bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Large-Eddy Simulation Study of Atmospheric Boundary Layer Influence on Stratified Flows over Terrain
Authors: Sauer Jeremy A. , Muñoz-Esparza Domingo , Canfield Jesse M. , Costigan Keeley R. , Linn Rodman R. , Kim Young-Joon 
Published: May 2016

Abstract
The impact of atmospheric boundary layer (ABL) interactions with large-scale stably stratified flow over an isolated, two-dimensional hill is investigated using turbulence-resolving large-eddy simulations. The onset of internal gravity wave breaking and leeside flow response regimes of trapped lee waves and nonlinear breakdown (or hydraulic-jump-like state) as they depend on the classical inverse Froude number, Fr−1 = Nh/Ug, is explored in detail. Here, N is the Brunt–Väisälä frequency, h is the hill height, and Ug is the geostrophic wind. The results here demonstrate that the presence of a turbulent ABL influences mountain wave (MW) development in critical aspects, such as dissipation of trapped lee waves and amplified stagnation zone turbulence through Kelvin–Helmholtz instability. It is shown that the nature of interactions between the large-scale flow and the ABL is better characterized by a proposed inverse compensated Froude number, = N(h − zi)/Ug, where zi is the ABL height. In addition, it is found that the onset of the nonlinear-breakdown regime, ≈ 1.0, is initiated when the vertical wavelength becomes comparable to the sufficiently energetic scales of turbulence in the stagnation zone and ABL, yielding an abrupt change in leeside flow response. Finally, energy spectra are presented in the context of MW flows, supporting the existence of a clear transition in leeside flow response, and illustrating two distinct energy distribution states for the trapped-lee-wave and the nonlinear-breakdown regimes.
An AIS-Based Site Planning Method to Help Minimize Collision Risk during Marine Autonomous Surface Craft Deployments
Authors: Filimon Michael A. , Codiga Daniel L. 
Published: May 2016

AbstractMarine autonomous surface crafts (MASCs), or unmanned surface vehicles as their precursors have traditionally been known, could cost effectively advance spatiotemporal coverage and resolution capabilities for oceanographic sampling in coastal and estuarine settings, if deployed for long durations (from days to weeks). Site planning for such deployments balances scientific goals against operational risk of collision avoidance (CA) maneuvers required by the MASC during encounters with other vessels. A method is developed and demonstrated in this paper, using archived Automatic Identification System (AIS) vessel tracking data, to quantify such potential encounters of a MASC on a repeat-transect survey. The demonstration site is Rhode Island Sound, where average vessel track frequencies are shown to range from about 8 to 0.01 or less per day, from inshore shipping lanes to areas farther offshore, respectively. Encounters per month ranged from 24 to 1 for increasingly offshore locations, based on a MASC repeatedly traversing an 18-km transect at an average speed of 2.5 m s−1 (~5 kt) over a one-month summer period and stopping at each of 10 equispaced stations in one direction to sample for 10 min. Crude estimates of non-AIS vessel traffic suggest total encounters (with vessels equipped by AIS or not) up to 3–4 times higher. The method can be applied anywhere AIS data are available and is generalizable to any survey configuration. It facilitates investigating sensitivity to choices of transect location and sampling configuration parameters, providing crucial information to guide deployment planning for a given level of confidence in CA capabilities of the MASC.
Life With Type 1 Diabetes
Authors: Reitblat Lital , Whittemore Robin , Weinzimer Stuart A. , Tamborlane William V. , Sadler Lois S. 
Published: May 2016

Purpose The purpose of this study was to describe the experience of Hispanic adolescents with type 1 diabetes (T1DM) from the perspectives of adolescents and their diabetes clinicians. Methods Nine Hispanic adolescents with T1DM and 7 clinicians at a tertiary academic medical center participated in in-depth individual semistructured interviews. Adolescents were purposively sampled to obtain a range in age and metabolic control. Based on interpretive descriptive methodology, data were coded and combined into themes, which were constructed separately for the 2 groups and then compared across groups. Data were analyzed concurrently with data collection. Results Adolescents and clinicians reported similar themes related to (1) cultural aspects of living with T1DM; (2) finding the balance of: food, insulin, and exercise; being “perfect at diabetes” versus being a “normal teenager”; and being independent versus needing support, and (3) ways to improve life for Hispanic adolescents with T1DM. Although there were some key cultural distinctions, Hispanic adolescents with T1DM and their clinicians described life and daily management issues as being similar to those of their non-Hispanic peers. Conclusions Hispanic adolescents with T1DM have unique experiences and beliefs that affect their living with T1DM, but in many respects, their experiences are similar to those of their non-Hispanic peers with T1DM. Hispanic adolescents with T1DM want their clinicians to learn about their personal lives. Preferably, clinicians and parents should speak the same language. If not possible, interpreters should be used instead of having adolescents translate during clinic appointments.
An individualized exercise programme with and without behavioural change enhancement strategies for managing fatigue among frail older people: a quasi-experimental pilot study
Authors: Liu Justina Y-W , Lai Claudia KY , Siu Parco M , Kwong Enid , Tse Mimi MY 
Published: May 2016

Objective: To evaluate the feasibility and preliminary effects of an individualized exercise programme with and without behavioural change enhancement strategies for frail older people with fatigue. Design: A three-arm, single-blinded, quasi-experimental pilot study. Setting: Community health centres. Participants: A total of 79 frail older people with fatigue, mean age 79.32 years (±7.72). Interventions: The combined group received a 16-week combined intervention consisting of exercise training and a behavioural change enhancement programme. The exercise group received exercise training and health talks, whereas the control group received only health talks. Main outcome measure(s): Feasibility was assessed through the participants’ recruitment, retention, attendance and adherence, feedback, and reports of adverse events. The preliminary effects were assessed by the participants’ level of fatigue, physical endurance, self-efficacy, and self-perceived compliance with exercise. Results: Feasibility was achievable with high recruitment (87.2%) and low overall attrition (7.1%) rates. A similar reduction in fatigue was identified in all groups, but a trend of greater improvement in physical endurance was observed in the combined group than in the other two groups. The combined group also had a significantly better attendance rate [F(2,76) = 5.64, p < 0.01)] and higher self-perceived exercise compliance than the exercise group. Conclusion: The combined intervention has the potential to enhance the participants’ adherence to exercise regimens by improving their attendance in training sessions and their self-perceived exercise compliance. They are important to maintaining an appropriate level of engagement in daily exercises, especially at the beginning stages of behavioural change, when the participants are establishing the habit of exercising daily.
Current understanding of decision-making in adolescents with cancer: A narrative systematic review
Authors: Day Emma , Jones Louise , Langner Richard , Bluebond-Langner Myra 
Published: May 2016

Background: Policy guidance and bioethical literature urge the involvement of adolescents in decisions about their healthcare. It is uncertain how roles and expectations of adolescents, parents and healthcare professionals influence decision-making and to what extent this is considered in guidance. Aims: To identify recent empirical research on decision-making regarding care and treatment in adolescent cancer: (1) to synthesise evidence to define the role of adolescents, parents and healthcare professionals in the decision-making process and (2) to identify gaps in research. Design: A narrative systematic review of qualitative, quantitative and mixed-methods research. We adopted a textual approach to synthesis, using a theoretical framework of interactionism to interpret findings. Data Sources: The databases MEDLINE, PsycINFO, SCOPUS, EMBASE and CINHAL were searched from 2001 through May 2015 for publications on decision-making for adolescents (13–19 years) with cancer. Results: Twenty-eight articles were identified. Adolescents and parents initially find it difficult to participate in decision-making due to a lack of options in the face of protocol-driven care. Parent and adolescent preferences for information and response to loss of control vary between individuals and over time. No studies indicate parental or adolescent preference for a high degree of independence in decision-making. Conclusion: Striving to make parents and adolescents fully informed or urge them towards more independence than they prefer may add to distress and confusion. This may interfere with their ability to participate in their preferred way in decisions about care and treatment. Future research should include analysis of on-ground interactions among parents, adolescents and clinicians across the trajectory.
Carers of people affected by cancer and other long-term conditions at end of life: A qualitative study of providing a bespoke package of support in a rural setting
Authors: Nelson David , Mansfield Paul , Kane Roslyn 
Published: May 2016

Background: A UK charity, Macmillan Cancer Support has funded a local intervention, whereby carers of people affected by cancer and other long-term conditions at end of life are offered a bespoke package of support. Aim: This short report describes the qualitative experiences of carers in receipt of the intervention. Design: Qualitative research utilising in-depth interviews. Discussions were digitally recorded and transcribed verbatim. Data were analysed using thematic analysis. Setting/participants: Participants were carers ( n = 10) in receipt of the intervention. Interviews were conducted between August and September 2014 in Lincolnshire (England). Results: Five themes from the interviews were identified: (1) Awareness and advertising, (2) focus of support on the carer, (3) modes of communication, (4) personal attributes and skills of the support worker (5) streamlining and signposting. Conclusion: The intervention was successful within a social care setting. The participants had no overtly negative opinions on the service in its current format and all held it in high regard. Carers felt a sense of reassurance from having background support and maintained that their situation would have been worse had this support not been there.
Information processing speed in multiple sclerosis: Past, present, and future
Authors: Costa Silvana L , Genova Helen M , DeLuca John , Chiaravalloti Nancy D 
Published: May 2016

Background: Information processing speed (IPS) is a prevalent cognitive impairment in multiple sclerosis (MS). Objectives: This review aims to summarize the methods applied to assess IPS in MS and its theoretical conceptualization. A PubMed search was performed to select articles published between 1 January 2004 and 31 December 2013, resulting in 157 articles included. Results: The majority (54%) of studies assessed IPS with heterogeneous samples (several disease courses). Studies often report controlling for presence of other neurological disorders (60.5%), age (58.6%), education (51.6%), alcohol history (47.8%), or use of steroids (39.5%). Potential confounding variables, such as recent relapses (50.3%), history of developmental disorders (19.1%), and visual problems (29.9%), were often neglected. Assessments used to study IPS were heterogeneous (ranging from simple to complex tasks) among the studies under review, with 62 different tasks used. Only 9.6% of articles defined the construct of IPS and 22.3% discussed IPS in relation to a theoretical model. Future directions: The challenges for the upcoming decade include clarification of the definition of IPS as well as its theoretical conceptualization and a consensus on assessment. Based on the results obtained, we propose a new theoretical model, the tri-factor model of IPS.
Investigation of the Impact of Cell Cycle Stage on Freeze Response Sensitivity of Androgen-Insensitive Prostate Cancer
Authors: Santucci Kimberly L. , Baust John M. , Snyder Kristi K. , Van Buskirk Robert G. , Baust John G. 
Published: May 2016

Background: Cryoablation, an effective means of ablating cancer, is often used in conjunction with adjuvants that target cancer cells in a specific cell cycle stage to increase treatment efficacy. The objective of this study was to investigate the impact of cell cycle stage on cancer freeze response as well as investigate the potential cellular kinetic effect of calcitriol, the active metabolic of vitamin D3, when used as a cryosensitizing adjuvant in order to maximize prostate cancer cell death. Methods: Cell cycle distribution of PC-3 cells was analyzed via flow cytometry to compare gap 1, synthesis, and gap 2/mitosis phase subpopulations pre- and postfreeze as well as changes elicited by calcitriol pretreatment. Distinct gap 1, synthesis, and gap 2/mitosis phase populations were obtained through fluorescence-activated cell sorting and synthesis phase thymidine synchronization. Posttreatment viability was assessed using alamarBlue and fluorescence microscopy to assess live, apoptotic, and necrotic subpopulations. Results: A small but statistically significant increase in synthesis phase and decrease in gap 2/mitosis phase populations was noted at 6 hours postfreeze in asynchronous samples. Synchronization in synthesis phase yielded an increase in cell death when combined with freezing to both −15°C and −20°C. Calcitriol pretreatment increased the gap 1 phase population by 20% and a synergistic decrease in viability following freezing. However, gap 1–sorted populations combined with calcitriol treatment did not exhibit this synergistic effect. Fluorescence microscopy of fluorescence-activated cell sorting-sorted cells revealed necrosis as the predominant form of cell death in all phases, though apoptosis did play a role. Conclusion: Although initial results suggested a potential sensitivity, PC-3 cells exposed to freezing as sorted populations did not reveal significant differences in cell death. As such, the data from this study suggest that there is no difference in cell cycle stage sensitivity to freezing injury.
Factors Associated With Callus in Patients with Diabetes, Focused on Plantar Shear Stress During Gait
Authors: Hamatani Masako , Mori Taketoshi , Oe Makoto , Noguchi Hiroshi , Takehara Kimie , Amemiya Ayumi , Ohashi Yumiko , Ueki Kohjiro , Kadowaki Takashi , Sanada Hiromi 
Published: May 2016

Background: The aim of this study is to identify whether plantar shear stress in neuropathic patients with diabetes with callus is increased compared with those without callus. Method: The differences in foot deformity, limited joint mobility, repetitive stress of walking, and ill-fitting shoes between patients with callus and those without callus were also determined. Subjects were recruited from the Diabetic Foot Outpatient Clinic. A newly developed in-shoe measurement system, which has flexible and thin insoles, enabled measurement of both plantar pressure and shear stress simultaneously when subjects walked as usual on a 10 m walkway. Results: It was found that plantar shear stress adjusted for weight during the push-off phase was increased by 1.32 times in patients with callus compared with those without callus (mean ± SD: 0.0500 ± 0.0160 vs 0.0380 ± 0.0144, P = .031). Moreover, hallux valgus deformity, reduction in dorsiflexion of the ankle joint and increase in plantar flexion were showed in feet with callus. Increased plantar shear stress may be caused by gait change that patients having callus push off with the metatarsal head instead of the toe as a result of foot deformity and limited joint mobility. Conclusions: It was found that plantar shear stress adjusted for weight during the push-off phase was increased in patients with callus compared with those without callus by using the newly developed measurement system. These results suggest that reduction of plantar shear stress during the push-off phase can prevent callus formation in neuropathic patients with diabetes.
Emergency Presentation and Short-Term Survival Among Patients With Colorectal Cancer Enrolled in the Government Health Plan of Puerto Rico
Authors: Ortiz-Ortiz Karen J. , Ríos-Motta Ruth , Marín-Centeno Heriberto , Cruz-Correa Marcia R. , Ortiz Ana P. 
Published: May 2016

Objective: In this study, we examine factors associated with the use of the emergency room (ER) as an entry point into the health-care system to initiate a cancer diagnosis among Puerto Rico’s Government Health Plan (GHP) patients and compare the 1-year survival of GHP patients that initiated cancer diagnosis in the emergency room (ER) presentation with those that initiated the diagnosis in a physician’s office. Methods: Data for patients with colorectal cancer (CRC) aged 50 to 64 years and diagnosed in 2012 were obtained from the Puerto Rico Central Cancer Registry and linked to the Puerto Rico Health Insurance Administration database (n = 190). Crude odds ratio, adjusted odds ratio, and their 95% confidence intervals were reported. We used the Kaplan-Meier method to generate survival curves. Multivariate Cox regression analysis was performed to evaluate the association between ER presentation and 1-year cause-specific survival. Results: We found that 37.37% of the study population had an ER presentation. Male patients had a higher occurrence of having an ER presentation (66.20%), while 76.06% of the patients with an ER presentation were diagnosed in late stage. Emergency room presentation was a highly predictive factor for cancer mortality in the year following the diagnosis. These patients had between 3.99 to 4.24 times higher mortality risk than non-ER presentation patients ( P < .05). Conclusion: Late presentation for CRC diagnosis through an ER visit is a significant concern that influences negatively on the patient’s outcome. Efforts at increasing primary care visits and routine screening tests among GHP beneficiaries could improve survival.
Dimers of oxocentred [OCu4]6+ tetrahedra in two novel copper selenite chlorides, K[Cu3O](SeO3)2Cl and Na2[Cu7O2] (SeO3)4Cl4, and related minerals and inorganic compounds
Authors: Kovrugin Vadim M. , Colmont Marie , Mentré Olivier , Siidra Oleg I. , Krivovichev Sergey V. 
Published: May 2016

AbstractTwo novel copper selenite chlorides, K[Cu3O](SeO3)2Cl (I) and Na2[Cu7O2](SeO3)4Cl4 (II), have been synthesized by the CVT method. Their crystal structures have been solved by direct methods and refined by least-squares techniques. I is triclinic, space group P1̄, a = 7.6821(5), b = 8.1179(5), c = 8.7836(6) Å, α = 113.193(3), β = 108.735(4), γ = 98.245(4)°, V = 453.32(5) Å3, R1 = 0.0481 for 1210 unique reflections with F≥4σ(F); II is triclinic, space group P1̄,a = 7.4362(6), b = 8.3361(7), c = 9.1343(11) Å,α = 110.277(6), β = 106.212(6), γ = 105.158(4)°, V = 467.94(8) Å3, R1 = 0.0265 for 2498 unique reflections with F≥4σ(F). The structures of I and II can be described in terms of dimers of copper oxocentred tetrahedra. In I, two (OCu4)6+ tetrahedra share a common Cu···Cu edge to form the [O2Cu6]8+ dimer, whereas the structure of II is based upon two (OCu4)6+ tetrahedra linked together by one common Cu atom resulting in the formation of the [O2Cu7]10+ dimer. A comparison with related minerals and inorganic compounds is given.
Vanadium, V – a new native element mineral from the Colima volcano, State of Colima, Mexico, and implications for fumarole gas composition
Authors: Ostrooumov M. , Taran Y. 
Published: May 2016

AbstractVanadium, V, is a new mineral found in sublimates of high-temperature fumaroles of the Colima volcano, Mexico. The mineral precipitates over a narrow temperature range of 550–680°C, and occurs in association with colimaite (K3VS4) and shcherbinaite (V2O5). Native vanadium was been found on the inner wall of an inserted silica tube and subsequently in the adjacent rock of the Z3 fumarole. Vanadium forms smooth, irregular to flattened crystals, 5–20 μm in diameter. Smaller irregular crystals have also been observed in silica tubes. Due to its small crystal size, its physical properties (hardness, cleavage and density) could not be determined. An EDS spectrum indicated the presence of V, Fe, Al and Ti with an empirical formula calculated on the basis of EPMA analyses of V0.86Fe0.09Al0.04Ti0.01. Gandolfi and glancing-angle X-ray diffraction data showed that the microcrystals were body-centred cubic, space group Im3̄m, a = 3.022(3) Å, V = 27.60 (5) Å3, Z = 2. The five strongest calculated diffraction lines are [ d spacings in Å, (I) (hkl)]: 2.1411 (100)(110), 1.5126 (12)(200), 1.2301 (19)(211), 0.9565 (8)(310) and 8.8090 (11)(321). The calculated density is 6.033 g cm–3. Thermochemical modelling was used to explain why very oxidized gas at Colima precipitates V-bearing minerals and some native elements (vanadium and gold). Vanadium, is the second newly recognized mineral species (after colimaite) collected from an active fumarole in this volcanic crater. The mineral and its name have been approved by the CNMNC (IMA 2012-021a).
SeqPurge: highly-sensitive adapter trimming for paired-end NGS data
Authors: Sturm Marc , Schroeder Christopher , Bauer Peter 
Published: May 2016

Abstract
Background
Trimming of adapter sequences from short read data is a common preprocessing step during NGS data analysis. When performing paired-end sequencing, the overlap between forward and reverse read can be used to identify excess adapter sequences. This is exploited by several previously published adapter trimming tools. However, our evaluation on amplicon-based data shows that most of the current tools are not able to remove all adapter sequences and that adapter contamination may even lead to spurious variant calls.

Results
Here we present SeqPurge (https://github.com/imgag/ngs-bits), a highly-sensitive adapter trimmer that uses a probabilistic approach to detect the overlap between forward and reverse reads of Illumina sequencing data. SeqPurge can detect very short adapter sequences, even if only one base long. Compared to other adapter trimmers specifically designed for paired-end data, we found that SeqPurge achieves a higher sensitivity. The number of remaining adapter bases after trimming is reduced by up to 90 %, depending on the compared tool. In simulations with different error rates, we found that SeqPurge is also the most error-tolerant adapter trimmer in the comparison.

Conclusion
SeqPurge achieves a very high sensitivity and a high error-tolerance, combined with a specificity and runtime that are comparable to other state-of-the-art adapter trimmers. The very good adapter trimming performance, complemented with additional features such as quality-based trimming and basic quality control, makes SeqPurge an excellent choice for the pre-processing of paired-end NGS data.