bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors
Authors: Lukeš Tomáš , Pospíšil Jakub , Fliegel Karel , Lasser Theo , Hagen Guy M 
Published: January 2018

Abstract

Background
Super-resolution single molecule localization microscopy (SMLM) is a method for achieving resolution beyond the classical limit in optical microscopes (approx. 200 nm laterally). Yellow fluorescent protein (YFP) has been used for super-resolution single molecule localization microscopy, but less frequently than other fluorescent probes. Working with YFP in SMLM is a challenge because a lower number of photons are emitted per molecule compared with organic dyes, which are more commonly used. Publically available experimental data can facilitate development of new data analysis algorithms.

Findings
Four complete, freely available single molecule super-resolution microscopy datasets on YFP-tagged growth factor receptors expressed in a human cell line are presented, including both raw and analyzed data. We report methods for sample preparation, for data acquisition, and for data analysis, as well as examples of the acquired images. We also analyzed the SMLM datasets using a different method: super-resolution optical fluctuation imaging (SOFI). The 2 modes of analysis offer complementary information about the sample. A fifth single molecule super-resolution microscopy dataset acquired with the dye Alexa 532 is included for comparison purposes.

Conclusions
This dataset has potential for extensive reuse. Complete raw data from SMLM experiments have typically not been published. The YFP data exhibit low signal-to-noise ratios, making data analysis a challenge. These datasets will be useful to investigators developing their own algorithms for SMLM, SOFI, and related methods. The data will also be useful for researchers investigating growth factor receptors such as ErbB3.
Successful Hand Replantation in a Case of Total Avulsion without Vein Graft
Authors: Sulaiman Shatha M. , Alkhodair Abdulmalik A. , Sulaiman Shahd M. , Sulaiman Lama M. , Elkafafy Ahmed S. 
Published: January 2018

Summary:
Replantation is the reattachment of a severed body part, with attempts to restore neurovascular and musculoskeletal integrity, function, and aesthetics. On September 7, 1964, the first extremity replantation—a completely amputated hand—by vascular anastomosis technique was successfully performed.
1
Soon after, the first replantation of a complete thumb amputation using microvascular anastomosis in a human was successfully conducted by Komatsu et al.
2
in 1968. The overall success rate of limb replantation surgery is around 83.2%.
3
The mechanism of injury plays a role in the outcome; guillotine amputations—for example—carry a better prognosis than crush amputations.
4
We present a case report of a 36-year-old male patient who presented with a total avulsion of the right hand with multiple fracture levels at the level of trans-carpal, distal radius extra-articulation fracture, and total avulsion of the hand. The patient was managed by a multidisciplinary team who were able to reattach his hand successfully with good functional outcome.
Statewide Inferior Vena Cava Filter Placement, Complications, and Retrievals
Authors: Charalel Resmi A. , Durack Jeremy C. , Mao Jialin , Ross Joseph S. , Meltzer Andrew J. , Sedrakyan Art 
Published: January 2018

Background:
Public awareness of inferior vena cava (IVC) filter-related controversies has been elevated by the Food and Drug Administration (FDA) safety communication in 2010.

Objectives:
To examine population level trends in IVC filter utilization, complications, retrieval rates, and subsequent pulmonary embolism (PE) risk.

Design:
A retrospective cohort study.

Subjects:
Patients receiving IVC filters during 2005–2014 in New York State.

Measures:
IVC filter-specific complications, new PE occurrences and IVC filter retrievals were evaluated as time-to-event data using Kaplan-Meier analysis. Estimated cumulative risks were obtained at various timepoints during follow-up.

Results:
There were 91,873 patients receiving IVC filters between 2005 and 2014 in New York State included in the study. The average patient age was 67 years and 46.6% were male. Age-adjusted rates of IVC filter placement increased from 48 cases/100,000 in 2005 to 52 cases/100,000 in 2009, and decreased afterwards to 36 cases/100,000 in 2014. The estimated risks of having an IVC filter-related complication and filter retrieval within 1 year was 1.5% [95% confidence interval (CI), 1.4%–1.6%] and 3.5% (95% CI, 3.4%–3.6%). One-year retrieval rate was higher post-2010 when compared with pre-2010 years (hazard ratio, 2.70; 95% CI, 2.50–2.91). Among the 58,176 patients who did not have PE events before or at the time of IVC filter placement, the estimated risk of developing subsequent PE at 1 year was 2.0% (95% CI, 1.9%–2.1%).

Conclusions:
Our findings suggest that FDA communications may be effective in modifying statewide clinical practices. Given the 2% observed PE rate following prophylactic IVC filter placement, large scale pragmatic studies are needed to determine contemporary safety and effectiveness of IVC filters.
Trends in Accreditation Council for Graduate Medical Education Accreditation for Subspecialty Fellowship Training in Plastic Surgery
Authors: Silvestre Jason , Serletti Joseph M. , Chang Benjamin 
Published: January 2018

Background:
The purposes of this study were to (1) determine the proportion of plastic surgery residents pursuing subspecialty training relative to other surgical specialties, and (2) analyze trends in Accreditation Council for Graduate Medical Education accreditation of plastic surgery subspecialty fellowship programs.

Methods:
The American Medical Association provided data on career intentions of surgical chief residents graduating from 2014 to 2016. The percentage of residents pursuing fellowship training was compared by specialty. Trends in the proportion of accredited fellowship programs in craniofacial surgery, hand surgery, and microsurgery were analyzed. The percentage of accredited programs was compared between subspecialties with added-certification options (hand surgery) and subspecialties without added-certification options (craniofacial surgery and microsurgery).

Results:
Most integrated and independent plastic surgery residents pursued fellowship training (61.8 percent versus 49.6 percent; p = 0.014). Differences existed by specialty from a high in orthopedic surgery (90.8 percent) to a low in colon and rectal surgery (3.2 percent). From 2005 to 2015, the percentage of accredited craniofacial fellowship programs increased, but was not significant (from 27.8 percent to 33.3 percent; p = 0.386). For hand surgery, the proportion of accredited programs that were plastic surgery (p = 0.755) and orthopedic surgery (p = 0.253) was stable, whereas general surgery decreased (p = 0.010). Subspecialty areas with added-certification options had more accredited fellowships than those without (100 percent versus 19.2 percent; p < 0.001).

Conclusion:
There has been slow adoption of accreditation among plastic surgery subspecialty fellowships, but added-certification options appear to be highly correlated.
Quantitative Trait Loci ControllingPhytophthora cactorumResistance in the Cultivated Octoploid Strawberry (Fragariaxananassa)
Authors: Nellist Charlotte F. , Vickerstaff Robert J. , Sobczyk Maria K. , Marina-Montes César , Brain Philip , Wilson Fiona M. , Simpson David W. , Whitehouse Adam B. , Harrison Richard J. 
Published: January 2018

ABSTRACTThe cultivated strawberry,Fragaria x ananassa(Fragariaspp.) is the most economically important global soft fruit.Phytophthora cactorum, a water-borne oomycete causes economic losses in strawberry production globally. A bi-parental cross of octoploid cultivated strawberry segregating for resistance toP. cactorum, the causative agent of crown rot disease, was screened using artificial inoculation. Multiple resistance quantitative trait loci (QTL) were identified and mapped. Three major effect QTL (FaRPc6C,FaRPc6DandFaRPc7D) explained 36% of the variation observed and in total, the detected QTL explained 86% of the variation observed. There were no epistatic interactions detected between the three major QTLs. Testing a subset of the mapping population progeny against a range ofP. cactorumisolates revealed no major differences in host response, however, some lines showed higher susceptibility than predicted, indicating that additional undetected factors may affect the expression of some quantitative resistance loci. Using historic crown rot disease score data from strawberry accessions, a preliminary genome-wide association study of 114 individuals revealed additional loci associated with resistance toP. cactorum. Mining ofFragaria vescaHawaii 4 v1.1 genome revealed candidate resistance genes in the QTL regions.
In vivomonitoring of plant small GTPase activation using a Förster resonance energy transfer biosensor
Authors: Wong Hann Ling , Akamatsu Akira , Wang Qiong , Higuchi Masayuki , Matsuda Tomonori , Okuda Jun , Kosami Ken-ichi , Inada Noriko , Kawasaki Tsutomu , Nagawa Shingo , Tan Li , Kawano Yoji , Shimamoto Ko 
Published: January 2018

ABSTRACTSmall GTPases act as molecular switches that regulate various plant responses such as disease resistance, pollen tube growth, root hair development, cell wall patterning and hormone responses. Thus, to monitor their activation status within plant cells is believed to be the key step in understanding their roles. We have established a plant version of a Förster resonance energy transfer (FRET) probe called Ras and interacting protein chimeric unit (Raichu) that can successfully monitor activation of the rice small GTPase OsRac1 during various defence responses in rice cells. Here, we describe the protocol for visualizing spatiotemporal activity of plant Rac/ROP GTPase in living plant cells, transfection of rice protoplasts withRaichu-OsRac1and acquisition of FRET images. Our protocol should be widely adaptable for monitoring activation for other plant small GTPases and for other FRET sensors in various plant cells.
HCAtk and pyHCA: A Toolkit and Python API for the Hydrophobic Cluster Analysis of Protein Sequences
Authors: Bitard-Feildel Tristan , Callebaut Isabelle 
Published: January 2018

AbstractMotivation: Detecting protein domains sharing no similarity to known domains, as stored in domain databases, is a challenging problem, particularly for unannotated proteomes, domains emerged recently, fast diverging proteins or domains with intrinsically disordered regions.Results: We developed pyHCA and HCAtk, a python API and standalone tool gathering together improved versions of previously developed methodologies, with new functionalities. The developed tools can be either used from command line or from a python API.Availability: HCAtk and pyHCA are available at https://github.com/T-B-F/pyHCA under the CeCILL-C license.
A hybrid global optimization method based on multiple metamodels
Authors: Cai Xiwen , Qiu Haobo , Gao Liang , Li Xiaoke , Shao Xinyu 
Published: January 2018

Purpose
This paper aims to propose hybrid global optimization based on multiple metamodels for improving the efficiency of global optimization.

Design/methodology/approach
The method has fully utilized the information provided by different metamodels in the optimization process. It not only imparts the expected improvement criterion of kriging into other metamodels but also intelligently selects appropriate metamodeling techniques to guide the search direction, thus making the search process very efficient. Besides, the corresponding local search strategies are also put forward to further improve the optimizing efficiency.

Findings
To validate the method, it is tested by several numerical benchmark problems and applied in two engineering design optimization problems. Moreover, an overall comparison between the proposed method and several other typical global optimization methods has been made. Results show that the global optimization efficiency of the proposed method is higher than that of the other methods for most situations.

Originality/value
The proposed method sufficiently utilizes multiple metamodels in the optimizing process. Thus, good optimizing results are obtained, showing great applicability in engineering design optimization problems which involve costly simulations.
RANS-based design optimization of dual-rotor wind turbines
Authors: Thelen Andrew , Leifsson Leifur , Sharma Anupam , Koziel Slawomir 
Published: January 2018

Purpose
An improvement in the energy efficiency of wind turbines can be achieved using dual rotors. Because of complex flow physics, the design of dual-rotor wind turbines (DRWTs) requires repetitive evaluations of computationally expensive partial differential equation (PDE) simulation models. Approaches for solving design optimization of DRWTs constrained by PDE simulations are investigated. The purpose of this study is to determine design optimization algorithms which can find optimal designs at a low computational cost.

Design/methodology/approach
Several optimization approaches and algorithms are compared and contrasted for the design of DRWTs. More specifically, parametric sweeps, direct optimization using pattern search, surrogate-based optimization (SBO) using approximation-based models and SBO using kriging interpolation models with infill criteria are investigated for the DRWT design problem.

Findings
The approaches are applied to two example design cases where the DRWT fluid flow is simulated using the Reynolds-averaged Navier−Stokes (RANS) equations with a two-equation turbulence model on an axisymmetric computational grid. The main rotor geometry is kept fixed and the secondary rotor characteristics, using up to three variables, are optimized. The results show that the automated numerical optimization techniques were able to accurately find the optimal designs at a low cost. In particular, SBO algorithm with infill criteria configured for design space exploitation required the least computational cost. The widely adopted parametric sweep approach required more model evaluations than the optimization algorithms, as well as not being able to accurately find the optimal designs.

Originality/value
For low-dimensional PDE-constrained design of DRWTs, automated optimization algorithms are essential to find accurately and efficiently the optimal designs. More specifically, surrogate-based approaches seem to offer a computationally efficient way of solving such problems.
A multi-block finite difference method for seismic wave equation in auxiliary coordinate system with irregular fluid–solid interface
Authors: Huang Jianping , Liao Wenyuan , Li Zhenchun 
Published: January 2018

Purpose
The purpose of this paper is to develop a new finite difference method for solving the seismic wave propagation in fluid-solid media, which can be described by the acoustic and viscoelastic wave equations for the fluid and solid parts, respectively.

Design/methodology/approach
In this paper, the authors introduced a coordinate transformation method for seismic wave simulation method. In the new method, the irregular fluid–solid interface is transformed into a horizontal interface. Then, a multi-block coordinate transformation method is proposed to mesh every layer to curved grids and transforms every interface to horizontal interface. Meanwhile, a variable grid size is used in different regions according to the shape and the velocity within each region. Finally, a Lebedev-standard staggered coupled grid scheme for curved grids is applied in the multi-block coordinate transformation method to reduce the computational cost.

Findings
The instability in the auxiliary coordinate system caused by the standard staggered grid scheme is resolved using a curved grid viscoelastic wave field separation strategy. Several numerical examples are solved using this new method. It has been shown that the new method is stable, efficient and highly accurate in solving the seismic wave equation defined on domain with irregular fluid–solid interface.

Originality/value
First, the irregular fluid–solid interface is transformed into a horizontal interface by using the coordinate transformation method. The conversion between pressures and stresses is easy to implement and adaptive to different irregular fluid–solid interface models, because the normal stress and shear stress vanish when the normal angle is 90° in the interface. Moreover, in the new method, the strong false artificial boundary reflection and instability caused by ladder-shaped grid discretion are resolved as well.
Evaluating quality of the didactics at university: the opportunities offered by latent class modeling
Authors: Bassi Francesca , Clerici Renata , Aquario Debora 
Published: January 2018

Purpose
Students’ evaluation of teaching quality plays a major role in higher education. Satisfaction is not directly observable, nevertheless it can be measured through multi-item measurement scales. These instruments are extremely useful and their importance requires accurate development and validation procedures. The purpose of this paper is to show how latent class (LC) analysis can improve the procedures for developing and validating a multi-item measurement scale for measuring students’ evaluation of teaching and, at the same time, provide a deeper insight in the phenomenon under investigation.

Design/methodology/approach
The traditional literature highlights specific protocols along with the statistical instruments to be used for achieving this goal. However, these tools are suited for metric variables but they are adopted even when the nature of the observed variables is different, as it often occurs, since in many cases the items are ordinal. LC analysis takes explicitly into account the ordinal nature of the variables and also the fact that the object of interest is unobservable.

Findings
The data refer to the questionnaire to evaluate didactics to the students of the University of Padua. Within LC analysis allows an insight of scale properties, such as dimensionality, validity and reliability. Moreover, the results provide a deeper view in the way students use the scale to report satisfaction suggesting to revise the instrument according to the suggestion by the National Agency for University Evaluation.

Originality/value
The paper gives an original contribution on two sides. On the side of methods, it introduces a more accurate methodology for evaluating scales to measure the students’ satisfaction. On the side of applications, it provides important suggestions to the university management to improve the process of quality of the didactics evaluation.
Speech and language therapists’ perspectives of therapeutic alliance construction and maintenance in aphasia rehabilitation post‐stroke
Authors: Lawton Michelle , Sage Karen , Haddock Gillian , Conroy Paul , Serrant Laura 
Published: January 2018

AbstractBackgroundTherapeutic alliance refers to the interactional and relational processes operating during therapeutic interventions. It has been shown to be a strong determinant of treatment efficacy in psychotherapy, and evidence is emerging from a range of healthcare and medical disciplines to suggest that the construct of therapeutic alliance may in fact be a variable component of treatment outcome, engagement and satisfaction. Although this construct appears to be highly relevant to aphasia rehabilitation, no research to date has attempted to explore this phenomenon and thus consider its potential utility as a mechanism for change.AimsTo explore speech and language therapists’ perceptions and experiences of developing and maintaining therapeutic alliances in aphasia rehabilitation post‐stroke.Methods & ProceduresTwenty‐two, in‐depth, semi‐structured interviews were conducted with speech and language therapists working with people with aphasia post‐stroke. Qualitative data were analysed using inductive thematic analysis.Outcomes & ResultsAnalysis resulted in the emergence of three overarching themes: laying the groundwork; augmenting cohesion; and contextual shapers. Recognizing personhood, developing shared expectations of therapy and establishing therapeutic ownership were central to laying the groundwork for therapeutic delivery. Augmenting cohesion was perceived to be dependent on the therapists’ responsiveness and ability to resolve both conflict and resistance, as part of an ongoing active process. These processes were further moulded by contextual shapers such as the patient's family, relational continuity and organizational drivers.Conclusions & ImplicationsThe findings suggest that therapists used multiple, complex, relational strategies to establish and manage alliances with people with aphasia, which were reliant on a fluid interplay of verbal and non‐verbal skills. The data highlight the need for further training to support therapists to forge purposive alliances. Training should develop: therapeutic reflexivity; inclusivity in goal setting, relational strategies; and motivational enhancement techniques. The conceptualization of therapeutic alliance, however, is only provisional. Further research is essential to elucidate the experiences and perceptions of alliance development for people with aphasia undergoing rehabilitation.
CEO Duality, Agency Costs, and Internal Capital Allocation Efficiency
Authors: Aktas Nihat , Andreou Panayiotis C. , Karasamani Isabella , Philip Dennis 
Published: January 2018

AbstractThis study examines the impact of CEO duality on firms’ internal capital allocation efficiency. We observe that when the CEO is also chair of the board, diversified firms make inefficient investments, as they allocate more capital to business segments with relatively low growth opportunities over segments with high growth opportunities. The adverse impact of CEO duality on investment efficiency prevails only among firms that face high agency problems, as captured by high free cash flows, staggered board structure and low board independence. Depending on the severity of the agency problem, CEO duality is associated with a decrease in industry‐adjusted investment in high‐growth segments of 1% to 2.1% over the following year, relative to that in low‐growth segments. However, CEOs’ equity‐based compensation curbs the negative effect of CEO duality on internal capital allocation efficiency. Overall, the findings of this study offer strong support for the agency theory and postulate the internal capital allocation policy as an important channel through which CEO duality lowers firm value in diversified firms.
Analysis of the Effect of Cyclophosphamide and Methotrexate on Chrysomya megacephala (Diptera: Calliphoridae),
Authors: Trivia Ana Letícia , de Carvalho Pinto Carlos José 
Published: January 2018

AbstractForensic entomotoxicology investigates the effects of chemical substances in the development of scavenger insects and the reflection on estimating the minimum postmortem interval (PMI). To evaluate the impact of the chemotherapeutic drugs cyclophosphamide (CF) and methotrexate (MTX) on the postembryonic development of Chrysomya megacephala, controlled experiments were performed by rearing the larvae on spiked minced beef with different concentrations of these drugs. The results indicated that CF significantly decreased their developmental rate up to 28 h but had no significant effect on larval and adult sizes, survival rate, and sex ratio, whereas MTX decreased larval and adult sizes, survival rate, and there was a deviation in the expected sex ratio toward females in MTX‐exposed larvae but had no significant impact on developmental rate. These negative interference factors should be considered in cases of suspected death of people that have undergone chemotherapy.