasi-analytical formula for the Gaussian sample variance properly taking into account the number of source pairs in the survey footprints. The standard Gaussian formula significantly overestimates or underestimates the mock results by 50 per cent level. We also show that different photo-z catalogues or the six disconnected fields, rather than a consecutive geometry, cause variations in the covariance by ${\sim } 5{{\ \rm per\ cent}}$. The mock catalogues enable us to study the chi-square distribution for ξ±. We find the wider distribution than that naively expected for the distribution with the degrees of freedom of data vector used. Finally, we propose a method to include non-zero multiplicative bias in mock shape catalogue and show that the non-zero multiplicative bias can change the effective shape noise in cosmic shear analyses. Our results suggest an importance of estimating an accurate form of the likelihood function (and therefore the covariance) for robust cosmological parameter inference from the precise measurements.
Faraday conversion and magneto-ionic variations in fast radio bursts
Authors: Vedantham H K , Ravi V
Published: March 2019

The extreme, time-variable Faraday rotation observed in the repeating fast radio burst (FRB) 121102 and its associated persistent synchrotron source demonstrates that some FRBs originate in dense, dynamic, and possibly relativistic magneto-ionic environments. Besides rotation of the linear polarization vector (Faraday rotation), such media can generally convert linear to circular polarization (Faraday conversion). We use non-detection of Faraday conversion, and the temporal variation in Faraday rotation and dispersion in bursts from FRB 121102 to constrain models where the progenitor inflates a relativistic nebula (persistent source) confined by a cold dense medium (e.g. supernova ejecta). We find that the persistent synchrotron source, if composed of an electron–proton plasma, must be an admixture of relativistic and non-relativistic (Lorentz factor γ < 5) electrons. Furthermore, we independently constrain the magnetic field in the cold confining medium, which provides the Faraday rotation, to be between 10 and 30 mG. This value is close to the equipartition magnetic field of the confined persistent source implying a self-consistent and overconstrained model that can explain the observations.
Impact of pretransplant mitral annular calcification on the incidence of cardiac events after renal transplantation
Authors: El Hangouche Nadia , Gomez Javier , Asfaw Addis , Sreenivasan Jayakumar , Akhtar Tauseef , Teshome Meron , Vij Aviral , Matar Ralph , Campagnoli Tania , Doukky Rami
Published: March 2019

Background

Mitral annular calcification (MAC) is associated with increased risk of major adverse cardiac events. We hypothesized that MAC, identified on a pretransplant transthoracic echocardiography (TTE), is predictive of cardiac events following renal transplantation (RT).

Methods

In a retrospective cohort of consecutive RT recipients, pretransplant MAC presence and severity were determined on TTE performed within 1 year prior to transplant. MAC severity was quantified based on the circumferential MAC extension relative to the mitral valve annulus. Post-transplant cardiac risk was assessed using the sum of risk factors (range: 0–8) set forth by the American Heart Association/American College of Cardiology Foundation consensus statement on the assessment of RT candidates. Subjects underwent pretransplant stress single-photon emission computed tomography myocardial perfusion imaging and followed for post-transplant composite outcome of cardiac death or myocardial infarction (CD/MI).

Results

Among 336 subjects (60.5% men; mean age 52 ± 12 years), MAC was present in 78 (23%) patients. During a mean follow-up of 3.1 ± 1.9 years, a total of 70 events were observed. Patients with MAC had a higher event rate compared with those without MAC (34.6% versus 17.8%, log-rank P = 0.001). There was a stepwise increase in CD/MI risk with increasing MAC severity (P for trend = 0.002). MAC-associated risk remained significant after adjusting for sex, duration of dialysis, sum of risk factors, ejection fraction and perfusion abnormality burden, providing an incremental prognostic value to these parameters (Δχ2 =4.63; P = 0.031).

Conclusion

Among RT recipients, the burden of pretransplant MAC is an independent predictor of post-transplant risk of CD/MI. MAC should be considered in the preoperative assessment of RT candidates.
Frock Coats against Brass Hats? Politicians, the Military and the War in Afghanistan 2001–2014
Authors: Dixon Paul
Published: March 2019

The ‘Dominant Military Narrative’ (DMN) on the Iraq and Afghan wars defends the effectiveness of the British military and its use of force by deflecting responsibility for failure onto the politicians and ‘Whitehall’. The politicians are blamed for over-stretching the military by fighting two wars, resulting in a shortage of equipment, inadequate troop numbers and without a clear ‘Strategic Narrative’. This article critiques the DMN and provides evidence to suggest that it was the military elite that sought maximum involvement in the Iraq and Afghan wars. The problem is that the military has too much rather than too little power to shape policy.
The Distortive Effects of Too Big To Fail: Evidence from the Danish Market for Retail Deposits
Authors: Iyer Rajkamal , Lærkholm Jensen Thais , Johannesen Niels , Sheridan Adam
Published: March 2019

We study the impact of too-big-to-fail (TBTF) guarantees on the market for retail deposits. Exploiting information about all personal deposit accounts in Denmark and salient changes to the deposit insurance limit, we provide evidence that systemically important banks successfully retain and attract uninsured deposits in a crisis at the expense of other banks even as they differentially lower their interest rates. The funding shock suffered by nonsystemic banks causes a decrease in their lending. The results point to the distortive effects of TBTF guarantees in the market for retail deposits.

Received March 15, 2018; editorial decision January 15, 2019 by Philip Strahan.
External Fixation as a Definitive Treatment for Humeral Shaft Fractures: Radiographic and Functional Results With Analysis of Outcome Predictors
Authors: Costa Giovan Giuseppe , Aloj Domenico Costantino , Cerbasi Simone , Rizzo Maria , Massè Alessandro , Pascarella Raffaele , Mariconda Massimo
Published: March 2019

Objectives:

To evaluate the results obtained using unilateral external fixation as a definitive treatment for humeral shaft fractures and to identify possible predictors of radiographic and functional outcomes.

Design:

Retrospective study.

Setting:

One large metropolitan hospital.

Patients:

A consecutive cohort of 107 patients who underwent external fixation for 109 humeral shaft fractures.

Main Outcome Measures:

Union rate, time to fracture healing, and functional assessment with disabilities of the arm, shoulder, and hand questionnaire, Constant score, Mayo Elbow Performance Index, and return to prefracture sports activity at a minimum of 2 years after surgery. Comorbidities were evaluated using the Cumulative Illness Rating Scale. Multiple linear regression analysis was used to determine whether any explanatory variables were significantly associated with the outcomes.

Results:

The union rate in 109 humeral shaft fractures was 97.2% (106/109) at a mean of 99.2 days. Two patients (1.8%) had delayed union, and 1 patient (0.9%) did not achieve union. At the latest follow-up, the mean Constant score, Mayo Elbow Performance Index, and disabilities of the arm, shoulder and hand questionnaire score was 85.6, 97.4, and 7.4 points, respectively. All patients engaged in sports activities before fracture resumed a sport activity. At the multiple linear regression analysis, obesity was directly related to a delayed healing of fracture (P = 0.010) and comorbidity was the most important determinant of the functional outcomes at follow-up (P < 0.001).

Conclusions:

These data support the use of unilateral external fixation as an effective therapeutic option in patients with humeral shaft fracture. Comorbidity as assessed by Cumulative Illness Rating Scale score is the most important determinant of functional outcomes.

Level of Evidence:

Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Current opinion about antimicrobial therapy in palliative care: an update
Authors: Macedo Filipa , Bonito Nuno
Published: March 2019

Purpose of review

The review englobes the latest studies published regarding the problem of antimicrobial usage with palliative intent.

Recent findings

In the advanced stages of illness like cancer, dementia, or neurodegenerative diseases, important decisions have to be made concerning the global treatment plan. Infections are very common among this kind of patients as they typically have multiple comorbidities and are incapacitated. These infections, in a majority of the cases, will be treated with antimicrobial therapy because this is a standard medical procedure. For a health professional, the decision of whether to treat, withhold, or withdraw a treatment can be difficult. In fact, in palliative care, the challenge is to balance compassionate care for people suffering from end-of-life diseases with the need for responsible antibiotic usage. Antimicrobial treatment could alleviate symptoms from an infection and make patients more comfortable, on the other hand, its overuse of it could bring a broader public health risk.

On the contrary, in 18 months there are few studies about this problem, what reveals no concern about the use of antimicrobians in end-of-life patients.
The Nurse-Chaplain-Family Spiritual Care Triad
Authors: Sonemanghkara Rocky , Rozo Jose Andres , Stutsman Sonja
Published: March 2019

This qualitative study utilized a phenomenological approach to better understand nurse, chaplain, and family member experiences with the delivery of spiritual services at the end of life in an inpatient intensive care unit. Triadic semistructured interviews (six with the patient's family members, six with nurses, and six with chaplains) were conducted. Family members perceived that the nurses' role was to care for the physical needs of their loved one, whereas chaplains were there to care for the emotional needs of those involved.
Impacting Depression in Homebound Elderly
Authors: Parson Laurie J.
Published: March 2019

Depression among homebound older adults is a significant problem. This pilot project examined the effect of a faith community nurse (FCN) educational intervention based on the CREATION Health Model, on depression in older homebound adults. Results showed a downward trend in depression scores on the Geriatric Depression Scale: Short Form, suggesting that FCN interventions and the CREATION Health Model may be helpful for decreasing depression in this group.
Fostering Cultural Competence in Nursing Students Through International Service Immersion Experiences
Authors: Dyches Cathy , Haynes-Ferere Angela , Haynes Twilla
Published: March 2019

Using an ethnographical case study method, faculty members examined senior nursing students' experiences and learning during a cultural immersion service-learning trip in Haiti. Pediatric care was emphasized, as well as cultural awareness and competency. Following thematic analysis, students' guided reflections revealed common themes: knowledge and skills, culture, healthcare, and challenges and opportunities. Students also reported improved cultural understanding and self-perception.
Medical Oversight and Scope of Practice of Medical Spas (Med-Spas)
Authors: Gibson Juliet F. , Srivastava Divya , Nijhawan Rajiv I.
Published: March 2019

BACKGROUND

The regulation of medical spas (med-spas) in the United States varies considerably from state to state with important ramifications for patient safety.

OBJECTIVE

To describe the current state of med-spas in the United States and degree of medical oversight in these facilities.

MATERIALS AND METHODS

Descriptive study based on web search and standardized phone interviews of med-spas in the most heavily populated cities in each state of the United States. Information obtained included the following: whether medical directors were listed; if so, whether they were advertised as being on site; medical directors' training and board certification; and services offered.

RESULTS

Of 247 medical spas reviewed, 72% advertised a medical director on their website, and 6.5% claimed that the director was on site. Of listed medical directors, 41% were trained in dermatology and/or plastic surgery. In phone interviews, 79% of med-spas endorsed the medical director to be board certified, and 52% stated that the medical director was on site less than 50% of the time.

CONCLUSION

There is significant variation in medical directorship and oversight among medical spas in the United States. Appropriate regulation of medical directors' training and the degree of oversight provided are warranted to optimize patient safety.
Phacoemulsification With 3.0 and 2.0 mm Opposite Clear Corneal Incisions for Correction of Corneal Astigmatism
Authors: Ren Yueping , Fang Xiuxiu , Fang Aiwu , Wang Le , Jhanji Vishal , Gong Xianhui
Published: March 2019

Purpose:

To compare the effect of 3.0 and 2.0 mm opposite clear corneal incisions (OCCIs) in phacoemulsification on reduction of preexisting corneal astigmatism, and their impact on corneal aberrations.

Methods:

This study is a prospective randomized controlled study that included 140 patients with age-related cataract and regular corneal astigmatism ≥0.75 diopter (D). Phacoemulsification was performed using on-meridian 3.0 or 2.0 mm corneal incision with or without an OCCI. Cases were divided into 4 groups: 3.0 mm OCCIs, 3.0 mm single clear corneal incision (3.0 mm SCCI), 2.0 mm OCCIs, and 2.0 mm SCCI. Keratometry and topography were performed at 3 months postoperatively. The variations in corneal astigmatism and aberrations were recorded. Surgically induced astigmatism was calculated using vector analysis.

Results:

The corneal astigmatism reduction was 0.61 ± 0.38 D in the 3.0 mm OCCIs group, significantly higher than the other groups (P ≤ 0.004); and 0.29 ± 0.29 D in the 2.0 mm OCCIs group. The mean surgically induced astigmatism was 1.07 ± 0.51 D in the 3.0 mm OCCIs group, higher than 0.61 ± 0.35 D in the 2.0 mm OCCIs group (P = 0.001). The root mean square values of corneal trefoil, spherical aberration, and total higher order aberrations increased at 3 months postoperatively, but there were no significant differences between OCCI and SCCI groups.

Conclusions:

On-meridian 3.0 mm OCCIs are effective for correcting mild-to-moderate corneal astigmatism during cataract surgery, exerting no additional impact on corneal aberration compared with SCCI.
Increased Serum Levels of Cortisol and Inflammatory Cytokines in People With Depression
Authors: Jia Yong , Liu Linlin , Sheng Chuqiao , Cheng Zhaohua , Cui Lianzhi , Li Min , Zhao Yawei , Shi Tongfei , Yau Tung On , Li Feng , Chen Li
Published: March 2019

This cross-sectional study aimed at measuring the correlation and association between serum levels of cortisol, inflammatory cytokines, and depression and to measure the detection accuracy of serum levels of cortisol in serum samples. In total, 89 male participants were recruited into this study from June 15, 2017, to September 31, 2017. The Hamilton Depression Rating Scale, Beck Anxiety Inventory, and Pittsburgh Sleep Quality Index were used to investigate the mental health status of the participants. Serum concentrations of cortisol and inflammatory cytokines were determined. The serum cortisol concentration, anxiety level, and sleep quality were included in the final logistic regression model. Serum cortisol was able to accurately distinguish between patients with depression and those without depression. There was a significant positive correlation between serum cortisol levels and Hamilton Depression Rating Scale scores.
Approaches to Recruitment of Postmenopausal Women for a Community-Based Study
Authors: Waltman Nancy L. , Smith Kara M. , Kupzyk Kevin A. , Lappe Joan M. , Mack Lynn R. , Bilek Laura D.
Published: March 2019

Background

Few researchers have focused on the challenges of recruiting postmenopausal women for community-based research. Researchers have reported that multiple methods may be needed to recruit the required number of subjects. One contemporary approach to recruitment is use of Facebook. More studies are needed examining Facebook as a recruitment strategy.

Objective

The aim of the study was to examine which recruitment methods were most successful and cost-effective in recruiting postmenopausal women for a randomized controlled trial on bone loss.

Methods

Subjects were 276 postmenopausal women who had osteopenia and were within 5 years of menopause. Multiple methods were used to recruit women. To determine which methods were successful, women were asked how they learned about the study. Descriptive data were used to examine recruitment numbers as well as to determine the cost-effectiveness and enrollment efficiency of recruitment methods.

Results

Healthcare provider letters yielded the highest number of enrolled subjects (n = 58), followed by postcard mailings (n = 47), and Facebook posts (n = 44). Eleven subjects were referred by family and friends, five subjects were from newspaper or television, and two were from digital ads. Cost of recruitment per subject enrolled was highest with digital ads and postcard mailings.

Discussion

Recruitment could be more costly and time-consuming than anticipated. Recruitment using direct-targeted mailings, such as provider letters and postcards, was successful in our study and has been effective in previous studies reviewed. Facebook was successful for recruitment in our study and may continue to be useful for recruitment in the future, as the number of women accessing Facebook continues to increase.
Understanding trauma systems
Authors: Miclau Theodore
Published: March 2019

Trauma is a leading cause of death worldwide. Many more survive their injuries and face lifelong disabilities, including limiting musculoskeletal conditions that significantly impact individuals and societies. According to the World Health Organization, the burden of injury resulting from trauma will continue to increase. Despite this expected increase, trauma systems remain poorly described and understood. This supplement, which represents a collaboration of member societies of the International Orthopaedic Trauma Association, will describe trauma systems in countries from 5 different continents. The expectation is that this work will assist in identifying existing trauma systems and developing strategies for improvements in post-injury care worldwide.
Arrhythmogenic Ventricular Cardiomyopathy Associated With Fibromuscular Dysplasia of Ostial Right Main Coronary Artery
Authors: Farkašová Iannaccone Silvia , Vasovčák Peter , Sopková Dorota , Švajdler Peter , Dettmeyer Reinhard , Rampazzo Alessandra , Farkaš Daniel
Published: March 2019

In this article, we report the autopsy findings of a 23-year-old woman, who was found unconscious at home by her relatives. During the transportation to the hospital, the woman was handed over to the ambulance personnel, who were the first to provide cardiopulmonary resuscitation. In the hospital, after an hour-lasting asystole, the heart activity was restored. Prolonged cardiac arrest led to hypoxic brain injury, which resulted in a persistent coma. Examinations carried out during hospitalization detected hypokinetic interventricular septum, frequent ventricular extrasystoles and ventricular fibrillation. The patient died within 35 hours of admission to the hospital. Gross findings of the heart included a noticeable increase of the adipose tissue in the right ventricular wall, where histologically focal myocardial atrophy with focal transmural lipomatosis reaching endocardium were detected. Death was attributed to arrhythmogenic ventricular cardiomyopathy. Pathogenic variants in JUP gene and KCNH2 gene confirmed the diagnosis. Other finding of note was fibromuscular dysplasia of ostial right main coronary artery causing a significant luminal narrowing.