bluuebunny/crossref_metadata_2025 huggingface dataset:
Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA
Authors: del Carmen Gomez Cabrera Maria , Young Jennifer M. , Roff George , Staples Timothy , Ortiz Juan Carlos , Pandolfi John M. , Cooper Alan
Published: February 2019

Marine environments face acute pressures from human impacts, often resulting in substantial changes in community structure. On the inshore Great Barrier Reef (GBR), palaeoecological studies show the collapse of the previously dominant coral Acropora from the impacts of degraded water quality associated with European colonization. Even more dramatic impacts can result in the replacement of corals by fleshy macroalgae on modern reefs, but their past distribution is unknown because they leave no fossil record. Here, we apply DNA metabarcoding and high‐throughput sequencing of the 18S rDNA gene on palaeoenvironmental DNA (aeDNA) derived from sediment cores at two sites on Pandora Reef (GBR), to enhance palaeoecological studies by incorporating key soft‐bodied taxa, including macroalgae. We compared temporal trends in this aeDNA record with those of coral genera derived from macrofossils. Multivariate analysis of 12 eukaryotic groups from the aeDNA community showed wide variability over the past 750 years. The occurrence of brown macroalgae was negatively correlated only with the dominant coral at both sites. The occurrence of coralline and green macroalgae was positively correlated with only the dominant coral at one of the sites, where we also observed a significant association between the whole coral community and the occurrence of each of the three macroalgae groups. Our results demonstrate that reef sediments can provide a valuable archive for understanding the past distribution and occurrence of important soft‐bodied reef dwellers. Combining information from fossils and aeDNA provides an enhanced understanding of temporal changes of reefs ecosystems at decadal to millennial timescales.
Oral Interaction in the EFL Classroom: The Effects of Instructional Focus and Task Type on Learner Affect
Authors: VAN BATENBURG ELINE S. L. , OOSTDAM RON J. , VAN GELDEREN AMOS J. S. , FUKKINK RUBEN G. , DE JONG NIVJA H.
Published: February 2019

Little is known about the effects of different instructional approaches on learner affect in oral interaction in the foreign language classroom. In a randomized experiment with Dutch pre‐vocational learners (N = 147), we evaluated the effects of 3 newly developed instructional programs for English as a foreign language (EFL). These programs differed in instructional focus (form‐focused vs. interaction strategies‐oriented) and type of task (pre‐scripted language tasks vs. information gap tasks). Multilevel analyses revealed that learners’ enjoyment of EFL oral interaction was not affected by instruction, that willingness to communicate (WTC) decreased over time, and that self‐confidence was positively affected by combining information gap tasks with interactional strategies instruction. In addition, regression analyses revealed that development in learners’ WTC and enjoyment did not have predictive value for achievement in EFL oral interaction, but that development in self‐confidence did explain achievement in EFL oral interaction in trained interactional contexts.
Material Moments: Teacher and Student Use of Materials in Multilingual Writing Classroom Interactions
Authors: MATSUMOTO YUMI
Published: February 2019

This qualitative study examines moments in the multilingual classroom when materials become prominent in whole‐class interactions. Despite the critical impact that materials can have on classroom discourse and learning/teaching, research onactual usageof materials in second language (L2) classroom interactions has been scarce compared with the effort devoted to the development and assessment of L2 materials (Guerrettaz & Johnston, 2013). This study examines students’ and instructors’ use of materials in a multilingual writing classroom, focusing on the roles of textbooks, teacher‐prepared worksheets, and a projection screen. The study illustrates the relationship between materials and miscommunication—specifically, how materials can contribute both to resolving miscommunication among students and their instructor and to creating miscommunication when students employ materials differently than intended by the instructor. This study employs the concepts ofadaptation, improvisation, andattractor statesfrom complexity theory (e.g., Larsen–Freeman, 2017) to analyze L2 classroom interactions. A sequential, multimodal analysis demonstrates that students and their instructor seem to be aware of materials as interactional resources and actively coordinate them with speech and nonverbal, embodied resources for meaning making. The findings improve our understanding of how L2 teachers and students can attend to materials and adapt such interactional resources for their own purposes.
Separation and identification of Brassica rapa BrAFP and its gene cloning and expression under freezing stress
Authors: Liu Zigang , Dong Xiaoyun , Ma Li , Sun Wancang , Yang Gang , Fang Yan , Wu Junyan , Li Xuecai
Published: February 2019

Antifreeze proteins (AFPs) are proteins that inhibit ice nucleation by non‐colligative combined with ice, to inhibit its growth and to modify ice crystal morphology. In this study, 'Longyou 6' (Brassica rapa) with the cold resistance was used as a model. A 38 kDa band of protein extracted from leaves of plants exposed to low temperature was enhanced on the electropherogram. The 38 kDa protein can significantly inhibit growth of ice crystals and modify its morphology, thus suggesting this protein has an AFP in winter turnip rape. The protein was identified as beta‐1,3‐glucanase by mass spectrometry, named BrAFP1. Its corresponding gene contains 1,032 bp bases, coding 343 amino acids with a molecular weight of 38,102 kDa. The BrAFP1 is a predicted hydrophobic protein with a signal peptide. Under cold stress, the plants showed morphological characteristics of cold resistance, and BrAFP expression was significantly up‐regulated at −4°C from 0.5 to 4 days compared with the control (at room temperature), suggesting that the BrAFP gene played an important role in cold acclimation in B. rapa.
Density enhancement of a faba bean genetic linkage map (Vicia faba) based on simple sequence repeats markers
Authors: Yang Tao , Jiang Junye , Zhang Hongyan , Liu Rong , Strelkov Stephen , Hwang Sheau‐Fang , Chang Kan‐Fa , Yang Feng , Miao Yamei , He Yuhua , Zong Xuxiao
Published: February 2019

Genetic mapping for faba bean lags far behind other major crops. Density enhancement of the faba bean genetic linkage map was carried out by screening 5,325 genomic SSR primers and 2033 expressed sequence tag (EST)‐SSR primers on the parental cultivars '91825' and 'K1563'. Two hundred and fifteen genomic SSR and 133 EST‐SSR primer pairs that detected polymorphisms in the parents were used to screen 129 F2 individuals. This study added 337 more SSR markers and extended the previous linkage map by 2928.45 cM to a total of 4516.75 cM. The number of SSR markers in the linkage groups varied from 12 to 136 while the length of each linkage group ranged from 129.35 to 1180.21 cM. The average distance between adjacent loci in the enhanced genetic linkage map was 9.71 cM, which is 2.79 cM shorter than the first linkage map of faba bean. The density‐enhanced genetic map of faba bean will be useful for marker‐assisted selection and breeding in this important legume crop.
Effectiveness of an educational program for mid‐level Japanese public health nurses to improve program planning competencies: A preliminary randomized control trial
Authors: Yoshioka‐Maeda Kyoko , Shiomi Misa , Katayama Takafumi , Hosoya Noriko , Kuroda Mariko
Published: February 2019

Objective

To evaluate the effectiveness of an education program for mid‐level Japanese public health nurses (PHNs) to improve their competencies in program planning, which will fulfill community health needs.

Design

Randomized control trial.

Sample

During 2017, 103 PHNs with 5–20 years of PHN work experience in Japan were enrolled and randomly allocated to the intervention (n = 51) or control group (n = 52).

Measurements

The primary outcome measured competency in program planning based on Competency Measurement of Creativity for PHNs (CMC), knowledge, and skills regarding program planning.

Intervention

Six web‐based learning modules followed by two face‐to‐face group sessions.

Results

The PHN participants averaged about 12 years of experience. In the intervention group, 25 PHNs completed all modules (49.0%). Post intervention, there were no statistically significant differences among any between‐group CMC scores. However, the intervention group's CMC 3 score was significantly higher than that of the control group of ≥12 years of experience. Total knowledge and skill scores also improved significantly in the intervention group compared with the control group.

Conclusions

The results suggest that PHNs with ≥12 years of experience are a suitable target of this educational program, and should play a key role in program planning.
Sexually transmitted disease services and third‐party payer reimbursement: Attitudes, knowledge, and current practices among 60 health departments/districts. Why does this matter to public health nurses?
Authors: Kovar Cheryl L. , Bynum Susan
Published: February 2019

Objective

To assess staff attitudes, knowledge, and current practices in billing third‐party payers for sexually transmitted disease (STD) services in public health departments/districts.

Design and Sample

A cross‐sectional, online survey was administered to staff at 60 urban and rural health departments/districts. Snowball sampling was used for greater representation. There were 311 staff responses from 56 agencies represented in the data analysis. Of the 311 responses, 106 were public health nurses and seven of the health directors had nursing backgrounds.

Measurement

The survey measured attitudes, knowledge, and current billing practices for STD services. Analysis of data was performed at both individual and agency level.

Results

Almost 90% reported it was acceptable to bill insurance. However, 56% felt these services should remain a “free” service in the agency. Most agencies were billing Medicaid for STD services (95%) and 70% bill private third‐party payers.

Conclusions

Current funding for public STD clinics is not sustainable and other viable income streams such as third‐party payer reimbursement must be utilized. Public health nurses play a pivotal role in developing policies and procedures in billing third‐party payers for STD and other clinical services. Understanding the interactions between attitudes, knowledge and practice are vital in this development.
Assessment of functional status and daily life problems faced by elderly in a North Indian city
Authors: Kaur Sukhpal , Bhalla Ashish , Kumari Savita , Singh Amarjeet
Published: February 2019

Background

The increase in proportion of elderly implies that their problems demand more attention of the administrators. The current study was carried out to assess the functional status of the elderly and to explore the extent and pattern of routine daily life problems faced by them.

Methods

An integrated qualitative and quantitative research design was employed. A stratified multistage random sampling technique was used to select the respondents from various areas of Chandigarh. The houses were selected randomly from where elderly persons (> 60 years) were identified. Katz Index of Independence in activities of daily living (ADL) was used to evaluate functional ability of the respondents. Instrumental ADLs (IADLs) were assessed using Lawton and Brody scale. Focus group discussions and in‐depth interviews were conducted among the elderly to explore their problems using an interview guide.

Results

One thousand and eighty elderly were enrolled in the study. Their mean age was 67.22 ± 7.54 years. (range 60–102 years). The majority (70%) were independent in carrying out their daily life activities. Financially, around one‐third were completely dependent and around half were partially dependent. Major dependence was in food preparation, housekeeping and laundry. From the qualitative data, four main themes were formulated, that is general personal problems of elderly; family problems; problems faced by elderly in hospitals and at public places. A feeling of purposelessness, financial insecurity, physical dependency, problems in hospitals and so on, emerged as the main problems.

Conclusions

Majority of the elderly considered their lives as problematic because they were dependent physically as well as financially. The main domains of dependency were problems related to bowel continence, food preparation, housekeeping and laundry.
Differences in coping strategies among young adults and the elderly with cancer
Authors: Hernández Raquel , Calderon Caterina , Carmona‐Bayonas Alberto , Rodríguez Capote Alejandra , Jara Carlos , Padilla Álvarez Airam , Gómez‐Camacho María de las Nieves , Beato Carmen , Castelo Beatriz , Majem Margarita , Muñoz María del Mar , Ivars Alejandra , Mangas‐Izquierdo Montserrat , Rogado‐Revuelta Jacobo , Jimenez‐Fonseca Paula
Published: February 2019

Background

Coping with cancer and the oncologist–patient relationship can vary depending on the patient's age. Our aim is to examine and compare young and elderly adults with non‐metastatic, resected cancer.

Methods

Two groups of patients were selected, young (< 40 years) and elderly (> 70) with a diagnosis of non‐metastatic, resected cancer requiring adjuvant chemotherapy from a pre‐exiting, national database (NEOCOPING Study). Epidemiological variables were collected and subjects’ emotional responses, perceptions of the physician–patient relationship, support network, fears, and regret about the decision to receive chemotherapy were assessed with questionnaires validated in previous studies: Mini‐Mental Adjustment to Cancer, Brief Summary Inventory (18 items), European Organization for the Research and Treatment of Cancer Quality of Life Questionnaire‐C30, Shared Decision‐Making Questionnaire‐Physician's version, Shared Decision‐Making Questionnaire‐Patient's version, and Informed Risk (physician and patient versions).

Results

Data from 46 young and 46 elderly participants were collected. The most common neoplasms in both groups were breast (50%) and colorectal (22%). The younger adults had a higher level of education and were actively employed (72% vs. 7%). The leading coping strategy in the younger cohort was hope, and resignation among the elderly. Young adults sought more social support and the impact of diagnosis was more negative for them than for older individuals. No significant differences were detected in quality of life; both age groups demanded more time at their first visit with the doctor, while the older group exhibited greater satisfaction with shared decision‐making. At the end of adjuvant chemotherapy, neither age group regretted their decision to receive said treatment.

Conclusion

Higher levels of education, greater demands of the labour market, and the advent of the age of information have entailed drastic changes in the physician–patient relationship paradigm. This is especially true in the younger cancer patient population, who require more information and active participation in decision‐making, can display more anxiety about their diagnosis, but also greater capacity to fight.
Cross‐sectional and longitudinal association of sports participation, media consumption and motor competence in youth
Authors: Drenowatz Clemens , Greier Klaus
Published: February 2019

The beneficial associations of physical activity (PA) and sports with motor competence have been well documented. Similarly, high media time has been associated with poor motor competence. Limited information, however, is available on the combined effects of sport participation and media consumption on motor competence. The present study followed 213 Austrian middle‐school students (57% male; age at baseline: 10.4 ± 0.6 years) over a 4‐year period. Annual assessments included the German Motor Test 6‐18, along with self‐reported participation in club sports, time spent watching TV and using the computer. There were no interaction effects between sports participation and media time on motor competence. Club sports participation, however, was associated with higher motor competence, while there was an inverse association between media time and motor competence. Further, motor competence affected future participation in club sports while club sports had limited effects on subsequent motor development. High media time, on the other hand, impaired subsequent motor development, while effects of motor competence on media time were limited. Taken together, these results emphasize the importance of motor competence in the facilitation of sports participation during adolescence. Accordingly, a wide variety of movement experiences should be provided at young ages to promote motor development. In addition, the detrimental effects of media time on motor competence warrant that sedentary behaviors are targeted separately, particularly in youth not participating in sports.
Correlates of Food–Energy–Water Nexus Awareness Among the American Public*
Authors: Hannibal Bryce , Portney Kent
Published: February 2019

Objective

Recently, much research in the physical sciences has been dedicated to identifying a nexus or connection between water, energy, and food. This research agenda, however, has not been sufficiently examined in the social sciences. This article examines the extent to which individuals demonstrate awareness of the three nexus elements: water–energy, energy–food, and food–water.

Methods

We use three awareness indexes as dependent variables and varying sociodemographic characteristics and aspects of environmental concern as predictors in the statistical analysis.

Results

Our results suggest that there are some patterned or systematic correlates with the nexus elements, although relationships do not always turn out as anticipated. Indeed, explanations of nexus awareness do not follow previously studies’ explanations of environmental concern, and vary depending on which elements of the nexus are analyzed.

Conclusion

We conclude with suggestions to raise awareness of the connections between natural resources among all populations. Such awareness will promote sustainable societies and reduce environmental inequality and issues of environmental justice
How Governance and Disasters Shape Renewable Energy Transitions: The Case of Japanese Mega‐Solar*
Authors: Fraser Timothy
Published: February 2019

Objectives

This mixed‐methods study examines whether governance and disasters affect towns that host more renewable power plants, focusing on solar facilities in Japan after the 3/11 disaster.

Methods

I tested the effects of various factors on multiple sizes of feed‐in tariff certified solar power plants with negative binomial models. I confirmed those effects through process tracing using 14 interviews with local stakeholders from two prefectural case studies.

Results

Most prefectures boost solar power plant siting, especially for small plants 10–499 kilowatts (kW) in size. However, towns more damaged by disaster host less 10–499 kW plants because disasters create land‐use problems for solar.

Conclusion

When prefectures share information about renewable resources with local residents, they can compete more evenly with extraprefectural companies. However, disaster areas face extra governance challenges when introducing solar. Good subnational governance is vital to creating a more equitable, locally engaged renewable energy transition.
An in vitro pilot study of apheresis platelets collected on Trima Accel system and stored in T‐PAS+ solution at refrigeration temperature (1‐6°C)
Authors: Reddoch‐Cardenas Kristin M. , Sharma Umang , Salgado Christi L. , Montgomery Robbie K. , Cantu Carolina , Cingoz Neslihan , Bryant Ron , Darlington Daniel N. , Pidcoke Heather F. , Kamucheka Robin M. , Cap Andrew P.
Published: February 2019

BACKGROUND

Using platelet additive solution (PAS) to dilute fibrinogen during long‐term cold storage of platelets (PLTs) decreases PLT activation and increases functional PLT shelf life. We performed a randomized, paired study to assess the in vitro quality of PLTs stored in the cold in T‐PAS+ for up to 18 days evaluated against PLTs stored under currently allowable conditions (5‐day room temperature–stored PLTs [RTP] and 3‐day cold‐stored PLTs [CSP]).

STUDY DESIGN AND METHODS

PLTs were collected from healthy volunteers (n = 10) and diluted to 65% T‐PAS+/35% plasma before cold storage. Double‐dose apheresis PLTs (in 100% plasma) were collected from the same donors and split into two bags (one bag RTP, one bag CSP). All bags were sampled on the day of collection (Day 0). CSP and RTP bags were sampled on Days 3 and 5, respectively. T‐PAS+ samples were assessed on Days 3, 5, 14, 16, and 18 of storage for metabolism, hemostatic function, and activation.

RESULTS

After 18 days of storage in T‐PAS+, pH was 6.71 ± 0.04, PLT count was comparable to Day 3 CSP, PLT function (aggregation and clot strength) was comparable to Day 5 RTP, and PLT activation was significantly increased.

CONCLUSION

Refrigerated PLTs stored in T‐PAS+ for 18 days met FDA pH standards. Functional metrics suggest activity of T‐PAS+‐stored PLTs and the potential to contribute to hemostasis throughout 18 days of storage. Extending the shelf life of PLTs would increase access to hemostatic resuscitation for bleeding patients in military and civilian settings.
Long‐term outcome of phacoemulsification in raptors—A retrospective study (1999‐2014)
Authors: Sigmund Alex B. , Jones Michael P. , Ward Daniel A. , Hendrix Diane V.H.
Published: February 2019

Objective

To determine long‐term outcome of phacoemulsification in raptors at the University of Tennessee Veterinary Medical Center.

Animals Studied

Seven nonreleasable diurnal raptors including, four bald eagles (Haliaeetus leucocephalus), two red‐tailed hawks (Buteo jamaicensis), and one peregrine falcon (Falco peregrinus) that had undergone phacoemulsification. All birds showed behavioral changes attributable to visual deficits prior to surgery.

Procedures

All birds underwent phacoemulsification for cataracts. Four underwent bilateral phacoemulsification, and three had unilateral surgery. Due to a low sample size, statistics were not done.

Results

Six raptors (nine eyes) had long‐term follow‐up (median 75 months, range 28 to 105 months). Seven of these eyes (78%) were visual at last examination. Of those visual eyes, two developed mild to moderate posterior synechiae, four had mild to moderate capsular opacities, and one developed a lipid keratopathy. The remaining two eyes with long‐term follow‐up were from the same red‐tailed hawk. Both eyes developed fibropupillary membranes that were blinding. One eye was pseudophakic, and the other was aphakic and also developed a rhegmatogenous retinal detachment. Another bald eagle was euthanized two months after surgery due to refractory glaucoma; one eye was pseudophakic.

Conclusions

Phacoemulsification is a viable treatment for captive raptors with cataracts. The most severe complications occurred relatively soon after surgery. Captive raptors appear to adapt well to aphakia.
Hydromorphological, hydraulic and ecological effects of restored wood: findings and reflections from an academic partnership approach
Authors: Pinto Carolina , Ing Rebecca , Browning Ben , Delboni Vinicius , Wilson Hazel , Martyn Dominic , Harvey Gemma L.
Published: February 2019

Large wood (re)introduction can deliver multiple benefits in river restoration, but there is a dearth of the detailed and longer‐term post‐project monitoring and evaluation required for improving best practice. We present findings from an academic partnership approach to post‐project evaluation, based on successive MSc research projects on restored large wood in the Loddon catchment, UK. Field and modelling data reveal: (i) key differences in large wood features between restored and natural reaches; (ii) increased hydraulic retention and changes to mesohabitats associated with large wood; (iii) differences in macroinvertebrate community composition around large wood but a lack of site‐level effects; (iv) interactions between macrophytes and large wood that may be specific to restored reaches; (v) a need for further field and modelling studies to inform the accurate representation of large wood in hydraulic models. Some key challenges in partnership working are identified to aid planning and effectiveness of future collaborations.
Cholinergic neurons in the pedunculopontine tegmental nucleus modulate breathing in rats by direct projections to the retrotrapezoid nucleus
Authors: Lima Janayna D. , Sobrinho Cleyton R. , Falquetto Barbara , Santos Leonardo K. , Takakura Ana C. , Mulkey Daniel K. , Moreira Thiago S.
Published: February 2019

Key points

Cholinergic projections from the pedunculopontine tegmental nucleus (PPTg) to the retrotrapezoid nucleus (RTN) are considered to be important for sleep–wake state‐dependent control of breathing.

The RTN also receives cholinergic input from the postinspiratory complex.

Stimulation of the PPTg increases respiratory output under control conditions but not when muscarinic receptors in the RTN are blocked.

The data obtained in the present study support the possibility that arousal‐dependent modulation of breathing involves recruitment of cholinergic projections from the PPTg to the RTN.

The pedunculopontine tegmental nucleus (PPTg) in the mesopontine region has important physiological functions, including breathing control. The PPTg contains a variety of cell types, including cholinergic neurons that project to the rostral aspect of the ventrolateral medulla. In addition, cholinergic signalling in the retrotrapezoid nucleus (RTN), a region that contains neurons that regulate breathing in response to changes in CO2/H+, has been shown to activate chemosensitive neurons and increase inspiratory activity. The present study aimed to identify the source of cholinergic input to the RTN and determine whether cholinergic signalling in this region influences baseline breathing or the ventilatory response to CO2 in conscious male Wistar rats. Retrograde tracer Fluoro‐Gold injected into the RTN labelled a subset of cholinergic PPTg neurons that presumably project directly to the chemosensitive region of the RTN. In unrestrained awake rats, unilateral injection of the glutamate (10 mm/100 nL) in the PPTg decreased tidal volume (VT) but otherwise increased respiratory rate (fR) and net respiratory output as indicated by an increase in ventilation (VE). All respiratory responses elicited by PPTg stimulation were blunted by prior injection of methyl‐atropine (5 mm/50–75 nL) into the RTN. These results show that stimulation of the PPTg can increase respiratory activity in part by cholinergic activation of chemosensitive elements of the RTN. Based on previous evidence that cholinergic PPTg projections may simultaneously activate expiratory output from the pFRG, we speculate that cholinergic signalling at the level of RTN region could also be involved in breathing regulation.
Joint Multifractal and Lacunarity Analysis of Image Profiles for Manufacturing Quality Control
Authors: Imani Farhad , Yao Bing , Chen Ruimin , Rao Prahalad , Yang Hui
Published: February 2019

The modern manufacturing industry faces increasing demands to customize products according to personal needs, thereby leading to the proliferation of complex designs. To cope with design complexity, manufacturing systems are increasingly equipped with advanced sensing and imaging capabilities. However, traditional statistical process control methods are not concerned with the stream of in-process imaging data. Also, very little has been done to investigate nonlinearity, irregularity, and inhomogeneity in the image stream collected from manufacturing processes. This paper presents the joint multifractal and lacunarity analysis to characterize irregular and inhomogeneous patterns of image profiles, as well as detect the hidden dynamics in the manufacturing process. Experimental studies show that the proposed method not only effectively characterizes surface finishes for quality control of ultraprecision machining but also provides an effective model to link process parameters with fractal characteristics of in-process images acquired from additive manufacturing. This, in turn, will allow a swift response to processes changes and consequently reduce the number of defective products. The proposed multifractal method shows strong potentials to be applied for process monitoring and control in a variety of domains such as ultraprecision machining and additive manufacturing.
How We Solve the Weights in Our Surrogate Models Matters
Authors: Correia Daniel , Wilke Daniel N.
Published: February 2019

The construction of surrogate models, such as radial basis function (RBF) and Kriging-based surrogates, requires an invertible (square and full rank matrix) or pseudoinvertible (overdetermined) linear system to be solved. This study demonstrates that the method used to solve this linear system may result in up to five orders of magnitude difference in the accuracy of the constructed surrogate model using exactly the same information. Hence, this paper makes the canonic and important point toward reproducible science: the details of solving the linear system when constructing a surrogate model must be communicated. This point is clearly illustrated on a single function, namely the Styblinski–Tang test function by constructing over 200 RBF surrogate models from 128 Latin Hypercubed sampled points. The linear system in the construction of each surrogate model was solved using LU, QR, Cholesky, Singular-Value Decomposition, and the Moore–Penrose pseudoinverse. As we show, the decomposition method influences the utility of the surrogate model, which depends on the application, i.e., whether an accurate approximation of a surrogate is required or whether the ability to optimize the surrogate and capture the optimal design is pertinent. Evidently the selection of the optimal hyperparameters based on the cross validation error also significantly impacts the utility of the constructed surrogate. For our problem, it turns out that selecting the hyperparameters at the lowest cross validation error favors function approximation but adversely affects the ability to optimize the surrogate model. This is demonstrated by optimizing each constructed surrogate model from 16 fixed initial starting points and recording the optimal designs. For our problem, selecting the optimal hyperparameter that coincides with the lowest monotonically decreasing function value significantly improves the ability to optimize the surrogate for most solution strategies.
Numerical Investigation of Added Mass and Hydrodynamic Damping on a Blunt Trailing Edge Hydrofoil
Authors: Zeng Yongshun , Yao Zhifeng , Gao Jiangyong , Hong Yiping , Wang Fujun , Zhang Fang
Published: February 2019

Added mass and hydrodynamic damping play significant roles in fluid-structure interaction (FSI) in hydraulic turbines. Added mass can reduce natural frequencies, while hydrodynamic damping could result in a higher amplitude decay speed of the vibration. In order to quantify the added mass and hydrodynamic damping of a three-dimensional (3D) NACA 0009 hydrofoil with a blunt trailing edge, a two-way FSI simulation method was employed. The effects of grid scale, time-step, turbulence model, exciting force, and numerical damping on the calculation accuracy of the two-way FSI numerical simulation were analyzed in great detail through comparison with the previously published experimental data. Hydraulic force was obtained by using a transitional shear stress transport model at the flow region of the Reynolds number ReL = 0.2 × 106–2 × 106. The vortex shedding frequency, the natural frequency of the first-order bending mode in water, and the hydrodynamic damping ratio obtained from the numerical simulations agree well with the experimental data, with maximum deviations in 6.12%, 4.53%, and 8.82%, respectively. As the flow velocity increases, the natural frequency may not significantly change, while the added mass coefficient gradually increases, considering the effect of added stiffness. Above the first-order bending mode lock-in region, the results indicate that the first-order bending mode hydrodynamic damping ratio increases linearly with velocity. The present numerical achievements offer a higher level of accuracy for predicting the added mass and hydrodynamic damping characteristics of a hydrofoil.
Hypoxic cancer–associated fibroblasts increase NCBP2-AS2/HIAR to promote endothelial sprouting through enhanced VEGF signaling
Authors: Kugeratski Fernanda G. , Atkinson Samuel J. , Neilson Lisa J. , Lilla Sergio , Knight John R. P. , Serneels Jens , Juin Amelie , Ismail Shehab , Bryant David M. , Markert Elke K. , Machesky Laura M. , Mazzone Massimiliano , Sansom Owen J. , Zanivan Sara
Published: February 2019

Analysis of the cancer-associated fibroblast secretome identifies an angiogenesis-promoting factor.
Interrogating B cell signaling pathways: A quest for novel therapies for mantle cell lymphoma
Authors: Ahmed Makhdum , Lorence Elizabeth , Wang Jeffrey , Jung Dayoung , Zhang Liang , Nomie Krystle , Wang Michael
Published: February 2019

Targeting B cell receptor signaling pathways may be effective at treating mantle cell lymphoma.
2-Hydroxylation of
Acinetobacter baumannii
Lipid A Contributes to Virulence
Authors: Bartholomew Toby L. , Kidd Timothy J. , Sá Pessoa Joana , Conde Álvarez Raquel , Bengoechea José A.
Published: February 2019

Acinetobacter baumannii
causes a wide range of nosocomial infections. This pathogen is considered a threat to human health due to the increasingly frequent isolation of multidrug-resistant strains.
Coxiella burnetii
RpoS Regulates Genes Involved in Morphological Differentiation and Intracellular Growth
Authors: Moormeier Derek E. , Sandoz Kelsi M. , Beare Paul A. , Sturdevant Daniel E. , Nair Vinod , Cockrell Diane C. , Miller Heather E. , Heinzen Robert A.
Published: February 2019

The Q fever bacterium
Coxiella burnetii
has spore-like environmental stability, a characteristic that contributes to its designation as a potential bioweapon. Stability is likely conferred by a highly resistant, small cell variant (SCV) stationary-phase form that arises during a biphasic developmental cycle. Here, we define the role of the alternative sigma factor RpoS in regulating genes associated with SCV development. Genes involved in stress responses, amino acid transport, cell wall remodeling, and type 4B effector secretion were dysregulated in the
rpoS
mutant. Cellular impairments included defects in intracellular growth, cell wall structure, and resistance to oxidants. These results support RpoS as a central regulator of the
Coxiella
developmental cycle and identify developmentally regulated genes involved in morphological differentiation.
Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance
Authors: Timme Ruth E. , Strain Errol , Baugher Joseph D. , Davis Steven , Gonzalez-Escalona Narjol , Sanchez Leon Maria , Allard Marc W. , Brown Eric W. , Tallent Sandra , Rand Hugh
Published: February 2019

Foodborne pathogen surveillance in the United States is transitioning from strain identification using restriction digest technology (pulsed-field gel electrophoresis [PFGE]) to shotgun sequencing of the entire genome (whole-genome sequencing [WGS]). WGS requires a new suite of analysis tools, some of which have long histories in academia but are new to the field of public health and regulatory decision making.
Draft Genome Assembly of the False Spider Mite
Brevipalpus yothersi
Authors: Navia Denise , Novelli Valdenice M. , Rombauts Stephane , Freitas-Astúa Juliana , Santos de Mendonça Renata , Nunes Maria Andreia , Machado Marcos A. , Lin Yao-Cheng , Le Phuong , Zhang Zaichao , Grbić Miodrag , Wybouw Nicky , Breeuwer Johannes A. J. , Van Leeuwen Thomas , Van de Peer Yves
Published: February 2019

The false spider mite
Brevipalpus yothersi
infests a broad host plant range and has become one of the most economically important species within the genus
Brevipalpus
. This phytophagous mite inflicts damage by both feeding on plants and transmitting plant viruses.
Diagnostic performance of optical coherence tomography angiography in glaucoma: a systematic review and meta-analysis
Authors: Miguel Ana I M , Silva André B , Azevedo Luis F
Published: February 2019

Background

Compared with current imaging methods, the diagnostic performance and the advantages and limitations of optical coherence tomography angiography (OCTA) remain unclear. We performed a systematic review and meta-analysis of studies investigating vessel density (VD) in patients with glaucoma using OCTA.

Methods

We conducted a literature search on PubMed, Scopus, Web of Science, ISI Conference Proceedings and Google Scholar, along with a manual search, from January 2006 to March 2018. We included prospective studies that used OCTA to compare the VD in glaucomatous eyes with healthy control eyes.

Results

Of 3045 screened articles, 24 were included in a broad characterisation and 18 in the meta-analysis. We observed a statistically significant reduction in the mean peripapillary VD (MPVD) in glaucoma (MPVD: 57.53%, 95% CI 52.60 to 62.46, p< 0.001) compared with controls (MPVD: 65.47%, 95% CI 59.82 to 71.11; standardised mean difference [SMD], –1.41, 95% CI –1.62 to –1.20, p< 0.001) for 888 glaucomatous and 475 healthy eyes, and also in the mean-whole optic nerve image VD (SMD, –9.63, 95% CI –10.22 to –9.03, p<0.001), mean inside-disc VD (SMD, − 9.51, 95% CI –12.66 to –6.36, p<0.05) and mean parafoveal VD (SMD, –3.92, 95% CI –4.73 to –3.12, p<0.001). Subgroup analyses revealed a significant difference in the MPVD across glaucoma subtypes and OCTA devices.

Conclusion

This suggests the diagnostic utility of OCTA in detecting glaucomatous eyes; however, further longitudinal prospective studies are welcomed to characterise vascular changes in glaucoma.
Cross-sectional study of the association between serum perfluorinated alkyl acid concentrations and dental caries among US adolescents (NHANES 1999–2012)
Authors: Puttige Ramesh Nithya , Arora Manish , Braun Joseph M
Published: February 2019

Study objectives

Perfluoroalkyl acids (PFAAs) are a class of anthropogenic and persistent compounds that may impact some biological pathways related to oral health. The objective of our study was to estimate the relationship between dental caries prevalence and exposure to four PFAA: perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorohexane sulfonic acid (PFHxS) and perfluorooctane sulfonic acid (PFOS) in a nationally representative sample of US adolescents.

Setting/Design

We analysed cross-sectional data from the National Health and Nutrition Examination Survey from 1999 to 2012 for 12–19-year-old US adolescents.

Participants

Of 10 856 adolescents aged 12 to 19 years who had a dental examination, we included 2869 with laboratory measurements for serum PFAA concentrations and complete covariate data in our study.

Primary and secondary outcome measures

Dental caries prevalence was defined as the presence of decay or a restoration on any tooth surface, or the loss of a tooth due to tooth decay. We used multivariable logistic regression to estimate the covariate-adjusted association between serum PFAA concentrations and dental caries prevalence, accounting for the complex National Health and Nutrition Examination Survey design.

Results

Of 2869 adolescents, 59% had one or more dental caries. We observed no associations between the prevalence of dental caries and serum concentrations of PFOA, PFOS or PFHxS. The adjusted odds of caries were 21% (OR 0.79; 95% CI 0.63 to 1.01), 15% (OR 0.85; 95% CI 0.67 to 1.08) and 30% (OR 0.7; 95% CI 0.55 to 0.90) lower among adolescents in the 2nd, 3rd and 4th serum PFNA concentration quartiles compared to adolescents in the first quartile, respectively. The linear trend for this association was not statistically significant.

Conclusion

PFOA, PFOS and PFHxS were not associated with prevalence of dental caries. The prevalence of caries was reduced with increasing serum PFNA concentrations; however, these results should be interpreted cautiously given that we were unable to adjust for several factors related to oral health.
Sharing individual participant data from clinical studies: a cross-sectional online survey among Italian patient and citizen groups
Authors: Colombo Cinzia , Roberto Anna , Krleza-Jeric Karmela , Parmelli Elena , Banzi Rita
Published: February 2019

Objectives

To gather knowledge on the current debate, opinions and attitudes of Italian patient and citizen groups on individual participant data (IPD) sharing from clinical studies.

Design

Cross-sectional online survey.

Setting and participants

A 22-item online questionnaire was sent by email to 2003 contacts of patient and citizen groups in Italy. We received 311 responses, checked for duplicate respondents (16); 295 single groups responded, 280 providing questionnaires eligible for analysis (response rate 15%). Ninety (32.1%) dealt with oncology and palliative care, 175 (46.2%) operated locally or regionally and 136 (48.6%) were involved in clinical research.

Outcome measure

Data on Italian patient and citizen groups’ self-reported knowledge, attitudes and opinions on IPD sharing, mechanisms for IPD access, advantages and risks.

Results

Half the respondents (144 out of 280, 51%) had some knowledge about the IPD sharing debate, and 60 (42%) stated they had an official position (35 in favour, 19 in favour with restrictions, 2 against, 1 neither for nor against, 3 missing). Nineteen discussed the topic encouraged by this survey; 39% approved broad access by researchers and other professions and identified information to participants, data de-identification, secure archives, access agreements and sanctions for misuse as important aspects of IPD sharing models. Respondents highlighted re-identification, privacy and re-use of data for purposes that participants do not agree on, as main risks, advancement of innovation and reducing waste in research as main advantages. Around half believed IPD sharing would not discourage study participation.

Conclusions

Half the respondents were aware of the debate. Those who had an official position were mainly in favour of IPD sharing. Many supported broad access, asking for conditions important for building trust in entities that handle IPD sharing.

Although limited by the low response rate, these findings reinforce the demand for reliable and transparent processes where accountabilities are clear.
‘Just because I’m old it doesn’t mean I have to be fat’: a qualitative study exploring older adults’ views and experiences of weight management
Authors: Jackson Sarah E , Holter Linn , Beeken Rebecca J
Published: February 2019

Objectives

The aim of this study was to explore older adults’ beliefs about the appropriateness of weight management, and how their experiences and expectations of weight management have changed as they have got older.

Design

Qualitative semistructured interview study.

Setting

UK.

Participants

Older adults (≥65 years) in the UK who had recent (<5 years) experience of trying to manage their weight (n=15; 12 women; 73% white British).

Results

Data were analysed using thematic analysis. Emergent themes highlighted that weight remained a concern for many older adults, although having a high body weight was seen to be more acceptable at older than younger ages. Excess weight was reported to have negative consequences for health and well-being which participants felt could be alleviated by losing weight. Participants were motivated to lose weight for appearance and health reasons, but mentioned finding it harder to lose weight as they had got older and generally felt they had received limited guidance on weight management from health professionals.

Conclusions

The views of our participants highlight the need for further research into safe and effective methods of weight loss for older people and indicate that advice and support from health professionals would be welcomed.
Precarious employment, business performance and occupational injuries: a study protocol of a register-based Swedish project
Authors: Orellana Cecilia , Kreshpaj Bertina , Johansson Gun , Burström Bo , Kjellberg Katarina , Hemmingsson Tomas , Axén Magnus , Davis Letitia , Wegman David , Bodin Theo
Published: February 2019

Introduction

There is uncertainty regarding the trends in occupational injuries (OIs) in Sweden due to a significant and increasing problem with under-reporting to injury registers. Under-reporting, in general, is likely to be exacerbated by the rise in precarious employment (PE), a set of unfavourable employment characteristics that would benefit from formal definition and study. PE and global trends are believed also to affect companies and their commitment to health and safety. The present study attempts to bridge these knowledge gaps and presents a study protocol for planned studies, with three main objectives: first, to review the literature for definitions of PE emphasising those that are multidimensional and operationalise components in routinely collected register data; second, to estimate the under-reporting of OI in Swedish registers and third, using results from the first objective, to conduct large, register-based prospective studies, designed to measure effect sizes and interactions between PE, business performance and OI.

Methods and analysis

First, a scientific literature review will be conducted, including scientific databases and grey literature. Second, data from two major OI registers will be used to estimate the magnitude of under-reporting using capture–recapture methodology. Finally, all residents aged 18–65 in Sweden with any registered income during 2003–2015 will be included. Data sources encompass Swedish population and labour market registers with linkage to both the main OI register with national coverage and hospital records. Trends in PE and OI will be explored, together with risk of OI associated with PE and business performance.

Ethics and dissemination

The project has been approved by the Regional Ethics Committee, Stockholm (dnr: 2016/2325–31; 2017/2173–32). Dissemination of study results will include a series of peer-reviewed papers, at least one PhD thesis and one report in Swedish, engaging relevant stakeholders. Results will be presented in national and international conferences and through press releases to mass media.