bluuebunny/crossref_metadata_2025 huggingface dataset:
Imaging the complex geometry of a magma reservoir using FEM-based linear inverse modeling of InSAR data: application to Rabaul Caldera, Papua New Guinea
Authors: Ronchin Erika , Masterlark Timothy , Dawson John , Saunders Steve , Martì Molist Joan
Published: March 2017

We test an innovative inversion scheme using Green's functions from an array of pressure sources embedded in finite-element method (FEM) models to image, without assuming an a-priori geometry, the composite and complex shape of a volcano deformation source. We invert interferometric synthetic aperture radar (InSAR) data to estimate the pressurization and shape of the magma reservoir of Rabaul caldera, Papua New Guinea. The results image the extended shallow magmatic system responsible for a broad and long-term subsidence of the caldera between 2007 February and 2010 December. Elastic FEM solutions are integrated into the regularized linear inversion of InSAR data of volcano surface displacements in order to obtain a 3-D image of the source of deformation. The Green's function matrix is constructed from a library of forward line-of-sight displacement solutions for a grid of cubic elementary deformation sources. Each source is sequentially generated by removing the corresponding cubic elements from a common meshed domain and simulating the injection of a fluid mass flux into the cavity, which results in a pressurization and volumetric change of the fluid-filled cavity. The use of a single mesh for the generation of all FEM models avoids the computationally expensive process of non-linear inversion and remeshing a variable geometry domain. Without assuming an a-priori source geometry other than the configuration of the 3-D grid that generates the library of Green's functions, the geodetic data dictate the geometry of the magma reservoir as a 3-D distribution of pressure (or flux of magma) within the source array. The inversion of InSAR data of Rabaul caldera shows a distribution of interconnected sources forming an amorphous, shallow magmatic system elongated under two opposite sides of the caldera. The marginal areas at the sides of the imaged magmatic system are the possible feeding reservoirs of the ongoing Tavurvur volcano eruption of andesitic products on the east side and of the past Vulcan volcano eruptions of more evolved materials on the west side. The interconnection and spatial distributions of sources correspond to the petrography of the volcanic products described in the literature and to the dynamics of the single and twin eruptions that characterize the caldera. The ability to image the complex geometry of deformation sources in both space and time can improve our ability to monitor active volcanoes, widen our understanding of the dynamics of active volcanic systems and improve the predictions of eruptions.
Agricultural Landscape and Pesticide Effects on Honey Bee (Hymenoptera: Apidae) Biological Traits
Authors: Alburaki Mohamed , Steckel Sandra J. , Williams Matthew T. , Skinner John A. , Tarpy David R. , Meikle William G. , Adamczyk John , Stewart Scott D.
Published: March 2017

Sixteen honey bee (Apis mellifera L.) colonies were placed in four different agricultural landscapes to study the effects of agricultural landscape and exposure to pesticides on honey bee health. Colonies were located in three different agricultural areas with varying levels of agricultural intensity (AG areas) and one nonagricultural area (NAG area). Colonies were monitored for their performance and productivity for one year by measuring colony weight changes, brood production, and colony thermoregulation. Palynological and chemical analyses were conducted on the trapped pollen collected from each colony and location. Our results indicate that the landscape’s composition significantly affected honey bee colony performance and development. Colony weight and brood production were significantly greater in AG areas compared to the NAG area. Better colony thermoregulation in AG areas’ colonies was also observed. The quantities of pesticides measured in the trapped pollen were relatively low compared to their acute toxicity. Unexplained queen and colony losses were recorded in the AG areas, while colony losses because of starvation were observed in the NAG area. Our results indicate that landscape with high urban activity enhances honey bee brood production, with no significant effects on colony weight gain. Our study indicates that agricultural crops provide a valuable resource for honey bee colonies, but there is a trade-off with an increased risk of exposure to pesticides.
Integrative Environmental Medicine
Authors: Weil Andrew
Published: March 2017

Integrative Environmental Medicine looks at the history and changing landscape of environmental issues in the United States, including water supply, air quality, extensive plastic pollution, harmful chemicals in cleaning and personal care products, radiofrequency radiation, food additives, pesticides, and medications. The unique properties of compounds such as endocrine-disrupting chemicals are explored along with their ability to disturb the body’s normal signaling pathways, genetic profile, and gut microbiome. Resulting molecular derangements promote thyroid and other autoimmune diseases, diabetes, cardiovascular disease, cancer, and influence developmental problems in children. Analysis of current research identifies ways to reduce exposures and health risks, improve regulations and appropriate testing for chemicals, remediate environmental pollution, and design healthier products for the future. Best practices are considered for clinicians to ascertain exposure history, test for toxins, and teach patients how to avoid harmful exposures. Patients will be prepared and empowered with information about healthier food choices and cooking practices, appropriate supplement use, water filtration, cleaning and personal care product selection, improved sleep, stress reduction, sauna, fasting, chelation, safe cell phone use, and other means of reducing harmful environmental exposures. Solutions at every level require interdisciplinary collaboration to advance assessment, design, stewardship, and regulation of chemicals to promote environmental and human health.
Entrustment Decisions: Bringing the Patient Into the Assessment Equation
Authors: ten Cate Olle
Published: March 2017

With the increased interest in the use of entrustable professional activities (EPAs) in undergraduate medical education (UME) and graduate medical education (GME) come questions about the implications for assessment. Entrustment assessment combines the evaluation of learners’ knowledge, skills, and behaviors with the evaluation of their readiness to be entrusted to perform critical patient care responsibilities. Patient safety, then, should be an explicit component of educational assessments. The validity of these assessments in the clinical workplace becomes the validity of the entrustment decisions.

Modern definitions of the validity of educational assessments stress the importance of the purpose of the test and the consequences of the learner’s score. Thus, if the learner is a trainee in a clinical workplace and entrusting her or him to perform an EPA is the focus of the assessment, the validity argument for that assessment should include a patient safety component.

While the decision to allow a learner to practice unsupervised is typically geared toward GME, similar decisions are made in UME regarding learners’ readiness to perform EPAs with indirect supervision (i.e., without a supervisor present in the room). Three articles in this issue address implementing EPAs in UME.

The author of this Commentary discusses the possibility of implementing true entrustment decisions in UME. He argues that bringing the patient into the educational assessment equation is marrying educational and health care responsibilities. Building trust in learners from early on, gradually throughout the continuum of medical education, may reframe our vision on assessment in the workplace.
Prospective Randomized Clinical Trial Investigating the Effect of the Reamer-Irrigator-Aspirator on the Volume of Embolic Load and Respiratory Function During Intramedullary Nailing of Femoral Shaft Fractures
Authors: Hall Jeremy A. , McKee Michael D. , Vicente Milena R. , Morison Zachary A. , Dehghan Niloofar , Schemitsch Christine E. , Kreder Hans J. , Petrisor Brad , Schemitsch Emil H.
Published: March 2017

Objectives:

We sought to determine whether the use of the Reamer-Irrigator-Aspirator (RIA) device resulted in a decreased amount of fat emboli compared with standard reaming (SR) when performing intramedullary (IM) nailing of femoral shaft fractures.

Design:

Prospective randomized clinical trial.

Setting:

Multi-centered trial, level I trauma centers.

Patients/Participants:

All eligible patients who presented to participating institutions with an isolated femoral shaft fracture amenable to fixation with antegrade IM nailing. Thirty-one patients were enrolled: nine were excluded because of technical difficulties with the transesophageal echocardiogram (TEE) recording. Therefore, the study comprised 22 patients: 11 patients randomized to the SR group and eleven patients randomized to the RIA group.

Intervention:

Antegrade IM nailing of a femoral shaft fracture with standard reamers or the RIA device. All patients were monitored intraoperatively with a continuous TEE to assess embolic events in the right atrium. A radial arterial line was used to monitor blood gases and potential systemic effects of emboli.

Main Outcome Measure:

Duration, size, and severity of emboli as measured by TEE. The operative procedure was divided into 6 distinct stages: preoperative, reduction, guidewire passage, reaming, nail insertion, and postoperative.

Results:

There was no significant difference in emboli between the RIA and SR groups preoperatively, during fracture reduction, guidewire insertion, or postoperatively. Measured with a standardized scoring system, there was a modest reduction in total emboli score in the RIA group during reaming (SR 5.30 [SD; 1.81] vs. RIA 4.05 [SD; 2.19], P = 0.005) and during nail insertion (SR 5.09 [SD; 1.74] vs. RIA 4.25 [SD; 1.89], P = 0.03). We were unable to correlate this reduction with any improvement in physiologic parameters (mean arterial pressure, end-tidal CO2, O2 saturation, pH, paO2, and paCO2).

Conclusions:

This study showed a modest reduction of embolic debris during the reaming and nail insertion segments of the operative procedure. We were unable to correlate this with any change in physiologic parameters.

Level of Evidence:

Therapeutic Level II. See Instructions for Authors for a complete description of levels of evidence.
The Trauma Collaborative Care Study (TCCS)
Authors: Wegener Stephen T. , Pollak Andrew N. , Frey Katherine P. , Hymes Robert A. , Archer Kristin R. , Jones Clifford B. , Seymour Rachel B. , O'Toole Robert V. , Castillo Renan C. , Huang Yanjie , Scharfstein Daniel O. , MacKenzie Ellen J. ,   METRC
Published: March 2017

Previous research suggests that the care provided to trauma patients could be improved by including early screening and management of emotional distress and psychological comorbidity. The Trauma Collaborative Care (TCC) program, which is based on the principles of well-established models of collaborative care, was designed to address this gap in trauma center care. This article describes the TCC program and the design of a multicenter study to evaluate its effectiveness for improving patient outcomes after major, high-energy orthopaedic trauma at level 1 trauma centers. The TCC program was evaluated by comparing outcomes of patients treated at 6 intervention sites (n = 481) with 6 trauma centers where care was delivered as usual (control sites, n = 419). Compared with standard treatment alone, it is hypothesized that access to the TCC program plus standard treatment will result in lower rates of poor patient-reported function, depression, and posttraumatic stress disorder.
Physeal and Subphyseal Distraction Osteogenesis in Atrophic-type Congenital Pseudarthrosis of the Tibia: Efficacy and Safety
Authors: Jang Woo Young , Choi Yoon Hyo , Park Moon Seok , Yoo Won Joon , Cho Tae-Joon , Choi In Ho
Published: March 2017

Purpose:

To examine the efficacy, safety, and clinical outcomes of distraction osteogenesis through the physis (PDO) or through subphyseal osteotomy (SPDO) in patients with atrophic-type congenital pseudarthrosis of tibia with proximal tibial dysplasia.

Methods:

To validate the efficacy and safety of PDO and SPDO, radiographic and clinical parameters were compared between 5 patients who underwent proximal tibial metaphyseal or metadiaphyseal lengthening as a control (group 1) and 7 patients who underwent PDO or SPDO (group 2). Postoperative complication was also compared between the groups.

Results:

A significant difference in terms of healing index (group 1, 83.3±24.7 d/cm; group 2, 35.0±11.1 d/cm; P=0.001) and percentage increase (11.0%±3.7% vs. 23.1%±10.5%, P=0.034) was observed between the 2 groups. According to the Paley classification, group 1 included 1 “problems” case and 3 “obstacles” cases, whereas group 2 included 2 “problems” cases and 1 “obstacles” case. According to the Lascombes classification, group 1 included 2 grade IIIb cases and 3 grade IV cases, whereas group 2 included 6 grade I cases and 1 grade IIa case. Severe complications were significantly higher in group 1 compared with the group 2 (P=0.007).

Conclusions:

This study demonstrated that PDO or SPDO can be effectively and safely performed for tibial lengthening in atrophic-type congenital pseudarthrosis of tibia patients with proximal tibial dysplasia.

Level of Evidence:

Level III.
TWENTY-FIVE–GAUGE PARS PLANA VITRECTOMY IN COMPLEX RETINAL DETACHMENTS ASSOCIATED WITH GIANT RETINAL TEAR
Authors: Kumar Vinod , Kumawat Devesh , Bhari Anju , Chandra Parijat
Published: March 2017

Purpose:

To study the structural and functional outcomes of 25-gauge pars plana vitrectomy in giant retinal tear–associated retinal detachments.

Methods:

Seventeen eyes of 17 patients with giant retinal tear, who underwent 25-gauge pars plana vitrectomy over a period of 15 months at a tertiary eye care center by a single surgeon, were recruited in this retrospective interventional study.

Results:

Giant retinal tears were mostly traumatic (35.3%) or associated with myopia (35.3%) and occurred in young (mean age 25.7 years) males (94.1%). Most eyes had best-corrected visual acuity ≤20/1,200 (in 82.3%), foveal detachment (in 88.2%), and proliferative vitreoretinopathy ≤Grade B (in 82.3%). The giant retinal tear extent was more than 180° in 29.4% and the fellow eye was involved in 35.2% of eyes. All eyes underwent 25-gauge pars plana vitrectomy with encircling band in 41.1%, perfluorocarbon liquid use in 82.3%, and endotamponade with sulphur hexafluoride (23.6%) or silicone oil (76.4%). At mean follow-up of 10.2 months, reattachment rate was 88.2%. Only 35.2% of eyes achieved final visual acuity ≥20/80 with a cause of poor vision being cataract, secondary glaucoma, macular pucker, and corneal edema.

Conclusion:

Twenty-five–gauge pars plana vitrectomy can achieve excellent attachment rates in eyes with giant retinal tear–associated retinal detachment. It can be as efficient as larger-gauge vitrectomy, at the same time retaining all advantages of smaller-gauge surgery.
Comparison of the Effects of Quetiapine XR and Lithium Monotherapy on Actigraphy-Measured Circadian Parameters in Patients With Bipolar II Depression
Authors: Hwang Jeong Yeon , Choi Jae-Won , Kang Seung-Gul , Hwang Su Hwan , Kim Seog Ju , Lee Yu Jin
Published: March 2017

Purpose/Background

The aim of this study was to evaluate the effects of quetiapine XR and lithium on actigraphy-measured circadian parameters in patients with bipolar II depression.

Methods/Procedures

This was an 8-week, open-label, prospective, randomized comparative study. The assessments included the 17-item Hamilton Depression Rating Scale score and actigraphic measures concerning the previous 7 days, collected at each visit (weeks 0 [baseline], 1, 2, 4, 6, and 8); the actigraphic data were analyzed with a cosinor analysis.

Findings/Results

Medication, time, and the interaction between medication and time were significantly associated with acrophase for the entire group (Ps = 0.003, 0.020, and 0.042, respectively). More specifically, acrophase was significantly delayed at weeks 1 and 6 (Ps = 0.004 and 0.039, respectively) in the quetiapine XR group. The F statistics significantly increased over time for the entire group (P < 0.001), and there was a significant increase in F statistics on weeks 4 and 6 in the quetiapine XR group (Ps = 0.016 and 0.020, respectively) and on weeks 4 and 8 in the lithium group (Ps = 0.001 and 0.016, respectively). In addition, scores on the 17-item Hamilton Depression Rating Scale were significantly associated with the F statistics during 8 weeks for the entire group (P = 0.008).

Implications/Conclusions

Both quetiapine XR and lithium affected several circadian parameters, including peak activity time and robustness of circadian rhythm, but exerted different effects on acrophase in patients with bipolar II depression. In particular, clinical depressive symptoms were associated with robustness of circadian rhythm during the course of the 8-week treatment.
The Normal Adult Human Internal Auditory Canal: A Volumetric Multidetector Computed Tomography Study
Authors: Essbaiheen Fahad , Hegazi Tarek , Rosenbloom Lorne
Published: March 2017

Objective:

The purpose of this study was to demonstrate that volumetric analysis of multidetector computed tomography (CT) images can be used to calculate the volume of the adult human internal auditory canal (IAC) reproducibly, and to describe the range of normal IAC volumes in the adult population with subgroup analysis of sex, age, and laterality.

Background:

Previous studies of the IAC have typically used measurements in two dimensions or by using casts of cadavers to measure IAC volumes. This study is the first to report the normal ranges of IAC volumes measured by CT.

Methods:

Two hundred eighty-one CT scans were assessed. Of the CT scans that met the inclusion criteria, a software package was used to manually contour the IACs in each subject to calculate the volumes in cubic millimeters. Subgroup analysis of laterality, sex, and age was evaluated. Interobserver agreement was calculated for the first 59 patients (118 canals).

Results:

Two hundred fifty-nine scans (518 canals) met the inclusion criteria. The volumes ranged from 74 to 502 mm3, with no statistically significant difference between left and right (p value = 0.69). In males, the range of volumes measured 74 to 502 mm3 while in females it ranged from 78 to 416 mm3. Males had larger IAC volumes than females (Wilcoxon rank-sum test: S = 14,845.0, p value = 0.01 on the right, and S = 14,646, p value = 0.004 on the left). No correlation was found with age (Spearman: −0.10, p value = 0.09 on the right and −0.04, p value = 0.50 on the left). Excellent interobserver agreement was found.

Conclusion:

IAC volumes of normal adult subjects, measured by CT, were larger in males and not significantly different with respect to age or laterality.
The Effect of Inflow Cannula Length on the Intraventricular Flow Field: An In Vitro Flow Visualization Study Using the Evaheart Left Ventricular Assist Device
Authors: May-Newman Karen , Moon Juyeun , Ramesh Varsha , Montes Ricardo , Campos Josue , Herold Brian , Isingoma Paul , Motomura Tadashi , Benkowski Robert
Published: March 2017

Left ventricular assist device (LVAD) inflow cannula malposition is a significant risk for pump thrombosis. Thrombus development is influenced by altered flow dynamics, such as stasis or high shear that promote coagulation. The goal of this study was to measure the intraventricular flow field surrounding the apical inflow cannula of the Evaheart centrifugal LVAD, and assess flow stasis, vortex structures, and pulsatility for a range of cannula insertion depths and support conditions. Experimental studies were performed using a mock loop with a customized silicone left ventricle (LV) and the Evaheart LVAD. A transparent inflow cannula was positioned at 1, 2, or 3 cm insertion depth into the LV and the velocity field in the LV midplane was measured for 2 levels of LVAD support: 1800 and 2300 rpm. The LV velocity field exhibits a diastolic vortex ring whose size, path, and strength are affected by the flow conditions and cannula position. During diastole, the large clockwise midplane vortex grows, but its circulation and kinetic energy are reduced with cannula insertion depth. The counterclockwise vortex is smaller and exhibits more complex behavior, reflecting a flow split at 3 cm. Overall, the 1 cm cannula insertion depth produces the flow pattern that exhibits the least apical flow stasis and greatest pulsatility and should correlate to a lower risk of thrombus formation.
Incidence of Low Seroimmunity to Hepatitis B Virus in Children With Inflammatory Bowel Disease
Authors: Watts Abhishek , Bennett William E. , Molleston Jean P. , Gupta Sandeep K. , Croffie Joseph M. , Waseem Shamaila , McFerron Brian A. , Steiner Steven J. , Kumar Sanjay , Vanderpool Charles P. , Hon Emily C. , Bozic Molly A. , Subbarao Girish C. , Pfefferkorn Marian D.
Published: March 2017

Objectives:

Patients with inflammatory bowel disease (IBD) often receive immunosuppressive therapy, which may make them vulnerable to infections such as hepatitis B. We hypothesized that hepatitis B virus titers are low in the vaccinated pediatric population with IBD. The aims of our study were to identify the incidence of lower titers of hepatitis B surface antibody (HBsAb) and determine which patient factors may be associated with lower HBsAb titers.

Methods:

Patients with diagnosis of IBD, ages 5 to 18 years, were prospectively enrolled. Patients were confirmed to have had a full series of hepatitis B vaccination. Quantitative serum HBsAb titers were measured and logistic regression analysis with independent variables of age, sex, race, disease phenotype, surgery, medications and a dependent variable of adequate HBsAb titers (> 10 mIU/mL) was performed.

Results:

Of the 116 patients enrolled, 57 were boys and 59 were girls. 75 patients had a diagnosis of Crohn disease; 32 had a diagnosis of ulcerative colitis; and 9 patients had been diagnosed as having indeterminate colitis. At the time of the study, 15 patients were taking corticosteroid, 66 on an immunomodulator, and 53 on a biologic. Sixty percent of patients in the 5‐ to 10‐year age group had protective titers versus 22% to 27% in the older groups, P = 0.04. Only 28% of the 116 patients had HBsAb titers of >10m IU/mL. Twenty percent of the patients taking corticosteroids, 27% taking immunomodulators, and 24% taking biologics were found to be seroimmune.

Conclusions:

Nearly two‐thirds of pediatric patients with IBD have low titers against hepatitis B virus. Titers were highest in the younger patients. No patient‐specific variable, such as the use of immunosuppressants, appeared to influence these low titers.
Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain
Authors: Dunne Karl A , Chaudhuri Roy R , Rossiter Amanda E , Beriotto Irene , Browning Douglas F , Squire Derrick , Cunningham Adam F , Cole Jeffrey A , Loman Nicholas , Henderson Ian R
Published: March 2017

In 1885, Theodor Escherich first described the Bacillus coli commune, which was subsequently renamed Escherichia coli. We report the complete genome sequence of this original strain (NCTC 86). The 5 144 392 bp circular chromosome encodes the genes for 4805 proteins, which include antigens, virulence factors, antimicrobial-resistance factors and secretion systems, of a commensal organism from the pre-antibiotic era. It is located in the E. coli A subgroup and is closely related to E. coli K-12 MG1655. E. coli strain NCTC 86 and the non-pathogenic K-12, C, B and HS strains share a common backbone that is largely co-linear. The exception is a large 2 803 932 bp inversion that spans the replication terminus from gmhB to clpB. Comparison with E. coli K-12 reveals 41 regions of difference (577 351 bp) distributed across the chromosome. For example, and contrary to current dogma, E. coli NCTC 86 includes a nine gene sil locus that encodes a silver-resistance efflux pump acquired before the current widespread use of silver nanoparticles as an antibacterial agent, possibly resulting from the widespread use of silver utensils and currency in Germany in the 1800s. In summary, phylogenetic comparisons with other E. coli strains confirmed that the original strain isolated by Escherich is most closely related to the non-pathogenic commensal strains. It is more distant from the root than the pathogenic organisms E. coli 042 and O157 : H7; therefore, it is not an ancestral state for the species.
The physical boundaries of public goods cooperation between surface-attached bacterial cells
Authors: Weigert Michael , Kümmerli Rolf
Published: March 2017

Bacteria secrete a variety of compounds important for nutrient scavenging, competition mediation and infection establishment. While there is a general consensus that secreted compounds can be shared and therefore have social consequences for the bacterial collective, we know little about the physical limits of such bacterial social interactions. Here, we address this issue by studying the sharing of iron-scavenging siderophores between surface-attached microcolonies of the bacterium Pseudomonas aeruginosa. Using single-cell fluorescent microscopy, we show that siderophores, secreted by producers, quickly reach non-producers within a range of 100 μm, and significantly boost their fitness. Producers in turn respond to variation in sharing efficiency by adjusting their pyoverdine investment levels. These social effects wane with larger cell-to-cell distances and on hard surfaces. Thus, our findings reveal the boundaries of compound sharing, and show that sharing is particularly relevant between nearby yet physically separated bacteria on soft surfaces, matching realistic natural conditions such as those encountered in soft tissue infections.
Multi-tissue DNA methylation age predictor in mouse
Authors: Stubbs Thomas M. , Bonder Marc Jan , Stark Anne-Katrien , Krueger Felix ,   Clock Team BI Ageing, von Meyenn Ferdinand , Stegle Oliver , Reik Wolf
Published: March 2017

Background

DNA-methylation changes at a discrete set of sites in the human genome are predictive of chronological and biological age. However, it is not known whether these changes are causative or a consequence of an underlying ageing process. It has also not been shown whether this ‘epigenetic clock’ is unique to humans or conserved in the more experimentally tractable mouse.

Results

We have generated a comprehensive set of genome-scale base-resolution methylation maps from multiple mouse tissues spanning a wide range of ages. Many CpG sites show significant tissue-independent correlations with age and allowed us to develop a multi-tissue predictor of age in the mouse. Our model, which estimates age based on DNA methylation at 329 unique CpG sites, has a median absolute error of 3.33 weeks, and has similar properties to the recently described human epigenetic clock. Using publicly available datasets, we find that the mouse clock is accurate enough to measure effects on biological age, including in the context of interventions. While females and males show no significant differences in predicted DNA methylation age, ovariectomy results in significant age acceleration in females. Furthermore, we identify significant differences in age-acceleration dependent on the lipid content of the offspring diet.

Conclusions

Here we identify and characterize an epigenetic predictor of age in mice, the mouse epigenetic clock. This clock will be instrumental for understanding the biology of ageing and will allow modulation of its ticking rate and resetting the clock in vivo to study the impact on biological age.
Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations
Authors: Nguyen Quan H. , Lukowski Samuel W. , Chiu Han Sheng , Senabouth Anne , Bruxner Timothy J. C. , Christ Angelika N. , Palpant Nathan J. , Powell Joseph E.
Published: March 2017

Heterogeneity of cell states represented in pluripotent cultures have not been described at the transcriptional level. Since gene expression is highly heterogeneous between cells, single-cell RNA sequencing can be used to identify how individual pluripotent cells function. Here, we present results from the analysis of single-cell RNA sequencing data from 18,787 individual WTC CRISPRi human induced pluripotent stem cells. We developed an unsupervised clustering method, and through this identified four subpopulations distinguishable on the basis of their pluripotent state including: a core pluripotent population (48.3%), proliferative (47.8%), early-primed for differentiation (2.8%) and late-primed for differentiation (1.1%). For each subpopulation we were able to identify the genes and pathways that define differences in pluripotent cell states. Our method identified four transcriptionally distinct predictor gene sets comprised of 165 unique genes that denote the specific pluripotency states; and using these sets, we developed a multigenic machine learning prediction method to accurately classify single cells into each of the subpopulations. Compared against a set of established pluripotency markers, our method increases prediction accuracy by 10%, specificity by 20%, and explains a substantially larger proportion of deviance (up to 3-fold) from the prediction model. Finally, we developed an innovative method to predict cells transitioning between subpopulations, and support our conclusions with results from two orthogonal pseudotime trajectory methods.
Phandango: an interactive viewer for bacterial population genomics
Authors: Hadfield James , Croucher Nicholas J. , Goater Richard J , Abudahab Khalil , Aanensen David M , Harris Simon R.
Published: March 2017

Fully exploiting the wealth of data in current bacterial population genomics datasets requires synthesising and integrating different types of analysis across millions of base pairs in hundreds or thousands of isolates. Current approaches often use static representations of phylogenetic, epidemiological, statistical and evolutionary analysis results that are difficult to relate to one another. Phandango is an interactive application running in a web browser allowing fast exploration of large-scale population genomics datasets combining the output from multiple genomic analysis methods in an intuitive and interactive manner.

Availability

Phandango is a web application freely available for use athttps://jameshadfield.github.io/phandangoand includes a diverse collection of datasets as examples. Source code together with a detailed wiki page is available on GitHub athttps://github.com/jameshadfield/phandango

Contact

jh22@sanger.ac.uk,sh16@sanger.ac.uk
Continuum approximations for lattice-free multi-species models of collective cell migration
Authors: Matsiaka Oleksii M , Penington Catherine J , Baker Ruth E , Simpson Matthew J
Published: March 2017

Abstract

Cell migration within tissues involves the interaction of many cells from distinct subpopulations. In this work, we present a discrete model of collective cell migration where the motion of individual cells is driven by random forces, short range repulsion forces to mimic crowding, and longer range attraction forces to mimic adhesion. This discrete model can be used to simulate a population of cells that is composed ofK≥ 1 distinct subpopulations. To analyse the discrete model we formulate a hierarchy of moment equations that describe the spatial evolution of the density of agents, pairs of agents, triplets of agents, and so forth. To solve the hierarchy of moment equations we introduce two forms of closure: (i) the mean field approximation, which effectively assumes that the distributions of individual agents are independent; and (ii) a moment dynamics description that is based on the Kirkwood superposition approximation. The moment dynamics description provides an approximate way of incorporating spatial patterns, such as agent clustering, into the continuum description. Comparing the performance of the two continuum descriptions confirms that both perform well when adhesive forces are sufficiently weak. In contrast, the moment dynamics description outperforms the mean field model when adhesive forces are sufficiently large. This is a first attempt to provide an accurate continuum description of a lattice-free, multi-species model of collective cell migration.
Building operation and maintenance: manpower in Hong Kong
Authors: Lai Joseph H.K.
Published: March 2017

Purpose

The study aims to reveal the state of building operation and maintenance (O&M) manpower in Hong Kong. In addition, the study included supply and demand of O&M practitioners, gaps between their required and possessed competences and ways to meet the manpower needs.

Design/methodology/approach

After developing a model that integrates manpower levels (L), trades (T) and natures (N) of O&M works (named as “LTN” model), a full spectrum of O&M jobs were established followed by collecting data of 75 organizations and 402 stakeholders through two surveys.

Findings

Besides the large O&M workforce, vacancy rates of the jobs were found to be significant. For the different trades and natures of O&M works, the knowledge/skills levels perceived by the stakeholders were lower than the corresponding importance levels.

Research limitations/implications

The methodology of the study can be used in future research for revealing the state of O&M manpower in Hong Kong and cities alike. The way in which the “LTN” model was developed may be used as a reference for constructing similar models for manpower research in other industries.

Practical implications

The findings and the measures for improving the O&M manpower can assist policymakers and human resources departments to formulate necessary education and training courses for the building industry.

Originality/value

The study is the first of its kind focusing on building O&M manpower. The state of the manpower it unveiled forms a basis for comparison with similar findings in future.
Modelling the relationship between green built environment and occupants’ productivity
Authors: Mallawaarachchi Harshini , De Silva Lalith , Rameezdeen Raufdeen
Published: March 2017

Purpose

The purpose of the study presented in this paper is to determine the relationship and effect of built environment on occupants’ productivity in green-certified office buildings in Sri Lanka.

Design/methodology/approach

Two research hypotheses were tested by approaching the survey method under the quantitative phenomenon. The questionnaire survey was conducted among randomly selected occupants in three selected green-rated office buildings in Sri Lanka. The survey data were analysed by using the Spearman correlation and ordinal logistic regression analysis techniques to model the relationship existing between the variables. The SPSS v20 software was used in data analysis.

Findings

The findings confirm the relationship between built environment and occupants’ productivity. As it further proves that, there is a significant effect of built environment on occupants’ productivity in green-certified office buildings. Thus, critical built environment factors influencing occupants’ productivity and their effect were determined.

Practical implications

The findings could be practically implied as bases to strengthen the evaluation criteria of indoor environmental quality in GREENSL® national green-rating system.

Originality/value

The evaluation of occupants’ productivity and the built environment factors has been at the focal point of research; however, most studies have focused on single aspects of the built environment. Further, no evidences were found on “which factors” can critically influence the occupants’ productivity in green buildings. The paper, therefore, seeks to fill this gap by proving the relationship between green built environment and occupants’ productivity.
Taxpayers’ perceptions on tax evasion behaviour: an empirical study in Malaysia
Authors: Pui Yee Chan , Moorthy Krishna , Choo Keng Soon William
Published: March 2017

Purpose

The success of self-assessment tax system is voluntary compliance with the tax laws. When tax evasion is seen as unacceptable, taxpayers will tend to evade tax less. Hence, the understanding of taxpayers’ attitude on tax morality towards a tax system has to be enhanced to minimize tax evasion cases. The purposes of this study are to examine the relationship between tax fairness, tax knowledge, enforcement level and social exchange towards taxpayers’ attitude of tax morality under the self-assessment system in Malaysia and also to identify the relationship between taxpayers’ attitude of tax morality and taxpayers’ perceptions on tax evasion.

Design/methodology/approach

Data were collected from 400 taxpayers through a questionnaire and analysed.

Findings

From the analysis, it has been found out that tax knowledge is the most important tax system characteristic that affects taxpayers’ attitude of tax morality. In addition, taxpayers’ attitude of tax morality is significant to taxpayers’ perceptions on tax evasion in Malaysia.

Originality/value

The findings of this study would be useful for the government to further improve the present tax system to increase voluntary tax compliance.
Consumer decision making when purchasing eco-friendly apparel
Authors: Rothenberg Lori , Matthews Delisia
Published: March 2017

Purpose

The purpose of this paper is to identify the realistic trade-offs young consumers make when purchasing organic T-shirts.

Design/methodology/approach

A full profile discrete choice design was used. The data were analysed using a multinomial logit model and desirability indices.

Findings

Price was the most important attribute to consumers followed by the place of production and then sustainability. Consumers were most willing to purchase T-shirts that are eco-friendly, Made In America, made from wrinkle-free technology and cotton jersey knit fabric, and have a price of $15. Although consumers were most willing to pay $15, some were still willing to pay $25 or even $35 for the same eco-friendly T-shirt.

Practical implications

Consumers in the current study were more willing to purchase eco-friendly as opposed to organic apparel. The findings suggest that retailers need to consider the language used when communicating with consumers. Also, consumers were more willing to purchase T-shirts Made In America. Retailers may want to promote their domestic manufacturing through in-depth branding and promotions.

Originality/value

In order to identify the attributes to be used in the current study, labels on T-shirts in stores were examined and then those attributes were verified in the literature. In addition, the inclusion of price as an attribute, rather than as a separate independent question, provides a more realistic view of young consumers’ decision making.
Stability evaluation of three-layered journal bearing with slip/partial slip
Authors: Rao T.V.V.L.N. , Rani A.M.A. , Awang M. , Hashim F.M.
Published: March 2017

Purpose

This paper aims to present stability of a three-layered journal bearing considering magnitude of the layers’ thicknesses and viscosities with slip/partial slip on the bearing surface.

Design/methodology/approach

Modified Reynolds equation based on one-dimensional analysis is derived for a three-layered journal bearing with slip/partial slip. Dynamic coefficients are derived based on infinitesimal perturbation method. Linearized stability analysis is presented taking into account slip/partial slip on bearing surface; thicknesses and viscosities of bearing surface layer; and core layer and journal surface layer.

Findings

Results of threshold speed and critical whirl frequency ratio coefficients (Cω, CΩ), stiffness (Kij for i = x,y) and damping (Bij for i = x, y) coefficients and threshold speed (ωs) and critical whirl frequency ratio (Ωs) are presented. The bearing surface is analyzed for slip (total surface with slip) and partial slip (partial surface with slip). The slip-on bearing surface reduces stability, while partial slip improves bearing stability. The threshold speed coefficient (Cω) decreases with slip on bearing surface. The threshold speed (ωs) and critical whirl frequency ratio (Ωs) are influenced by the variation of threshold speed coefficient (Cω) and critical whirl frequency ratio coefficient (CΩ), respectively. A three-layered journal bearing with partial slip and thick high viscosity bearing surface layer results in higher threshold speed coefficient and has a potential to improve stability of journal bearing. The analyses indicate that optimal angular extent of partial slip region (θs) enhances the stability of journal bearing.

Originality/value

The paper presents parametric study of stability coefficients (Cω and CΩ) and evaluation of threshold speed (ωs) and critical whirl frequency ratio (Ωs) of a three-layered journal bearing with slip/partial slip.
XPS characterization of tribo-layer formation on the steel lubricated with crude and epoxidized jatropha oil under boundary lubrication
Authors: Lubis Abdul Munir Hidayat Syah , Ariwahjoedi Bambang , Sudin Mustafar
Published: March 2017

Purpose

This study aims to characterize the composition of the tribo-layer formed during sliding of steel in the presence of crude jatropha oil (CJO) and epoxidized jatropha oil (EJO) under boundary lubricant application.

Design/methodology/approach

CJO was obtained from a local market and used as received. EJO was obtained by epoxidation process with peroxyformic acid catalyzed by acidic ion exchange resin. The tribological test was conducted by the four ball method according to ASTM 4192. Wear scars generated on the lower balls were used to characterize the tribo-layer. Energy-dispersive X-ray and X-ray photo spectroscopy analysis were conducted to characterize the tribo-layer composition.

Findings

EJO shows a lower friction coefficient compared to CJO. Moreover, EJO also shows better wear preventive properties compared to CJO. The oxidation of CJO and EJO has lead chemisorption of the oil to steel surface to cause formation of protective layers for the steel surface. The layers were constructed from inorganic oxide in the form of iron oxides and silicon oxide together with organic layers in form of aldehyde, ketone and carboxylic acid. The formation and removal of this layer from rubbing sites are considered to affect wear-preventive and friction behaviour of steel lubricated with CJO and EJO.

Originality/value

This works highlights friction and anti-wear characteristics of CJO and EJO. This work also presents the composition of the tribo-layer that formed because of the sliding of steel lubricated with CJO and EJO. The method and result can be used for further investigation and development of lubricant.
Maintenance backlog for improving integrated planning
Authors: Rødseth Harald , Schjølberg Per
Published: March 2017

Purpose

The purpose of this paper is to develop a novel model for maintenance backlog (MB) of physical assets and structure it in a framework for integrated planning (IPL).

Design/methodology/approach

Reliability theory principles for modelling MB are used. Furthermore, to structure a framework for IPL, literature study combined with earlier case studies is used.

Findings

The framework for IPL facilitates the model of MB. In addition to providing real-time diagnosis indicators, MB is regarded as valuable information for decision support in IPL.

Originality/value

Development of MB applied to IPL.
Understand what your maintenance service partners value
Authors: Ali-Marttila Maaren , Marttonen-Arola Salla , Kärri Timo , Pekkarinen Olli , Saunila Minna
Published: March 2017

Purpose

The purpose of this paper is to identify what is currently valued in maintenance services. The study first conceptualizes the value construct through an examination of its elements, including both financial and non-financial elements, and second provides insight into its actors’ (i.e. customer companies, service providers, equipment providers) attitudes toward value creation.

Design/methodology/approach

The study uses data collected from maintenance service professionals by an online survey. First an explorative factor analysis is conducted to examine the value construct. After this cluster analysis is conducted to define the actors.

Findings

The empirical findings suggest seven main elements that capture maintenance service value: relationship synergies, reliability of the service partner, development, availability, service solutions and problem solving ability, environment, health, safety and quality, and adaptability to suit different situations. Further analysis reveals that the actors can be divided into three main strategy types: basic, quality- and collaboration-oriented partners.

Originality/value

In previous studies the comprehensive nature of maintenance service value has received less attention, and the literature has focused on the technical and financial aspects. This paper provides a new conceptualization of the value creating elements, including also non-financial elements, and offers an integrated measure for the actors to identify the comprehensive value construct around maintenance services. In addition, the findings show that the actors in the field still have varying strategies when considering value creation. Communication and mutual understanding of the value creating elements are important so that right services are carried out and developed with the right partners.