bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential variation and expression analysis
Authors: Bar Haim , Schifano Elizabeth D.
Published: March 2018

We propose an empirical Bayes approach using a three-component mixture model, the L2N model, that may be applied to detect both differential expression (mean) and variation. It consists of two log-normal components (L2) for the differentially expressed (dispersed) features (one component for under-expressed [dispersed] and the other for over-expressed [dispersed] features), and a single normal component (N) for the null features (i.e., non-differentially expressed [dispersed] features). Simulation results show that L2N can capture asymmetries in the numbers of over-and under-expressed (dispersed) features (e.g., genes) when they exist, can provide a better fit to data in which the distributions of the null and non-null features are not well-separated, but can also perform well under symmetry and separation. Thus the L2N model is particularly appealing when no a priori biological knowledge about the mixture density is available. The L2N model is implemented in an R package called DVX, for Differential Variation and eXpression analysis. The package also includes an implementation of differential expression analysis via the limma package, and a differential variation and expression analysis using a three-way normal mixture model. DVX is a user-friendly, graphical interface implemented via the ‘Shiny’ package [6], so that a user is not required to have R programming knowledge. It offers a set of diagnostics plots, data transformation tools, and report generation in Microsoft Excel- and Word-compatible formats. The package is available on the web, at https://haim-bar.uconn.edu/software/DVX/.
Where and how our brain represents the temporal structure of observed action
Authors: Thomas R.M. , Sanctis T. De , Gazzola V. , Keysers C.
Published: March 2018

Reacting faster to the behavior of others provides evolutionary advantages. Reacting to unpredictable events takes hundreds of milliseconds. Understanding where and how the brain represents what actions are likely to follow one another is therefore important. Everyday actions are predictable sequences of acts, yet neuroscientists focus on how brains responds to unexpected, individual motor acts. Using fMRI we show the brain encodes sequence-specific information in the motor system. Using EEG, we show visual responses were faster and smaller for predictable sequences that recruit the motor system. This study shifts the study of action observation from single acts to motor sequences, informs how we adapt to the actions of others and suggests the motor system may implement perceptual predictive coding.
Model for breast cancer diversity and spatial heterogeneity
Authors: Romero-Arias J. Roberto , Ramírez-Santiago Guillermo , Velasco-Hernández Jorge X. , Ohm Laurel , Hernández-Rosales Maribel
Published: March 2018

We present and analyze a growth model of an avascular tumor that considers the basic biological principles of proliferation, motility, death and genetic mutations of the cell. From a regulatory network analysis and an analysis of genomic data we identify two sets of genes-a set of six genes and a set of sixteen genes-that are believed to play an important role in the evolution of breast cancer. Considering that cancer cells shape the tissue microenvironment and niches to their competitive advantage, the model assumes that cancer and normal cells compete for essential nutrients and that the rate of the “driver” mutations depends on nutrient availability. To this end, we propose a coupling between the transport of nutrients and gene mutations dynamics. Gene mutation dynamics are modeled as a Yule-Furry Markovian process, while transport of nutrients is described with a system of reaction-diffusion equations. For each representative tumor we calculate its diversity, represented by the Shannon index, and its spatial heterogeneity, measured by its fractal dimension. These quantities are important in the clinical diagnosis of tumor malignancy. A tumor malignancy diagram, obtained by plotting diversity versus fractal dimension, is calculated for different values of a parameter β, which is related to the occurrence of driver mutations. It is found that when β < 1, tumors show greater diversity and more spatial heterogeneity as compared with β > 1. More importantly, it is found that the results and conclusions are similar when we use the six-gene set versus sixteen-gene set.
The AOPOntology: A Semantic Artificial Intelligence Tool for Predictive Toxicology
Authors: Burgoon Lyle D.
Published: March 2018

Introduction

Toxicology needs artificial intelligence tools that can automate the prediction of toxicity. Today we are at an interesting nexus. We have thousands of chemicals in the environment that lack regulatory thresholds for determining risk. New high throughput in vitro testing methods are becoming available to test these chemicals. Causal Adverse Outcome Pathway Networks (CAOPN) are emerging that will allow us to make predictions based on perturbations of specific key events within the network. The AOPOntology was developed as infrastructure for this nexus, providing the ability to model and marry the data from the in vitro tests for the thousands of chemicals and place them within the CAOPN framework to facilitate adverse outcome predictions.

Materials and Methods

The AOPN is a functional specialized ontology that creates classes that model biological pathways and CAOPNs. Adverse outcome predictions are based on mathematical determinations of key events that are sufficient to infer adverse outcomes will occur, or biological information. These sufficiency relationships are captured in the AOPOntology and used by the semantic reasoners to make predictions.

Results

The AOPOntology version 1.0 architecture is in place, and a CAOPN for steatosis demonstrates how causal network theory is used to make predictions. The AOPOntology is available at https://github.com/DataSciBurgoon/aop-ontology.

Discussion

The AOPOntology is a knowledge base for CAOPNs that one can use to make predictions about a chemical’s potential toxicity using in vitro high throughput and other assays.

Conclusions

Using CAOPNs and causal network theory one is able to predict potential toxicity for chemicals using in vitro high throughput and various high content screens.
Crystal structure of aquachlorido(nitrato-κ2
O,O′)[1-(pyridin-2-yl-κN)-2-(pyridin-2-ylmethylidene-κN)hydrazine-κN
2]manganase(II)
Authors: Sarr Mamour , Diop Mayoro , Thiam Elhadj Ibrahima , Barry Aliou Hamady , Gaye Mohamed , Retailleau Pascal
Published: March 2018

The search for novel manganese(II) compounds having interesting magnetic properties, using 1-(pyridin-2-yl)-2-(pyridin-2-ylmethylidene)hydrazine (HL) as a tridendate ligand, led to the preparation of the title mononuclear material, [MnCl(NO3)(C11H10N4)(H2O)], and the determination of its structure by XRD. The asymmetric unit comprises a discrete molecule in which the cation MnII is heptacoordinated. The environment around the cation is an almost perfect pentagonal bipyramid. The base is defined by the two N atoms of the pyridine rings, the N atom of the imino function of the ligand and the two O atoms of the chelating bidentate nitrate ligand. The apical positions are occupied by a Cl atom and a water molecule. In the crystal, there are numerous hydrogen bonds of the types Ow—H...ONO2 and C—H...ONO2, which generate layers parallel to the bc plane in which the ligands in the axial positions point into the interlayer space. These axial ligands give rise to hydrogen bonds of the types Ow—H...ONO2, Ow—H...Cl, N—H...Cl and C—H...Cl, leading to a three-dimensional framework. The chain bridging the two pyridine rings is disordered over two sets of sites in a 0.53 (2):0.47 (2) ratio.
Impact of quality management systems on firm performance
Authors: Kumar Pankaj , Maiti J. , Gunasekaran Angappa
Published: March 2018

Purpose

Within the operations management literature, quality management (QM) has been one of the most popular research areas over the last few decades. The impact of QM systems on firm performance has been the subject of constant interest and challenge among researchers. Last such review was done in 2002 based on QM-related articles published between 1994 and 1999 and these were primarily on Total Quality Management (TQM). In the last 18 years, a large number of empirical studies have been attempted to investigate QM system-performance relationships in different contexts, covering not only TQM but also other QM systems such as ISO 9001, Total Productive Maintenance (TPM), Lean Manufacturing, Theory of Constraints (TOC), and Six Sigma Continuous Improvement projects. The paper aims to discuss these issues.

Design/methodology/approach

Based on an extensive review of 263 papers published in 17 reputed journals during the period 2000 to 2017, this paper shows the reflections of QM systems with respect to study of different QM systems, type of research designs being used, performance categories and metrics being used, and application of tools/techniques.

Findings

The literature review has revealed several gaps in research in the area of QM and calls for research on: empirical longitudinal case studies; implementation of multiple QM systems; identification of leading indicators of firm’s performance; standardization of performance measures; safety, environment and health-related performance measures; the differences in the QM systems on firm’s performance for manufacturing vs service organizations; application of QM systems in developing countries including Asian countries; and impact of ISO 9001 QM system on firm’s performance.

Originality/value

The literature reviews in the past had considered only the TQM-related articles published in reputed journals and did not cover other QM systems such as TPM, TOC, Toyota Production System, Six Sigma, ISO 9001 QMS, etc., which have also been widely used in many organizations, more so in the last 15 years.
Role of internal and external organizational factors in TQM implementation
Authors: Nasim Kanwal
Published: March 2018

Purpose

The purpose of this paper is to provide a conceptual framework for the development of total quality management (TQM) model for service organizations considering both internal and external environmental factors.

Design/methodology/approach

Through an extensive literature search, it is found that despite a large body of knowledge on TQM, there is hardly any research undertaken on the model of service quality including all external and internal factors that can affect the impact of soft and hard TQM factors on organizations performance. So, a systematic literature review has been conducted to extract the relevant journal articles for the study purpose.

Findings

The conceptual model fills this yawning gap and presents a framework of integrated relationships based on several constituent models. These are soft TQM factors, hard TQM factors and organizational performance. Moreover, quality improvement, market benefits, R&D performance and quality performance are used as mediators while industry rivalry and entry barriers are used as moderators between soft and hard TQM and organizational performance. The seven propositions, derived from these elements, highlight the dynamic relationship between above mentioned constructs.

Research limitations/implications

One major limitation is the testing of this model. It has not been tested in any environment or organization to assess its validity. Future research can be done to test the developed hypotheses. Besides three journals, other journals can also be focused in future to get detailed insight into different factors. Impact of IT on organizational processes toward TQM can also be studied in future. More rigorous statistical tests can also be applied to generate more findings with an extension of review time period and selection of more journals.

Practical implications

The model developed in this study can be applied in any service organization with slight modifications to enhance the service quality of organizations by integrating both internal and external aspects for quality improvement. By adopting this framework, organizations can increase their production quality.

Originality/value

This proposed framework will help organizations to effectively implement TQM in their organizations considering internal and external organizational factors.
Productivity changes in Indian steel plants: DEA approach
Authors: Kumar Pankaj , Maiti J.
Published: March 2018

Purpose

The purpose of this paper is to evaluate the technical efficiency and productivity changes in the integrated steel plants in India over a period of five years.

Design/methodology/approach

Since this evaluation of integrated steel plants needs consideration of multiple input and output factors, data envelopment analysis (DEA) has been employed including bootstrapping (to account for statistical noise) to evaluate the relative efficiency of the steel manufacturing units. The efficiency and Malmquist productivity indices of a sample of ten integrated steel plants producing around 55 percent of the industry’s output were determined for the period 2008-2013. The results of these changes were further categorized according to the management control, route followed to produce crude steel, size and age of these steel plants, for gaining insights.

Findings

The study finds that private sector steel plants with larger capacity and which have adopted the latest and most modern technologies are more efficient and productive over the study period.

Practical implications

Public sector steel plants should therefore be provided with more autonomy and delegation of power and should be agiler in responding to market requirements as well as increasing their installed capacities to be competitive in technical efficiency and productivity as well as profitability in the long term to ensure sustainable achievements.

Originality/value

Productivity changes over time, both with respect to technological and efficiency changes, for the Indian integrated steel plants producing comparable products using DEA.
Knowledge transfer between projects within project-based organizations: the project nature perspective
Authors: Ren Xu , Deng Xiaofang , Liang Lihua
Published: March 2018

Purpose

This paper aims to investigate how project nature affects the effectiveness of knowledge transfer between projects in project-based organizations (PBOs) and to analyze the roles of inter-project communication, transfer intention and information technology (IT) in the influencing process.

Design/methodology/approach

This paper adopted a questionnaire survey method to collect data from construction enterprises in China and subsequently proceeded to structural equation modeling analysis with a total of 261 samples.

Findings

The results indicate that the similarity of projects could promote the inter-project communication and improve transfer intention, which further influences knowledge transfer effectiveness positively within PBOs. The urgency of projects has a negative impact on inter-project communication and transfer intention. The temporality of projects also negatively affects inter-project communication. They consequently hinder the knowledge transfer behaviors between projects. Additionally, the application of IT improves the frequency of communication and makes up for the negative impact of geographical distance between projects on knowledge transfer.

Practical implications

Based on the results, a series of strategies is recommended to improve knowledge transfer effectiveness between projects, including standardizing project management, promoting information construction, establishing a post-project evaluation system and creating a shared culture, so that the competitive advantages of PBOs could be improved.

Originality/value

The study explores the factors influencing knowledge transfer between projects from the perspective of project nature and provides guidance for enhancing knowledge management and project management practices.
Interviewer-respondent interaction and rapport in PIAAC
Authors: Maddox Bryan
Published: March 2018

Purpose

This paper aims to investigate small-scale, qualitative observations of interviewer–respondent interaction in the Organisation for Economic Co-operation and Development’s Programme for the International Assessment of Adult Competencies (PIAAC).

Design/methodology/approach

The paper uses video-ethnographic methods to document talk and gesture in assessment in Slovenian household settings. It presents an in-depth case study of interaction in a single testing situation.

Findings

Observing interaction in assessment captures data on assessment performance that is not available in quantitative analysis of assessment response processes. The character of interviewer–respondent interaction and rapport is shaped by the cognitive demands of assessment and the distinctive ecological setting of the household.

Research limitations/implications

Observational data on assessment response processes and interaction in real-life assessments can be integrated into and synthesized with other sources of “process data”.

Practical implications

Assessment programs such as PIAAC should consider the significance of the household setting on assessment quality and observations of interaction in assessment as a valid source of paradata.

Social implications

There is a place for small-scale observational studies of assessment to inform public understanding of assessment quality and validity.

Originality/value

The paper provides qualitative insights into the significance of interaction and “interviewer effects” in household assessment settings.
The Effect of Health Insurance on the Substitution between Public and Private Hospital Care
Authors: Doiron Denise , Kettlewell Nathan
Published: March 2018

Researchers have long been interested in estimating the causal effect of health insurance on health‐care utilisation. Less attention has been given to measuring the impact of insurance on the substitution between private and public sector care. We estimate this effect for hospital admissions in Australia. To identify causal effects we use household variables as instruments, namely, information on partner's health and family aspirations. We find that having private health insurance increases the probability of a hospital admission by 5–6 percentage points. This net effect is the result of a considerable substitution from public to private care, which has important policy implications.
Effects of Processing Conditions During Manufacture on Retronasal‐Aroma Compounds from a Milk Coffee Drink
Authors: Ikeda Michio , Akiyama Masayuki , Hirano Yuta , Miyazi Kazuhiro , Kono Masaya , Imayoshi Yuriko , Iwabuchi Hisakatsu , Onodera Takeshi , Toko Kiyoshi
Published: March 2018

To develop a ready‐to‐drink (RTD) milk coffee retaining the original coffee flavor, the effects of processing conditions during manufacture on retronasal‐arma (RA) compounds from the milk coffee were investigated by gas chromatography‐mass spectrometry using an RA simulator (RAS). Thirteen of 46 detected compounds in the RAS effluent (RAS compounds) decreased significantly following pH adjustment of coffee (from pH 5.1 to 6.8) and 5 compounds increased. RAS compounds from coffee tended to decrease through the pH adjustment and subsequent sterilization. Significantly higher amounts of 13 RAS compounds were released from the milk coffee produced using a blending‐after‐sterilization (BAS) process without the pH adjustment than from that using a blending‐before‐sterilization (BBS) process with the pH adjustment. In BAS‐processed milk coffee, significantly lower amounts of 8 high‐volatility compounds and 1H‐pyrrole were released from coffee containing infusion‐sterilized (INF) milk than from coffee containing plate‐sterilized (PLT) milk, whereas 3 low‐volatility compounds were released significantly more from coffee using PLT milk. Principal component analysis revealed that the effect of the manufacturing process (BAS, BBS, or homemade (blending unsterilized coffee without pH adjustment with sterilized milk)) on milk coffee volatiles was larger than that of the sterilization method (INF or PLT) for milk, and that the sterilization method could result in different RAS volatile characteristics in BAS and homemade processes. In conclusion, a BAS process was found to be superior to a BBS process for the manufacture of an RTD milk coffee that retains volatile characteristics similar to that of a homemade milk coffee.

Practical Application

Ready‐to‐drink (RTD) milk coffee manufactured using the conventional blending‐before‐sterilization process does not retain its original coffee flavor due to pH adjustment of the coffee during the process. The new blending‐after‐sterilization (BAS) process enabled the production of RTD milk coffee whose volatiles are closer to that of homemade milk coffee, as demonstrated by the results of RAS‐GC‐MS analysis. The BAS process has already been applied to the manufacture of RTD milk coffees in Japan.
Influence of Expectation Measure on the Sensory Acceptance of Petit Suisse Product
Authors: Teixeira Lopes Maria Micheline , Passos Rodrigues Maria do Carmo , Souza de Araújo Ana Maria
Published: March 2018

The consumer's expectation has an important role in the consumption of food products. It is one of the factors that influence the perception of sensory attributes and interact with the physiological, behavioral and cognitive factors influencing consumer decisions. The present study aimed to analyze the influence of consumer's expectations on the acceptance of Petit Suisse. Products of 4 different brands were used for the sensory analysis, 2 international brands and 2 regional ones. The 9‐point regular hedonic scale was employed to carry out affective sensory and expectation measure tests (with and without product information). Concerning the present research, photos of the packaging of each product were printed in color and presented to the participants. These photos displayed the following pieces of information: the product brand, pictures, colors, product name, nutritional information and date of manufacture. International samples obtained higher grades when presented with their packaging, and obtained lower values both in the blind test and in the real expectation test evaluation. It can be concluded that the sensory analysis of the expectation measure showed that the brand influences the acceptance of the product, for the consumer's expectations for international brands had positively confirmed and disconfirmed acceptance.

Practical Application

This study generated a significant contribution, especially for companies that aim for a wider market. The application of sensory analysis with a focus on expectation measure, it shows that the brand determines the purchase, based on the results of this study. Therefore, the product's visual identity must be invested in; it must arouse children and adults’ attention. That is, it reinforces that the image of the product, the label and what it arouses in the consumers are extremely important for the final choice.
Understanding Kombucha Tea Fermentation: A Review
Authors: Villarreal‐Soto Silvia Alejandra , Beaufort Sandra , Bouajila Jalloul , Souchard Jean‐Pierre , Taillandier Patricia
Published: March 2018

Kombucha is a beverage of probable Manchurian origins obtained from fermented tea by a microbial consortium composed of several bacteria and yeasts. This mixed consortium forms a powerful symbiosis capable of inhibiting the growth of potentially contaminating bacteria. The fermentation process also leads to the formation of a polymeric cellulose pellicle due to the activity of certain strains of Acetobacter sp. The tea fermentation process by the microbial consortium was able to show an increase in certain biological activities which have been already studied; however, little information is available on the characterization of its active components and their evolution during fermentation. Studies have also reported that the use of infusions from other plants may be a promising alternative.

Practical Application

Kombucha is a traditional fermented tea whose consumption has increased in the recent years due to its multiple functional properties such as anti‐inflammatory potential and antioxidant activity. The microbiological composition of this beverage is quite complex and still more research is needed in order to fully understand its behavior. This study comprises the chemical and microbiological composition of the tea and the main factors that may affect its production.
Association between type 2 diabetes mellitus and disability: What is the contribution of diabetes risk factors and diabetes complications?
Authors: Tabesh Maryam , Shaw Jonathan E. , Zimmet Paul Z. , Söderberg Stefan , Koye Digsu N. , Kowlessur Sudhir , Timol Maryam , Joonas Noorjehan , Sorefan Ameena , Gayan Praneel , Alberti K. George M.M. , Tuomilehto Jaakko , Magliano Dianna J.
Published: March 2018

Background

The aim of this study was to evaluate the association between type 2 diabetes and disability in Mauritius and to assess the extent to which the effect of diabetes is explained by diabetes risk factors and concomitant complications.

Methods

Data from a national survey in the multiethnic nation of Mauritius, which comprises South Asians and African Creoles, were analyzed. Disability was measured using the Katz activities of daily living questionnaire in participants aged >50 years.

Results

Among 3692 participants, 487 (13.2%) had some level of disability. Diabetes was associated with significantly higher risk of disability (odds ratio [OR] 1.67; 95% confidence interval [CI] 1.34–2.08). After adjusting for demographic, behavioral, and metabolic factors, as well as comorbidities, disability was significantly associated with diabetes among African Creoles (OR 2.03; 95% CI 1.16–3.56), but not South Asians (OR 1.27; 95% CI 0.98–1.66). Obesity explained much of the association between diabetes and disability (excess percentage of risk: 26.3% in South Asians and 12.1% in African Creoles). Obesity, history of cardiovascular disease (CVD), asthma‐like symptoms, and depression together explained 46.5% and 29.0% of the excess risk in South Asians and African Creoles, respectively.

Conclusions

Diabetes is associated with a 67% increased risk of disability. Diabetes risk factors and comorbidities explain more of the association between diabetes and disability among South Asians than Africans. Obesity and history of CVD explained the largest percentage of the relationship between diabetes and disability, indicating that weight and CVD management may be helpful in controlling disability related to diabetes.
Case sharing of a patient re‐challenged with afatinib for EGFR‐mutated advanced non–small cell lung cancer
Authors: Lee Victor H.F.
Published: March 2018

A 65‐year‐old female with diabetes mellitus but otherwise good health in the past suffered from cough with occasional blood‐stained sputum during initial presentation. The patient was diagnosed with pulmonary poorly differentiated adenocarcinoma with an epidermal growth factor receptor (EGFR) exon 19 deletion and hence received afatinib therapy for 25 months without obvious adverse events except for a grade 1–2 acneiform rash. The disease was stabilized after subsequent cycles of chemotherapy with pemetrexed and carboplatin followed by maintenance pemetrexed. The patient was rechallenged with afatinib treatment as a named‐patient drug in July 2014 (after approval) and later received afatinib in combination with palliative radiation. A blood test confirmed the presence of the T790M mutation and the patient was on osimertinib as part of a compassionate use program. The patient experienced good drug tolerance and eventually had a significant drop in tumor marker levels. This case provides insight into the use of afatinib in first‐line setting of EGFR‐mutated lung cancer.
ARE COOPERATIVES MORE PRODUCTIVE THAN INVESTOR‐OWNED FIRMS? CROSS‐INDUSTRY EVIDENCE FROM PORTUGAL
Authors: MONTEIRO Natália P. , STRAUME Odd Rune
Published: March 2018

We analyse empirically whether cooperatives and investor‐owned firms differ in terms of productive efficiency. Using rich Portuguese panel data covering a wide range of industries, we apply two different empirical approaches to estimate potential differences in productive efficiency. The results from our benchmark random‐effects model show that cooperatives are significantly less productive, on average, than investor‐owned firms, both at the aggregate level and for most of the industries considered. However, the results derived from a System‐GMM approach, which is our preferred empirical strategy, are much less conclusive, and we cannot conclude that cooperatives are generally less efficient that investor‐owned firms. With either approach, though, we find no evidence that cooperatives are more productive than investor‐owned firms in any industry.
RESILIENCE MEASUREMENT AND CONCEPTUAL FRAMEWORKS: A REVIEW OF THE LITERATURE
Authors: SERFILIPPI Elena , RAMNATH Gayatri
Published: March 2018

The lack of consensus and consistency in measuring resilience undermines the ability of the development aid community to objectively monitor and verify the effects of programs that are intentionally designed to build resilience. In this paper we compare conceptual and analytical models of resilience used by various development organizations, critically evaluating their strengths and weaknesses from a program implementation and measurement point of view. We provide the reader with a clear synthesis of the literature and a classification system for these resilience models. Lastly, we bridge the ‘measurement gap’ by mapping each resilience model to their set of indicators and by building a list of indicators and metrics directly distilled from the literature and classified using SMART filters.
Proton pump inhibitor use and risk of hip fractures among community‐dwelling persons with Alzheimer's disease—a nested case‐control study
Authors: Torvinen‐Kiiskinen S. , Tolppanen A.‐M. , Koponen M. , Tanskanen A. , Tiihonen J. , Hartikainen S. , Taipale H.
Published: March 2018

Background

Hip fractures are a major health concern among older persons with Alzheimer's disease, who usually use many concomitant drugs for several diseases. Evidence of the association between proton pump inhibitor use and risk of hip fracture is contradictory.

Aim

To investigate whether the long‐term use of proton pump inhibitor is associated with risk of hip fractures among community‐dwelling persons with Alzheimer's disease.

Methods

In this nested case‐control study, the nationwide MEDALZ data were utilised. Community‐dwelling persons with Alzheimer's disease who encountered incident hip fracture (N = 4818; mean age 84.1) were included as cases. Four controls were matched for each case at the date of hip fracture (N = 19 235; mean age 84.0). The association between hip fracture and duration of current PPI use (ongoing use during 0‐30 days before the index date), and cumulative duration of use during 10 years before was investigated with conditional logistic regression.

Results

Long‐term or cumulative proton pump inhibitor use was not associated with an increased risk of hip fracture. Current proton pump inhibitor use was associated with an increased risk of hip fracture (adjusted OR 1.12, 95% CI 1.03‐1.22). The risk was increased in short‐term current use (<1 year) (adjusted OR 1.23, 95% CI 1.10‐1.37).

Conclusions

The increased risk of hip fracture was evident only in short‐term proton pump inhibitor use, but no association was found for long‐term or cumulative use. Thus, our findings do not support previous assumptions that long‐term proton pump inhibitor use would be associated with an increased risk of hip fractures.
Genetic Variations, Exposure to Persistent Organic Pollutants and Breast Cancer Risk – A Greenlandic Case–Control Study
Authors: Wielsøe Maria , Eiberg Hans , Ghisari Mandana , Kern Peder , Lind Ole , Bonefeld‐Jørgensen Eva Cecilie
Published: March 2018

This study investigated the effects of single nucleotide polymorphisms (SNPs) in xenobiotic and steroid hormone‐metabolizing genes in relation to breast cancer risk and explored possible effect modifications on persistent organic pollutants (POPs) and breast cancer associations. The study also assessed effects of Greenlandic BRCA1 founder mutations. Greenlandic Inuit women (77 cases and 84 controls) were included. We determined two founder mutations in BRCA1: Cys39Gly (rs80357164) and 4684delCC, and five SNPs in xenobiotic and oestrogen‐metabolizing genes: CYP17A1 ‐34T>C (rs743572), CYP19A1 *19C>T (rs10046), CYP1A1 Ile462Val (rs1048943), CYP1B Leu432Val (rs1056836) and COMT Val158Met (rs4680). We used chi‐square test for comparison of categorical variables between groups. Odds ratio (OR) estimates with 95% confidence interval (95%CI) were obtained using logistic regression models. The variant allele of BRCA1 Cys39Gly increased breast cancer risk (Gly/Cys versus Cys/Cys, OR: 12.2, 95%CI: 1.53; 98.1), and carriers of the variant allele of CYP17A1 ‐34T>C had reduced risk (CT+CC versus TT, OR: 0.44, 95%CI: 0.21; 0.93). CYP17A1 ‐34T>C was an effect modifier on the association between perfluoroalkyl acids (PFAAs) and breast cancer risk (∑PFAA, ratio of OR: 0.18, 95%CI: 0.03; 0.97). Non‐significant modifying tendencies were seen for the other SNPs on the effect of polychlorinated biphenyls, organochlorine pesticides and PFAAs. In summary, the BRCA1 Cys39Gly and CYP17A1 ‐34T>C genetic variations were associated with breast cancer risk. Our results indicate that the evaluated genetic variants modify the effects of POP exposure on breast cancer risk; however, further studies are needed to document the data from the relatively small sample size.
Information matrix estimation procedures for cognitive diagnostic models
Authors: Liu Yanlou , Xin Tao , Andersson Björn , Tian Wei
Published: March 2018

Two new methods to estimate the asymptotic covariance matrix for marginal maximum likelihood estimation of cognitive diagnosis models (CDMs), the inverse of the observed information matrix and the sandwich‐type estimator, are introduced. Unlike several previous covariance matrix estimators, the new methods take into account both the item and structural parameters. The relationships between the observed information matrix, the empirical cross‐product information matrix, the sandwich‐type covariance matrix and the two approaches proposed by de la Torre (2009,J. Educ. Behav. Stat.,34, 115) are discussed. Simulation results show that, for a correctly specifiedCDMandQ‐matrix or with a slightly misspecified probability model, the observed information matrix and the sandwich‐type covariance matrix exhibit good performance with respect to providing consistent standard errors of item parameter estimates. However, with substantial model misspecification only the sandwich‐type covariance matrix exhibits robust performance.
Elevated CO2 and water addition enhance nitrogen turnover in grassland plants with implications for temporal stability
Authors: Dijkstra Feike A. , Carrillo Yolima , Blumenthal Dana M. , Mueller Kevin E. , LeCain Dan R. , Morgan Jack A. , Zelikova Tamara J. , Williams David G. , Follett Ronald F. , Pendall Elise
Published: March 2018

Temporal variation in soil nitrogen (N) availability affects growth of grassland communities that differ in their use and reuse of N. In a 7‐year‐long climate change experiment in a semi‐arid grassland, the temporal stability of plant biomass production varied with plant N turnover (reliance on externally acquired N relative to internally recycled N). Species with high N turnover were less stable in time compared to species with low N turnover. In contrast, N turnover at the community level was positively associated with asynchrony in biomass production, which in turn increased community temporal stability. Elevated CO2 and summer irrigation, but not warming, enhanced community N turnover and stability, possibly because treatments promoted greater abundance of species with high N turnover. Our study highlights the importance of plant N turnover for determining the temporal stability of individual species and plant communities affected by climate change.
The need for an extensive neuropsychological assessment for a reliable diagnosis of mild cognitive impairment in patients with Parkinson's disease
Authors: Daniele A. , Lacidogna G.
Published: March 2018

Click here to view the accompanying paper in this volume.
Redesigning technology integration into world language education
Authors: Rodríguez Julio C.
Published: March 2018

This article describes how a multi‐institutional, proficiency‐based program engages stakeholders in design thinking to discover and explore solutions to perennial problems in technology integration into world language education (WLE). Examples of replicable activities illustrate the strategies used to fuel innovation efforts, including fostering the creation of partnerships that engage government, academia, and the private sector as well as processes that may result in innovation in the way that technology is integrated into WLE.
A Multivariable Prediction Model for Mortality in Individuals Admitted for Heart Failure
Authors: Bowen Garrett S. , Diop Michelle S. , Jiang Lan , Wu Wen‐Chih , Rudolph James L.
Published: March 2018

Objectives

To derive and validate a 30‐day mortality clinical prediction rule for heart failure based on admission data and prior healthcare usage. A secondary objective was to determine the discriminatory function for mortality at 1 and 2 years.

Design

Observational cohort.

Setting

Veterans Affairs inpatient medical centers (n=124).

Participants

The derivation (2010–12; n=36,021) and validation (2013–15; n=30,364) cohorts included randomly selected veterans admitted for HF exacerbation (mean age 71±11; 98% male).

Measurements

The primary outcome was 30‐day mortality. Secondary outcomes were 1‐ and 2‐year mortality. Candidate variables were drawn from electronic medical records. Discriminatory function was measured as the area under the receiver operating characteristic curve.

Results

Thirteen risk factors were identified: age, ejection fraction, mean arterial pressure, pulse, brain natriuretic peptide, blood urea nitrogen, sodium, potassium, more than 7 inpatient days in the past year, metastatic disease, and prior palliative care. The model stratified participants into low‐ (1%), intermediate‐ (2%), high‐ (5%), and very high‐ (15%) mortality risk groups (C‐statistic=0.72, 95% confidence interval (CI)=0.71–0.74). These findings were confirmed in the validation cohort (C‐statistic=0.70, 95% CI=0.68–0.71). Subgroup analysis of age strata confirmed model discrimination.

Conclusion

This simple prediction rule allows clinicians to risk‐stratify individuals on admission for HF using characteristics captured in electronic medical record systems. The identification of high‐risk groups allows individuals to be targeted for discussion of goals and treatment.
Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content
Authors: Tran Hue T.M. , Ramaraj Thiruvarangan , Furtado Agnelo , Lee Leonard Slade , Henry Robert J.
Published: March 2018

Arabica coffee (Coffea arabica) has a small gene pool limiting genetic improvement. Selection for caffeine content within this gene pool would be assisted by identification of the genes controlling this important trait. Sequencing of DNA bulks from 18 genotypes with extreme high‐ or low‐caffeine content from a population of 232 genotypes was used to identify linked polymorphisms. To obtain a reference genome, a whole genome assembly of arabica coffee (variety K7) was achieved by sequencing using short read (Illumina) and long‐read (PacBio) technology. Assembly was performed using a range of assembly tools resulting in 76 409 scaffolds with a scaffold N50 of 54 544 bp and a total scaffold length of 1448 Mb. Validation of the genome assembly using different tools showed high completeness of the genome. More than 99% of transcriptome sequences mapped to the C. arabica draft genome, and 89% of BUSCOs were present. The assembled genome annotated using AUGUSTUS yielded 99 829 gene models. Using the draft arabica genome as reference in mapping and variant calling allowed the detection of 1444 nonsynonymous single nucleotide polymorphisms (SNPs) associated with caffeine content. Based on Kyoto Encyclopaedia of Genes and Genomes pathway‐based analysis, 65 caffeine‐associated SNPs were discovered, among which 11 SNPs were associated with genes encoding enzymes involved in the conversion of substrates, which participate in the caffeine biosynthesis pathways. This analysis demonstrated the complex genetic control of this key trait in coffee.
Classification of facial vitiligo: A cluster analysis of 473 patients
Authors: Bae Jung Min , Jung Yu Seok , Jung Han Mi , Park Ji Hun , Hann Seung‐Kyung
Published: March 2018

Vitiligo has a substantial negative impact on quality of life in affected patients, especially those with the involvement of the face. However, the current system can barely distinguish between specific patterns of facial involvement except for the segmental type when focusing only on facial lesions. We classified facial vitiligo into three distinct subtypes using cluster analysis based on facial topography (n = 473): centrofacial vitiligo (72.9%), panfacial vitiligo (18.0%), and hairline vitiligo (9.1%). Centrofacial vitiligo was the most common type and is thought to comprise the typical facial involvement of generalized vitiligo. Panfacial vitiligo was a distinct subtype with onset in old age and less involvement of other body parts. Hairline vitiligo was another distinct subtype with onset in old age and a poor response to conventional phototherapy. A relevant classification system could help us to explore the causes, anticipate the prognosis, and manage the condition in patients with vitiligo.
Is there an established hemoglobin target range for patients undergoing chronic dialysis?
Authors: Shah Hitesh H. , Fishbane Steven
Published: March 2018

Anemia is a common complication of advanced chronic kidney disease (CKD). Treatment with erythropoiesis‐stimulating agents (ESAs) remains a common approach in managing anemia of CKD. The 2012 Kidney Disease Improving Global Outcomes Clinical Practice Guideline for Anemia in CKD suggests avoiding ESA therapy use to maintain Hb level above 11.5 g/dL. However, optimal Hb target range in adult patients undergoing chronic dialysis remains unknown. Clinical studies suggest risks associated with normalization of Hb levels in adult patients with CKD. In this article, we briefly review some of these studies and the concerns associated with higher Hb targets in this patient population. We also suggest a target Hb range for adult chronic dialysis patients receiving ESAs. It is currently undetermined if this target Hb range would apply to newer agents that are being studied for anemia management in this population.
Major haemorrhage protocols
Authors: Booth C. , Allard S.
Published: March 2018

Major haemorrhage protocols are aimed at optimizing the care of patients suffering life‐threatening bleeding. They should clearly set out the responsibilities of all of the staff involved including clinical and laboratory teams and other support staff with explicit lines of communication to support a prompt response without delays. The emphasis is on ready access to blood and components to limit coagulopathy in conjunction with definitive methods of controlling haemorrhage. High‐quality evidence for the early use of tranexamic acid strongly supports the inclusion of this drug in protocols for trauma and obstetric haemorrhage. Although national and international guidelines recommend the use of MHPs, they are not without drawbacks. Much of the evidence for their use comes from studies of trauma haemorrhage, and although the principles are widely applied to other clinical settings, there is a lack of data to guide practice in bleeding from other causes. Initial empirical replacement of red cells and plasma in fixed ratios largely based on experience from the military is now common in trauma, but this approach might result in overtreatment of some patients. As hypofibrinogenaemia is a poor prognostic factor, the inclusion of early fibrinogen replacement deserves attention and is the subject of active research. Further studies are examining the use of targeted transfusion strategies based on near‐patient testing, use of whole blood and chilled platelets, expanding indications for tranexamic acid and component use in the prehospital setting. MHPs should be reviewed regularly following local audit with ongoing update to reflect new research findings.
Does patients’ opinion of remission in rheumatoid arthritis overlap ultrasound “true” remission? – a pilot study
Authors: Vlad Violeta , Berghea Florian , Iorgoveanu Vasilia , Popescu Mihaela , Predeteanu Denisa , Ionescu Ruxandra
Published: March 2018

Aim: Patients describe rheumatoid arthritis (RA) remission as the absence of any symptoms or return to normality. Residual ultrasound (US) synovitis was frequently described in remission cohorts in previous studies. US tenosynovitis evaluation and scoring seems to better follow clinical remission scores compared with synovitis in RA. Our objective was to verify the presence of US findings suggestive of persistent inflammation in a cohort of patients in remission according to their own opinion.Materials and methods: Forty-three RA patients were prospectively enrolled in this pilot study between 2015-2017 according to their positive answer to the question “Are you feeling free of symptoms, just like before your RA symptomsstarted?”. Clinical evaluation of tender and swollen joints was performed in the same day with US evaluation of 24 joints and 26 tendon sites and lab C-reactive protein (CRP) evaluation. DAS28-CRP and SDAI were calculated. Results: A total of 72.9% (35 of 43) of patients were in remission per DAS28 criteria. Except for CRP value, no other variables were significantly different in the 35 of 43. PD scoring in tenosynovitis of the ankle and feet was 100% overlapping remission felt by patients. PD tenosynovitis in both upper and lower limbs was found in less than 10% of patients, and only grade 1 (minimal).Conclusion: A combination of patients’ opinion and PDUS evaluation could be a starting point for RA treatment tapering.
The value of global longitudinal strain and galectin-3 for predicting cardiovascular events in patients with severe aortic stenosis
Authors: Agoston-Coldea Lucia , Bheecarry Kunal , Petra Cristian , Strambu Lelia , Ober Camelia , Revnic Radu , Lupu Silvia , Mocan Teodora , Fodor Daniela
Published: March 2018

Aims: Left ventricular global longitudinal strain (GLS) was shown to predict outcomes after valve replacement in patients with aortic stenosis (AS). In the current study, we aimed to test the combined use of GLS and a marker of fibrosis – Galectin-3 – for predicting major cardiovascular adverse events (MACEs) in patients with severe AS.Materials and methods: We conducted a prospective study on 42 patients with severe AS and 42 volunteers. Patient evaluation included biochemistry tests, electrocardiogram, 24-hour Holter monitoring, the 6-minute walk test, and echocardiography. Outcomes of AS patients were defined as the composite of MACEs – sudden cardiac death, non-fatal myocardial infarction, sustained ventricular arrhythmias,atrial arrhythmias, and hospitalization for heart failure.Results: Patients with severe AS had lower GLS, and increased levels of both biomarkers compared to the control group. Both biomarkers correlated to echocardiographic parameters such as left ventricular (LV) mass index, relative wall thickness, GLS, as well as with the 6-minute walk test distance, and glomerular filtration rate (eGFR). GLS and NT-proBNP predicted MACEs reasonably well, while Galectin-3 did not, after adjustments for confounding factors. Kaplan–Meier analysis showed that the probability of freedom from MACEs was significant in patients who exhibited lower GLS [HR 2.73 (95% CI 1.01-7.53), p<0.05] and higher levels of NT-proBNP [HR 5.22 (95% CI 1.85- 14.51), p=0.001].Conclusions: Among tested parameters, GLS and NT-proBNP were the most reliable predictors of MACEs in patients with severe AS, while Galectin-3 performed more poorly.