bluuebunny/crossref_metadata_2025 huggingface dataset:
Lag Penalized Weighted Correlation for Time Series Clustering
Authors: Chandereng Thevaa , Gitter Anthony
Published: March 2018

Motivation

The similarity or distance measure used for clustering can generate intuitive and interpretable clusters when it is tailored to the unique characteristics of the data. In time series datasets, measurements such as gene expression levels or protein phosphorylation intensities are collected sequentially over time, and the similarity score should capture this special temporal structure.

Results

We propose a clustering similarity measure called Lag Penalized Weighted Correlation (LPWC) to group pairs of time series that exhibit closely-related behaviors over time, even if the timing is not perfectly synchronized. LPWC aligns pairs of time series profiles to identify common temporal patterns. It down-weights aligned profiles based on the length of the temporal lags that are introduced. We demonstrate the advantages of LPWC versus existing time series and general clustering algorithms. In a simulated dataset based on the biologically-motivated impulse model, LPWC is the only method to recover the true clusters for almost all simulated genes. LPWC also identifies distinct temporal patterns in our yeast osmotic stress response and axolotl limb regeneration case studies.

Availability

The LPWC R package is available at https://github.com/gitter-lab/LPWC and CRAN under a MIT license.

Contact

chandereng@wisc.edu or gitter@biostat.wisc.edu

Supplementary information

Supplementary files are available online.
Functional genomics identifies AMPD2 as a new prognostic marker for undifferentiated pleomorphic sarcoma
Authors: Orth Martin F. , Gerke Julia S. , Knösel Thomas , Altendorf-Hofmann Annelore , Musa Julian , Alba Rubio Rebeca , Stein Stefanie , Dallmayer Marlene , Baldauf Michaela C. , Marchetto Aruna , Sannino Giuseppina , Ohmura Shunya , Li Jing , Hakozaki Michiyuki , Kirchner Thomas , Dandekar Thomas , Butt Elke , Grünewald Thomas G. P.
Published: March 2018

Soft-tissue sarcomas are rare, heterogeneous and often aggressive mesenchymal cancers. Many of them are associated with poor outcome, in part because biomarkers that can reliably identify high-risk patients are lacking. Studies on sarcomas often are limited by small sample sizes rendering the identification of novel biomarkers difficult when focusing only on individual cohorts. However, the increasing number of publicly available ‘omics’ data opens inroads to overcome this obstacle.

Here, we combine high-throughput transcriptome analyses, immunohistochemistry, and functional assays to show that high adenosine monophosphate deaminase 2 (AMPD2) is a robust prognostic biomarker for worse patient outcome in undifferentiated pleomorphic sarcoma (UPS). Publicly available gene expression and survival data for UPS from two independent studies, The Cancer Genome Atlas (TCGA) and the CINSARC reference dataset, were subjected to survival association testing. Genes, whose high expression was significantly correlated with worse outcome in both cohorts (overall and metastasis-free survival), were considered as prognostic marker candidates. The best candidate, AMPD2, was validated on protein level in an independent tissue microarray. Analysis of DNA copy-number and matched gene expression data indicated that high AMPD2 expression is significantly correlated with copy-number gains at the AMPD2 locus. Gene-set enrichment analyses of AMPD2 co-expressed genes in both UPS gene expression datasets suggested that highly AMPD2 expressing tumors are enriched in gene signatures involved in tumorigenesis. Consistent with this prediction in primary tumors, knockdown of AMPD2 by RNA interference with pooled siRNAs or a doxycycline-inducible shRNA construct in the UPS cell line FPS-1 markedly inhibited proliferation in vitro and tumorigenicity in vivo.

Collectively, these results provide evidence that AMPD2 may serve as a novel biomarker for outcome prediction in UPS. Our study exemplifies how the integration of available ‘omics’ data, immunohistochemical analyses, and functional experiments can identify novel biomarkers even in a rare sarcoma, which may serve as a blueprint for biomarker identification for other rare cancers.
Visual physiology of the Layer 4 cortical circuitin silico
Authors: Arkhipov Anton , Gouwens Nathan W. , Billeh Yazan N. , Gratiy Sergey , Iyer Ramakrishnan , Wei Ziqiang , Xu Zihao , Berg Jim , Buice Michael , Cain Nicholas , da Costa Nuno , de Vries Saskia , Denman Daniel , Durand Severine , Feng David , Jarsky Tim , Lecoq Jerome , Lee Brian , Li Lu , Mihalas Stefan , Ocker Gabriel K. , Olsen Shawn R. , Reid R. Clay , Soler-Llavina Gilberto , Sorensen Staci A. , Wang Quanxin , Waters Jack , Scanziani Massimo , Koch Christof
Published: March 2018

Despite advances in experimental techniques and accumulation of large datasets concerning the composition and properties of the cortex, quantitative modeling of cortical circuits under in-vivo-like conditions remains challenging. Here we report and publicly release a biophysically detailed circuit model of layer 4 in the mouse primary visual cortex, receiving thalamo-cortical visual inputs. The 45,000-neuron model was subjected to a battery of visual stimuli, and results were compared to published work and new in vivo experiments. Simulations reproduced a variety of observations, including effects of optogenetic perturbations. Critical to the agreement between responses in silico and in vivo were the rules of functional synaptic connectivity between neurons. Interestingly, after extreme simplification the model still performed satisfactorily on many measurements, although quantitative agreement with experiments suffered. These results emphasize the importance of functional rules of cortical wiring and enable a next generation of data-driven models of in vivo neural activity and computations.

AUTHOR SUMMARY

How can we capture the incredible complexity of brain circuits in quantitative models, and what can such models teach us about mechanisms underlying brain activity? To answer these questions, we set out to build extensive, bio-realistic models of brain circuitry employing systematic datasets on brain structure and function. Here we report the first modeling results of this project, focusing on the layer 4 of the primary visual cortex (V1) of the mouse. Our simulations reproduced a variety of experimental observations in a large battery of visual stimuli. The results elucidated circuit mechanisms determining patters of neuronal activity in layer 4 – in particular, the roles of feedforward thalamic inputs and specific patterns of intracortical connectivity in producing tuning of neuronal responses to the orientation of motion. Simplification of neuronal models led to specific deficiencies in reproducing experimental data, giving insights into how biological details contribute to various aspects of brain activity. To enable future development of more sophisticated models, we make the software code, the model, and simulation results publicly available.
iTOP: Inferring the Topology of Omics Data
Authors: Aben Nanne , Westerhuis Johan A. , Song Yipeng , Kiers Henk A.L. , Michaut Magali , Smilde Age K. , Wessels Lodewyk F.A.
Published: April 2018

Motivation

In biology, we are often faced with multiple datasets recorded on the same set of objects, such as multi-omics and phenotypic data of the same tumors. These datasets are typically not independent from each other. For example, methylation may influence gene expression, which may, in turn, influence drug response. Such relationships can strongly affect analyses performed on the data, as we have previously shown for the identification of biomarkers of drug response. Therefore, it is important to be able to chart the relationships between datasets.

Results

We present iTOP, a methodology to infera topology of relationships between datasets. We base this methodology on the RV coefficient, a measure of matrix correlation, which can be used to determine how much information is shared between two datasets. We extended the RV coefficient for partial matrix correlations, which allows the use of graph reconstruction algorithms, such as the PC algorithm, to infer the topologies. In addition, since multi-omics data often contain binary data (e.g. mutations), we also extended the RV coefficient for binary data. Applying iTOP to pharmacogenomics data, we found that gene expression acts as a mediator between most other datasets and drug response: only proteomics clearly shares information with drug response that is not present in gene expression. Based on this result, we used TANDEM, a method for drug response prediction, to identify which variables predictive of drug response were distinct to either gene expression or proteomics.

Availability

An implementation of our methodology is available in the R package iTOP on CRAN. Additionally, an R Markdown document with code to reproduce all figures is provided as Supplementary Material.

Contact

a.k.smilde@uva.nl and l.wessels@nki.nl

Supplementary information

Supplementary data are available at Bioinformatics online.
Benchmarking New CEASIOM with CPACS adoption for aerodynamic analysis and flight simulation
Authors: Jungo Aidan , Zhang Mengmeng , Vos Jan B. , Rizzi Arthur
Published: April 2018

Purpose

The purpose of this paper is to present the status of the on-going development of the new computerized environment for aircraft synthesis and integrated optimization methods (CEASIOM) and to compare results of different aerodynamic tools. The concurrent design of aircraft is an extremely interdisciplinary activity incorporating simultaneous consideration of complex, tightly coupled systems, functions and requirements. The design task is to achieve an optimal integration of all components into an efficient, robust and reliable aircraft with high performance that can be manufactured with low technical and financial risks, and has an affordable life-cycle cost.

Design/methodology/approach

CEASIOM (www.ceasiom.com) is a framework that integrates discipline-specific tools like computer-aided design, mesh generation, computational fluid dynamics (CFD), stability and control analysis and structural analysis, all for the purpose of aircraft conceptual design.

Findings

A new CEASIOM version is under development within EU Project AGILE (www.agile-project.eu), by adopting the CPACS XML data-format for representation of all design data pertaining to the aircraft under development.

Research limitations/implications

Results obtained from different methods have been compared and analyzed. Some differences have been observed; however, they are mainly due to the different physical modelizations that are used by each of these methods.

Originality/value

This paper summarizes the current status of the development of the new CEASIOM software, in particular for the following modules: CPACS file visualizer and editor CPACSupdater (Matlab) Automatic unstructured (Euler) & hybrid (RANS) mesh generation by sumo Multi-fidelity CFD solvers: Digital Datcom (Empirical), Tornado (VLM), Edge-Euler & SU2-Euler, Edge-RANS & SU2-RANS Data fusion tool: aerodynamic coefficients fusion from variable fidelity CFD tools above to compile complete aero-table for flight analysis and simulation.
Team learning behaviours and innovative work behaviour in work teams
Authors: Widmann Andreas , Mulder Regina H.
Published: April 2018

Purpose

The purpose of this paper is to get deeper insight into the complex nature of the relationship between team learning conditions, team learning behaviours (TLBs) and innovative work behaviour (IWB) by considering and combining different neglected aspects in research.

Design/methodology/approach

A questionnaire was filled out by 593 vocational educators of 117 interdisciplinary work teams in vocational colleges in Germany. Correlations were calculated and structural equation modelling at two levels was conducted.

Findings

The results indicate that TLBs, especially team reflexivity and boundary spanning, relate positively to IWB. Furthermore, team structure, task interdependence and group potency relate positively to TLBs. It means that TLBs can be fostered by establishing these team learning conditions and, thus, IWB can be fostered.

Research limitations/implications

The main limitation of the study is that the data collection was cross-sectional. Longitudinal studies are required to capture the dynamic character of team learning and to identify causal relationships.

Practical implications

It is important to make all employees in vocational education aware of the importance of TLBs especially of team reflexivity and boundary spanning.

Originality/value

This study provides practical implications for organisations to foster IWB and indications for a better understanding of the relationship between team learning conditions, TLBs and IWB considering and combining different neglected aspects such as examining TLBs separated in one study.
Integrated work-based placements – shifting the paradigm
Authors: Smith Sara
Published: April 2018

Purpose

The role of higher education institutions in enhancing capability development of the healthcare professionals workforce has resulted in work-based learning becoming an essential component of awards linked to professional registration. The purpose of this paper is to explore how key stakeholders (academics, workplace tutors and students) on a programme leading to registration as a Biomedical Scientist (BMS) position themselves in their role and the subsequent impact of this upon delivery of pre-registration training and the development of professional capability.

Design/methodology/approach

Constructivist grounded theory methodology and a mixed-methods approach were drawn upon for the study.

Findings

Findings expose the challenges of a positivist focus and assumptions around workplace learning and professional development presenting a barrier to developing professional capability. In addressing this barrier, two strategies of “doing the portfolio” and “gaining BMS currency” are adopted. The registration portfolio has become an objective reductionist measure of learning, reflecting the positivist typology of practice in this profession.

Practical implications

To ensure that students are supported to develop not only technical skills but also professional capability there is a need for a paradigm shift from a positivist episteme to one that embraces both the positivist and socio-cultural paradigms, viewing them as complimentary and parallel.

Originality/value

The study provides a novel insight into how stakeholders interact with the pressures of internal and external influences and the impact this has upon behaviours and strategies adopted. The theoretical understanding proposed has a range of implications for practice and for the development of practitioner capability through pre-registration training and beyond.
Gendered patterning of relationships
Authors: Bhatia Bhanu , Salignac Fanny
Published: April 2018

Purpose

Social capital has become a general tool for policy interventions in developing countries – often put forward as empowering and improving women’s socioeconomic position. Using the framework of gendered manifestations of networks in patriarchal setting of Bangladesh, the authors argue that while networks are crucial building blocks of social capital they are bound to manifest differently depending on the context in which they are embedded. The paper aims to discuss this issue.

Design/methodology/approach

By combining methods of social networks and spatial analysis, this study provides insights into the embeddedness of networks in gender norms. The authors conduct the study in the context of reproductive health networks in rural Bangladesh.

Findings

The findings suggest that networks mirror the structure of the society in which they evolve, reproducing rather than challenging disadvantage.

Research limitations/implications

The authors call for a more nuanced view of social capital leading to policy design that is sensitive to different manifestations of networks.

Originality/value

This study is the first to combine novel methods of social networks and spatial analysis to quantify the complex interplay between social networks and gender norms. This study further contributes to the diffusion literature by providing the first comparative view of women’s and men’s reproductive health networks that extend beyond actors’ direct tie.
Public attitudes towards the poor in the South Caucasus: a matter of solidarity and conditionality
Authors: Gugushvili Dimitri
Published: April 2018

Purpose

The purpose of this paper is to explore public attitudes towards poor people in the South Caucasian countries.

Design/methodology/approach

The paper is based on an analysis of data from the tenth round of the Caucasus Barometer survey, one of the most reliable sources of public opinion data in the region.

Findings

The majority of the population in Azerbaijan and Georgia would consent to paying higher taxes or reducing public services if their governments used the extra resources to provide cash assistance to more poor people, but in Armenia the level of solidarity is considerably lower. However, the majority in each of the countries supports assistance being conditional on beneficiaries actively searching for work. In contrast to conventional wisdom, some better-off groups are more in favour of supporting the poor than those who face a higher risk of poverty. The author hypothesises that this may be driven by self-interest, as in relative terms the welfare sacrifices required for financing the extension of schemes might be higher for the vulnerable than for the better-off.

Originality/value

This paper is the first to provide a comparative analysis of public attitudes towards vulnerable groups in the South Caucasus. It also contributes to the scarce literature on perceived welfare deservingness of social assistance recipients and public preferences for imposing conditionality on them. In addition, it presents a strong case for using more comprehensive questions to construct measurements of people’s welfare attitudes than those commonly used.
Formal controls and team adaptability in new product development projects
Authors: Detzen Nina , Verbeeten Frank H.M. , Gamm Nils , Möller Klaus
Published: April 2018

Purpose

The purpose of this paper is to investigate the effects of two formal controls, namely target rigidity and process autonomy, on team adaptability and project success in new product development (NPD) projects. Target rigidity refers to performance goals that are non-negotiable once they have been set. Process autonomy refers to the extent to which a project team is free to choose ways to achieve its goals. Team adaptability is considered a key factor that explains the relationship between formal controls and project success.

Design/methodology/approach

Two separate models related to resource and cost measures are analysed, since different target types may influence managerial perceptions. This study uses data collected from a survey with 113 project managers as respondents.

Findings

The findings show that target rigidity and process autonomy support team adaptability. Furthermore, team adaptability mediates the impact of formal controls on project success. The effects are more pronounced for cost targets as compared to resource targets.

Practical implications

Firms can increase project success by using formal controls in such a way that they allow project managers to provide their teams with motivating guidelines (target rigidity) and discretion (process autonomy) to adapt to new circumstances.

Originality/value

This study reveals the impact of formal controls on NPD project success through team adaptability. A balanced use of target rigidity and process autonomy may help improving NPD project success.
Optimizing the use of topical retinoids in Asian acne patients
Authors: See Jo‐Ann , Goh Chee Leok , Hayashi Nobukazu , Suh Dae Hun , Casintahan Flordeliz Abad
Published: April 2018

Acne vulgaris is a common disease among people in Asia. International guidelines and treatment recommendations emphasize the central role of topical retinoids in the management of acne. However, topical retinoids remain underutilized in clinical practise, which may be in part due to fear of retinoid‐associated dermatitis/lack of experience, particularly in Asian patients. There is a perception that Asian skin has a greater tendency toward sensitivity compared with Caucasian skin. In our clinical experience, topical retinoid therapy can be used with excellent effect to treat Asians with acne. This article discusses available published work regarding the use of topical retinoids in Asian populations, and presents tips for utilizing these important agents in daily practise. Optimizing use of topical retinoids may improve adherence and, in turn, therapeutic outcomes and patient satisfaction.
Thirty‐two Japanese cases of infantile hemangiomas treated with oral propranolol
Authors: Kagami Shinji , Kaneko Masahide , Katori Tatsuo
Published: March 2018

Infantile hemangiomas undergo rapid growth during early infancy followed by gradual involution. Infantile hemangiomas sometimes impair vital functions or cause disfigurement. Thirty‐two Japanese patients between the ages of 1 and 4 months with proliferating infantile hemangiomas received oral propranolol on an outpatient basis. The success rate (complete or nearly complete resolution) at week 25 was 56% (18/32). Two patients dropped out because of a personal reason and moving out. Recurrence after termination of treatment was seen in six patients. Adverse events occurred in 16 patients. There were no adverse events on day 1 (initiation of treatment at a dose of 1 mg/kg per day) and day 8 (dose increase to 2 mg/kg per day). One patient was hospitalized due to pneumonia, and suspended propranolol for 26 days. Oral propranolol at 2 mg/kg per day is effective and safe in Japanese patients with infantile hemangiomas.
Moving from frugivory to seed dispersal: Incorporating the functional outcomes of interactions in plant–frugivore networks
Authors: Simmons Benno I. , Sutherland William J. , Dicks Lynn V. , Albrecht Jörg , Farwig Nina , García Daniel , Jordano Pedro , González‐Varo Juan P.
Published: March 2018

There is growing interest in understanding the functional outcomes of species interactions in ecological networks. For many mutualistic networks, including pollination and seed dispersal networks, interactions are generally sampled by recording animal foraging visits to plants. However, these visits may not reflect actual pollination or seed dispersal events, despite these typically being the ecological processes of interest.

Frugivorous animals can act as seed dispersers, by swallowing entire fruits and dispersing their seeds, or as pulp peckers or seed predators, by pecking fruits to consume pieces of pulp or seeds. These processes have opposing consequences for plant reproductive success. Therefore, equating visitation with seed dispersal could lead to biased inferences about the ecology, evolution and conservation of seed dispersal mutualisms.

Here, we use natural history information on the functional outcomes of pairwise bird–plant interactions to examine changes in the structure of seven European plant–frugivore visitation networks after non‐mutualistic interactions (pulp pecking and seed predation) have been removed. Following existing knowledge of the contrasting structures of mutualistic and antagonistic networks, we hypothesized a number of changes following interaction removal, such as increased nestedness and lower specialization.

Non‐mutualistic interactions with pulp peckers and seed predators occurred in all seven networks, accounting for 21%–48% of all interactions and 6%–24% of total interaction frequency. When non‐mutualistic interactions were removed, there were significant increases in network‐level metrics such as connectance and nestedness, while robustness decreased. These changes were generally small, homogenous and driven by decreases in network size. Conversely, changes in species‐level metrics were more variable and sometimes large, with significant decreases in plant degree, interaction frequency, specialization and resilience to animal extinctions and significant increases in frugivore species strength.

Visitation data can overestimate the actual frequency of seed dispersal services in plant–frugivore networks. We show here that incorporating natural history information on the functions of species interactions can bring us closer to understanding the processes and functions operating in ecological communities. Our categorical approach lays the foundation for future work quantifying functional interaction outcomes along a mutualism–antagonism continuum, as documented in other frugivore faunas.
Enhanced reproductive success revealed key strategy for persistence of devastated populations in Himalayan food‐deceptive orchid, Dactylorhiza hatagirea
Authors: Thakur Dinesh , Rathore Nikita , Sharma Manish K. , Chawla Amit
Published: March 2018

Anthropogenic disturbances adversely affect populations of rare and endemic plants, resulting in reduction of their population size and performance. Among different plant groups, deceptive terrestrial orchids are vulnerable and possess greater extinction risks because of rarity in occurrence. To understand the response of food‐deceptive terrestrial orchids to disturbances, we selected Dactylorhiza hatagirea as our representative species, which is endemic to Himalaya, and studied its natural populations. This species is rare for being habitat specific, pollination limited and threatened in its natural habitats. We tested the hypothesis that disturbances lead to reduction in population size and plant performance of food‐deceptive terrestrial orchids. For assessing the impact of disturbance, two contrasting groups, heavily devastated (HD) and lightly devastated (LD), were identified on the basis of frequency and intensity of disturbance (harvesting of plant for tubers) by interviewing local people, medicinal plant extractors and shepherds. HD sites, in comparison to LD sites, were found to have smaller population sizes, but showed an increase in plant growth traits (plant height, specific leaf area, leaf N and specific shoot length). Similarly, plants at HD sites were found to have invested less in inflorescence (inflorescence size, inflorescence length, inflorescence length fraction and flowers per length), but despite that showed higher reproductive success. This was a clear indication of enhanced performance of its populations driven by disturbances. Our findings suggested that food‐deceptive species in small populations tend to reduce the probability of population extinction and have the capability to recover rapidly if conserved in time.
Mobility closure in the upper class: assessing time and forms of capital
Authors: Toft Maren
Published: March 2018

Most understandings of the ways classes become social groupings centre on processes of mobility closure whereby mutual appreciation and recognition within classes arise from homogenous experiences over time. The mapping of such structured biographies, however, remains understudied. This paper explores intra‐ and intergenerational mobility patterns in the upper strata of the Norwegian class structure and aims to include temporal processes and multiple forms of capital in the quantification of class trajectories. By combining multiple correspondence analysis and social sequence analysis, two important but often neglected aspects of recruitment to the upper class are emphasized: first, by introducing multiple forms of capital, different ways of maintaining mobility closure are demonstrated; second, different pathways to power are highlighted by distinguishing between divergent class careers. A key aim of the analysis is to explore internal divisions within the upper class in forms of parental capital (an ‘origin space’) and link these divisions to a typology of ‘destination careers’ in adulthood. The analysis suggests that individuals from modest origins are more likely to have careers that feature a biographically late arrival and/or short‐term affiliations to upper‐class positions whereas individuals from families rich in capital are more likely to have stable careers in the upper‐class fractions from which they originate. The analysis thus reveals important divisions in the trajectories of Norwegians who reach the upper class; not only are there differences in their upbringing in terms of the availability of different amounts and types of capital but such divisions also seem linked to their own class careers later in adulthood.
Flying solo: Explaining single‐party cabinets under minority presidentialism
Authors: CHAISTY PAUL , POWER TIMOTHY J.
Published: March 2018

In recent years, the comparative literature on presidential democracy has emphasised the role of coalitional politics in attenuating the ‘perils’ facing minority presidents. Yet since the beginning of the Third Wave of democratisation in 1974, a surprising number of minority presidents have eschewed cabinet coalitions (defined minimally as the awarding of at least one portfolio to a party other than the nominal party of the president). Unipartisan governments are observed just under half of the time. What explains the adoption of single‐party cabinets by minority presidents? Cross‐sectional time‐series analysis is employed to address this question. Hypotheses are tested that relate to the size and distribution of the formateur (presidential) and largest non‐formateur parties that make up the legislature; the nature of party linkages and ideological distance between the president and possible partisan allies; and the extent of reactive veto powers held by the president.
Employment inequality among women migrant workers in China: comparative analysis from the 2014 Guangdong Migrant Workers Survey
Authors: An Fansuo , Broadbent Kaye , Yuan Fang
Published: March 2018

Early studies on women migrant workers in China focused largely on thedagongmei,or single young women, and the general poverty of their employment conditions. Recent trends, however, indicate that the number of married women migrant workers, ordagongsao, is increasing. But the paid work experiences of married women migrant workers are largely under‐researched. In order to address this gap, we analyse data from the 2014 Guangdong Migrant Workers Survey (GMWS2014) and focus on workers employed in the formal sector. In comparing the employment conditions of single and married women migrant workers, the findings reveal that the working conditions of married women migrant workers are worse, particularly with respect to pay, social security benefits and the workplace environment. This research makes a significant contribution to the literature on migrant workers in China, and offers a different perspective to the traditional stereotype of women migrant workers.
Assessment of Beer Quality Based on a Robotic Pourer, Computer Vision, and Machine Learning Algorithms Using Commercial Beers
Authors: Gonzalez Viejo Claudia , Fuentes Sigfredo , Torrico Damir D. , Howell Kate , Dunshea Frank R.
Published: March 2018

Sensory attributes of beer are directly linked to perceived foam–related parameters and beer color. The aim of this study was to develop an objective predictive model using machine learning modeling to assess the intensity levels of sensory descriptors in beer using the physical measurements of color and foam‐related parameters. A robotic pourer (RoboBEER), was used to obtain 15 color and foam‐related parameters from 22 different commercial beer samples. A sensory session using quantitative descriptive analysis (QDA®) with trained panelists was conducted to assess the intensity of 10 beer descriptors. Results showed that the principal component analysis explained 64% of data variability with correlations found between foam‐related descriptors from sensory and RoboBEER such as the positive and significant correlation between carbon dioxide and carbonation mouthfeel (R = 0.62), correlation of viscosity to sensory, and maximum volume of foam and total lifetime of foam (R = 0.75, R = 0.77, respectively). Using the RoboBEER parameters as inputs, an artificial neural network (ANN) regression model showed high correlation (R = 0.91) to predict the intensity levels of 10 related sensory descriptors such as yeast, grains and hops aromas, hops flavor, bitter, sour and sweet tastes, viscosity, carbonation, and astringency.

Practical Applications

This paper is a novel approach for food science using machine modeling techniques that could contribute significantly to rapid screenings of food and brewage products for the food industry and the implementation of Artificial Intelligence (AI). The use of RoboBEER to assess beer quality showed to be a reliable, objective, accurate, and less time‐consuming method to predict sensory descriptors compared to trained sensory panels. Hence, this method could be useful as a rapid screening procedure to evaluate beer quality at the end of the production line for industry applications.
Publication rates of abstracts presented at the Royal Australian and New Zealand College of Radiologists annual scientific meetings: Any change since 2004?
Authors: Croker Jeremy D , Bydder Sean A
Published: March 2018

Introduction

The aim of this study was to determine the publication rate of abstracts presented at annual Royal Australian and New Zealand College of Radiologists (RANZCR) conferences.

Methods

The College's Annual Scientific Meetings (ASMs) from 2010 to 2013 were examined, with the goal of comparing these results to the findings of an earlier identical study that examined RANZCR ASMs from 1996 to 1999.

Results

Of the 1152 research abstracts presented, 468 (41%) had been published as full articles. The overall abstract to publication ratio (APR) for radiology was 34% and for radiation oncology was 57%. For oral presentations, these were 44% for radiology and 55% for radiation oncology. Papers were published in a wide variety of journals but 23% of articles appeared in the College's journal, the Journal of Medical Imaging and Radiation Oncology. The mean time between presentation and publication was 16.5 months (median 17 months).

Conclusion

Publication rates are comparable with international reports. The APR has increased since the previous study for both disciplines, but more so for Radiation Oncology.
Outcome and predictors of renal survival in patients with lupus nephritis: Comparison between cyclophosphamide and mycophenolate mofetil
Authors: Joo Young Bin , Kang Young Mo , Kim Hyoun‐Ah , Suh Chang‐Hee , Kim Tae‐Jong , Park Yong‐Wook , Lee Jisoo , Lee Joo‐Hyun , Yoo Dae Hyun , Bae Sang‐Cheol , Lee Hye‐Soon , Bang So‐Young
Published: April 2018

Aim

To compare renal outcomes between cyclophosphamide (CYC) and mycophenolate mofetil (MMF), and attempt to identify a predictor of renal survival.

Methods

A total of 99 patients with class III–V lupus nephritis (LN) and treated with CYC or MMF were enrolled. The remission rate and predictors of poor renal outcomes in LN were assessed.

Results

The mean age at LN diagnosis was 31.7 years. The baseline characteristics of the two groups were similar except for the chronicity index (3.1 ± 2.4 and 2.3 ± 0.8 for CYC and MMF, respectively, P = 0.007). The overall remission rate was 76.8% and 77.7% after 6 and 12 months, respectively, with no significant difference between the two groups at these time points. After a median follow‐up of 36 months (interquartile range 12–60), eight (8.1%) patients had chronic kidney disease, four (4.1%) were dialyzed permanently, and seven (7.1%) suffered a relapse, with no significant difference in these final outcomes between the two groups. Adverse events included infection (CYC group), and rash and neutropenia (MMF group), with no significant difference in frequency between the two groups. Failure of induction therapy (hazards ratio [HR] = 10.626, P = 0.022) and the creatinine level at diagnosis of LN (HR = 8.397, P = 0.007) were significantly associated with renal survival adjusted for age at LN diagnosis, disease duration and proteinuria.

Conclusion

Response to current induction therapy for LN was favorable, and 6 months response following induction therapy was the most important predictor for renal survival.
Vascular smooth muscle cells direct extracellular dysregulation in aortic stiffening of hypertensive rats
Authors: Hays Tristan T. , Ma Ben , Zhou Ning , Stoll Shaunrick , Pearce William J. , Qiu Hongyu
Published: March 2018

Aortic stiffening is an independent risk factor that underlies cardiovascular morbidity in the elderly. We have previously shown that intrinsic mechanical properties of vascular smooth muscle cells (VSMCs) play a key role in aortic stiffening in both aging and hypertension. Here, we test the hypothesis that VSMCs also contribute to aortic stiffening through their extracellular effects. Aortic stiffening was confirmed in spontaneously hypertensive rats (SHRs) vs. Wistar‐Kyoto (WKY) rats in vivo by echocardiography and ex vivo by isometric force measurements in isolated de‐endothelized aortic vessel segments. Vascular smooth muscle cells were isolated from thoracic aorta and embedded in a collagen I matrix in an in vitro 3D model to form reconstituted vessels. Reconstituted vessel segments made with SHR VSMCs were significantly stiffer than vessels made with WKY VSMCs. SHR VSMCs in the reconstituted vessels exhibited different morphologies and diminished adaptability to stretch compared to WKY VSMCs, implying dual effects on both static and dynamic stiffness. SHR VSMCs increased the synthesis of collagen and induced collagen fibril disorganization in reconstituted vessels. Mechanistically, compared to WKY VSMCs, SHR VSMCs exhibited an increase in the levels of active integrin β1‐ and bone morphogenetic protein 1 (BMP1)‐mediated proteolytic cleavage of lysyl oxidase (LOX). These VSMC‐induced alterations in the SHR were attenuated by an inhibitor of serum response factor (SRF)/myocardin. Therefore, SHR VSMCs exhibit extracellular dysregulation through modulating integrin β1 and BMP1/LOX via SRF/myocardin signaling in aortic stiffening.
Differences in the placebo response in duloxetine and venlafaxine trials
Authors: Breilmann J. , Furukawa T. A. , Becker T. , Koesters M.
Published: March 2018

Objective

Our analysis aimed at comparing the placebo effect sizes from randomized controlled trials (RCTs) of two widely prescribed antidepressants, namely duloxetine and venlafaxine, and at analysing a potential influence of the investigated drugs on the placebo response.

Method

We conducted a comprehensive systematic review and meta‐analysis of placebo‐controlled, double‐blind RCTs, which examined the efficacy of duloxetine and venlafaxine in the acute treatment of major depressive disorder.

Results

We included 71 studies (29 duloxetine trials and 43 venlafaxine trials; one study provided data for the duloxetine and the venlafaxine data set). The placebo effect sizes, defined as pre‐postscore change divided by baseline standard deviation, differed significantly between venlafaxine and duloxetine studies (−2.51 vs. −2.09; test for subgroup differences P = 0.028; high heterogeneity). The analysis of effect modifiers and the metaregression analyses confirmed the drug, next to baseline depression severity and publication status, as the most influential independent predictor.

Conclusion

Our analyses show a significant difference in the placebo response between venlafaxine and duloxetine trials and suggest that the investigated drug has an influence on the placebo response that is not related to baseline severity, changes over the years or other variables we included.
Discovery of a new species ofStromatiumAudinet‐Serville, 1834 (Coleoptera: Cerambycidae) native to Australia, based on morphology and DNA barcoding
Authors: Jin Mengjie , Weir Tom , Cameron Stephen L , Lemann Catherine , Ślipiński Adam , Pang Hong
Published: March 2018

StromatiumAudinet‐Serville 1834 is considered to be one of the most economically important genera of Cerambycidae. Three species of this genus,Stromatium barbatum(Fabricius),Stromatium longicorne(Newman 1842) andStromatium auratum(Böber 1793), are able to develop to maturity in seasoned timber and are distributed worldwide due to human commerce. We clarified here the status of wild populations ofStromatiumin Australia.Stromatium darwinenseJin & Weir sp. nov. is described from the Northern Territory in Australia, based on evidence from morphological characters and mtDNA barcode sequences (421 bp fragment of COI). The new species is morphologically very similar toS. longicorne, which is native to Christmas Island but not to mainland Australia. We redescribeS. barbatumandS. longicorne, the introductions of which still remain high risks for Australian biosecurity.
Functional diversity of macroinvertebrates on abandoned cattle enclosures in a semi‐arid African savannah
Authors: Chikorowondo Gift , Muvengwi Justice , Mbiba Monicah , Gandiwa Edson
Published: April 2018

Zimbabwe is experiencing a shift in land‐use, away from livestock farming and towards wildlife conservation. The abandonment of livestock farming may have unforeseen consequences on biodiversity and ecosystem functioning, as cattle kraals create valuable nutrient‐rich patches across the semi‐arid savannah. It is unclear how macroinvertebrates functionally respond to such nutrient‐rich patches in semi‐arid savannahs. We analysed functional diversity of both aboveground and belowground taxa on abandoned cattle kraals and savannah control plots in Save valley Conservancy (SVC). We used distance‐based multivariate techniques to estimate indices of functional diversity. Our results indicated that after two decades of abandonment, kraals had higher functional richness (FRic), functional divergence (FDiv) and functional dispersion (FDis) of macroinvertebrates when both aboveground and belowground species are combined. When aboveground macroinvertebrates were considered alone, no difference was observed for all the considered functional indices. However, only FRic was higher on kraals when belowground macroinvertebrates were separately considered. Our results suggest that two‐decade‐old abandoned kraals may have recovered enough for aboveground species to match the surrounding savannah plot and even surpassed the savannah control for belowground species functional diversity.
Lymphocytes immunotherapy for preserving pregnancy: Mechanisms and Challenges
Authors: Hajipour Hamed , Nejabati Hamid Reza , Latifi Zeinab , Hamdi Kobra , Bahrami‐asl Zahra , Fattahi Amir , Nouri Mohammad
Published: March 2018

Due to the expression of paternal antigens by the embryo, pregnancy is considered as a semi‐allograft and so immunological dysregulation is considered as one of the important causes in repeated implantation failure (RIF) and recurrent pregnancy loss (RPL). It has been revealed that lymphocytes immunotherapy (LIT) could be an appropriate approach to prevent pregnancy loss in such patients. Various mechanisms have been suggested for effectiveness of LIT such as enhancing expression of anti‐paternal cytotoxic antibodies (APCA), progesterone‐induced blocking factor (PIBF), anti‐idiotypic antibodies (Ab2), and mixed lymphocyte reaction blocking antibodies (MLR‐Bf), as well as reduction in the T helper 1/T helper 2 ratio and deviation in the pattern of cytokines production. However, there are controversial results about the beneficial effect of LIT treatment in RIF and RPL patients. In the current study, we reviewed findings of LIT in RIF and RPL patients with a focus on possible mechanisms of alloimmunization in preserving pregnancy. Besides, we highlighted possible reasons for mixed results about the effectiveness of LIT and way of solving the problem. Also, we proposed potential laboratory and clinical criteria to recruit patients for LIT.
A direct‐to‐patient telemedicine abortion service in Australia: Retrospective analysis of the first 18 months
Authors: Hyland Paul , Raymond Elizabeth G. , Chong Erica
Published: March 2018

Background

In 2015, the Tabbot Foundation launched a nationwide direct‐to‐patient telemedicine service to enable women to obtain medical abortion without visiting an abortion provider.

Aims

We aimed to describe results from the first 18 months of this service.

Materials and Methods

To have an abortion through the Foundation, a woman obtained screening tests locally and had a telephone consultation with a Foundation doctor. If she was eligible, mifepristone, misoprostol and other medications were sent to her by mail. After taking the drugs, the woman obtained follow‐up tests at local facilities and had a consultation with Foundation professionals. The Foundation charged $250 to patients with Medicare eligibility and $600 otherwise. We summarised clinical data collected by the service.

Results

Between June 2015 and December 2016, 1010 women received medications, of whom 56% lived outside of major cities. Ninety‐five percent of packages were sent within 15 days after registration. Of the 965 women who took misoprostol, outcomes were definitively documented for 754 (78%), of whom 96% had a complete abortion without surgical intervention, and 95% had no face‐to‐face clinical encounter after treatment. Of women with Medicare cards, 72% paid no out‐of‐pocket charges other than to the Foundation. Nearly all women (781/802; 97%) were highly satisfied.

Conclusions

The direct‐to‐patient telemedicine medical abortion service was effective, safe, inexpensive and satisfactory. It disproportionately served women in parts of Australia with limited access to abortion facilities. This experience may be instructive for others desiring to use telemedicine to enhance access to abortion.