bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling and simulation of filling in dual-scale fibrous reinforcements: state of the art and new methodology to quantify the sink effect
Authors: Patiño-Arcila Iván D , Vanegas-Jaramillo Juan D
Published: October 2017

The main advances in the modeling and simulation of the filling phenomenon that takes place in dual-scale fibrous reinforcements used in liquid composites molding processes are grouped and classified in the present work. Special emphasis is done in the classification of the simulation methods according to the dimension of the mesh, the identification of the interface conditions porous medium-free fluid, the comparison between the most used fluid-front tracking techniques and the survey of researches dealing with the non-uniform filling of representative unitary cells, which in turn is responsible for the void formation at mesoscopic scale and the sink effect at macroscopic scale. As an original contribution to this field of study, a new methodology to quantify the sink effect in macroscopic fillings is presented and subsequently assessed by comparing the results of experimental radial injections with numerical results obtained by the dual reciprocity-boundary element method. The proposed methodology is physically consistent and leads to results that are closer to the experimental ones than the results obtained when the sink effect is neglected; however, the accuracy is liable to be improved.
Novel Translucent and Strong Submicron Alumina Ceramics for Dental Restorations
Authors: Zhao M. , Sun Y. , Zhang J. , Zhang Y.
Published: October 2017

An ideal ceramic restorative material should possess excellent aesthetic and mechanical properties. We hypothesize that the high translucency and strength of polycrystalline ceramics can be achieved through microstructural tailoring. The aim of this study is to demonstrate the superior optical and mechanical properties of a new class of submicron grain-sized alumina ceramics relative to the current state-of-the-art dental ceramic materials. The translucency, the in-line transmission ( TIT) in particular, of these submicron alumina ceramics has been examined with the Rayleigh-Gans-Debye light-scattering model. The theoretical predictions related very well with the measured TIT values. The translucency parameter ( TP) and contrast ratio ( CR) of the newly developed aluminas were measured with a reflectance spectrophotometer on a black-and-white background. For comparison, the TIT, TP, and CR values for a variety of dental ceramics, mostly measured in-house but also cited from the literature, were included. The flexural strength of the aluminas was determined with the 4-point bending test. Our findings have shown that for polycrystalline alumina ceramics, an average grain size <1 µm coupled with a porosity level <0.7% could yield translucency values ( TIT, TP, CR) similar to those of the commercial high-translucency porcelains. These values are far superior to the high-translucency lithium disilicate glass-ceramic and zirconias, including the most translucent cubic-containing zirconias. The strength of these submicron grain-sized aluminas was significantly higher than that of the cubic-containing zirconia (e.g., Zpex Smile) and lithia-based glass-ceramics (e.g., IPS e.max CAD HT). A coarse-grained alumina could also reach a translucency level comparable to that of dental porcelain. However, the relatively low strength of this material has limited its clinical indications to structurally less demanding applications, such as orthodontic brackets. With a combined high strength and translucency, the newly developed submicron grain-sized alumina may be considered a suitable material for dental restorations.
Racial/Ethnic Differences in Cigarette Use Trends in the United States among Multiracial and Other Youth, 1994-2008
Authors: Goings Trenette Clark , Hidalgo Sebastian Teran , McGovern Patricia P.
Published: October 2017

Tobacco use among the multiracial population is grossly underresearched. This study explored the cigarette-smoking trends of multiracial individuals over time in comparison with monoracial individuals and assessed the relationship between cigarette smoking and factors at the individual, family, peer, school, and state levels. This study used data collected by the National Longitudinal Study of Adolescents and Adult Health from 1994 to 2008. This study examined a subsample of 9,421 respondents who self-identified as Black, Asian, American Indian, Hispanic, White, or multiracial. Generalized estimating equations were used to analyze the population-level data. Findings suggest that multiracial individuals reported high rates of cigarette use over time. The most consistent correlates of cigarette use were family factors, peer cigarette use, and school policies that prohibit staff from smoking on school premises. Additional research is needed to identify the correlates and causes of cigarette use among multiracial adolescents and young adults.
How Immigration Reforms Affect Voting Behavior
Authors: Abou-Chadi Tarik , Helbling Marc
Published: October 2017

This article investigates how changes in immigration policies affect migration as a vote-defining issue at upcoming elections. So far, the literature on issue voting has mostly focused on the role of issue entrepreneurs in politicizing new issues. In this article, however, we introduce policy change as a new potential determinant in the process of issue evolution. Moreover, in contrast to most of the literature that investigates the role of policy outcomes (such as economic growth or unemployment) on voting decisions, we analyze the effect of laws which can be directly attributed to governments and political parties. We focus on within-country variation and analyze national election surveys from the Netherlands, Denmark, and Germany between 1994 and 2011. These surveys include information on both self- and party-placements regarding immigration issues. To measure policy changes, we use data on immigration policies from the newly built Immigration Policies in Comparison dataset. While we expect a general reform effect, we investigate in more detail whether liberal and restrictive reforms have a similar effect on votes for left/right, government/opposition parties. It is shown that both liberal and restrictive reforms lead to increasing issue voting. While we show that government parties are not more affected than opposition parties, we see that party ideology partly plays a role.
Becoming a “Better” Father: Supporting the Needs of Incarcerated Fathers
Authors: Fowler Cathrine , Rossiter Chris , Dawson Angela , Jackson Debra , Power Tamara
Published: October 2017

Given the importance of fathering to the well-being and development of children, paternal incarceration has a major impact on children and families. Drawing on interviews with 64 incarcerated fathers in New South Wales, Australia, this article explores their experiences. The men’s childhood familial separation and disconnection is frequently repeated in adulthood, with limited contact with their own families even when not in custody. Despite barriers to connection, the interviewees express strong aspirations to be “good” fathers and to achieve a “better life” for their children. The absence of stable models of responsive fathering in early life is a common theme that has implications for the development of education and support programs for imprisoned fathers.
A New Way to View the Magnitude of the Difference between the Arithmetic Mean and the Geometric Mean and the Difference between the Slopes When a Continuous Dependent Variable Is Expressed in Raw Form Versus Logged Form
Authors: Goodman Leo A.
Published: October 2017

In Trond Petersen’s “Multiplicative Models for Continuous Dependent Variables: Estimation on Unlogged versus Logged Form” (this volume, pp. 113–164), the following phenomenon is noted: With the arithmetic and geometric means of a nonnegative quantitative variable measured for two groups (say, groups 1 and 2), it is possible for the arithmetic mean [Formula: see text] for group 1 to be larger than the arithmetic mean [Formula: see text] for group 2 and the geometric mean [Formula: see text] for group 1 to be smaller than the geometric mean [Formula: see text] for group 2. In the present note, some new formulas are introduced that will help to make clear when this phenomenon will occur and when it will not occur. The phenomenon considered here is of interest in situations where, for example, as noted in Petersen’s paper, results obtained using the raw form for a continuous dependent variable are compared with the corresponding results obtained using the logged form for the dependent variable. In addition, the formulas that are introduced in the present note also provide a new way to view the magnitude of the difference between the arithmetic mean and the geometric mean.
Accommodating binary and count variables in mediation
Authors: Geldhof G. John , Anthony Katherine P. , Selig James P. , Mendez-Luck Carolyn A.
Published: October 2017

The existence of several accessible sources has led to a proliferation of mediation models in the applied research literature. Most of these sources assume endogenous variables (e.g., M, and Y) have normally distributed residuals, precluding models of binary and/or count data. Although a growing body of literature has expanded mediation models to include more diverse data types, the nonlinearity of these models presents a substantial hurdle to their implementation and interpretation. The present study extends the existing literature (e.g., Hayes & Preacher, 2010; Stolzenberg, 1980) to propose conditional indirect effects as a useful tool for understanding mediation models that include paths estimated using the Generalized Linear Model (e.g., logistic regression, Poisson regression). We briefly review the relevant literature, culminating in a discussion of conditional indirect effects and their importance when examining nonlinear associations. We present a simple extension of the equations presented by Hayes and Preacher (2010) and provide an applied example of the technique.
The basic continuity hypothesis of L1 to L2 production
Authors: Romano Francesco
Published: October 2017

To what extent can second language (L2) speakers acquire a syntactic representation for an L2 structure absent in the first language (L1)? Findings from L2 structural priming studies are in conflict inasmuch as evidence for and against continuity between L1 and L2 sentence production has been shown. Furthermore, previous investigations have not adequately controlled for well-known animacy effects on choice of syntactic frames. I address the conflict of views in the field via three experiments of structural priming with native, Chinese, and Turkish speakers of English by means of an oral sentence-recall production task. The structure tested, the English genitive alternation, is subject to animacy effects as in the waiter’s photo / the photo of the waiter. Chinese and Turkish have no equivalent to English of genitives nor animacy effects in their genitive structure. Experiment 1 showed priming within-L1 English and found evidence of an animacy effect, albeit only numerical. Likewise, Experiment 2 showed priming within-L2 English and found the L1 Chinese were similarly susceptible to animacy effects. Experiment 3 also showed clear within-L2 English priming in Turkish speakers but the effects of animacy differed from the other groups. I argue the similarities between the native and L2 groups to constitute grounds for a basic continuity in L1 to L2 production.
Blood asymmetric dimethylarginine and nitrite/nitrate concentrations in short-stature children born small for gestational age with and without growth hormone therapy
Authors: Nagasaka Hironori , Morioka Ichiro , Takuwa Mayuko , Nakacho Mariko , Yoshida Mayumi , Ishida Akihito , Hirayama Satoshi , Miida Takashi , Tsukahara Hirokazu , Yorifuji Tohru , Iijima Kazumoto
Published: October 2017

Objective

To investigate the basal amino acid metabolism and impact of growth hormone (GH) therapy in short-stature children born small for gestational age (short SGA children).

Methods

In this age-matched case-control study, the basal blood levels of amino acids, asymmetric dimethylarginine (ADMA), and nitrite/nitrate (NOx) were compared between 24 short SGA children and 25 age-matched normal children. Changes in these parameters were assessed for 12 months in 12 short SGA children initiating GH therapy (Group A) and 12 age-matched short SGA children without GH therapy (Group B).

Results

The arginine levels were significantly lower in the short SGA than in normal children. The ADMA levels were significantly higher and NOx levels were significantly lower in the short SGA than normal children. In Group A, the ADMA level was significantly lower and NOx level was significantly higher at 6 months than at baseline. At 12 months, the ADMA level in Group A began to increase, but the NOx level remained the same. Group B showed no significant changes.

Conclusions

This study is the first to show that ADMA is promoted and nitric oxide is suppressed in short SGA children and that GH therapy affects the production of ADMA and nitric oxide.
Optimization of machining parameters of composites using multi-attribute decision-making techniques: A review
Authors: Arun Ramnath R , Thyla PR , Mahendra Kumar N , Aravind S
Published: October 2017

An in-depth literature survey of machining study on fiber-matrix composites is presented in this review paper. The review work mainly focuses on optimization of machining parameters in composite materials with different machining factors. Conventional machining processes such as turning, drilling and milling as well as composite materials which are reinforced with fibers are considered in this study. Machining aspects on various fiber matrix composites has been carried out over a long period of time. In this review work, conflicting conditions of multi-attribute decision-making techniques and machining conditions are focused. The optimization study on machining parameters is done, considering both priori and posteriori approach including advanced optimization techniques. Optimization of machining parameters in fiber reinforced particulate composites has not been explored earlier. The review work on machining study of composites was not attempted earlier and hence this work provides valuable information for subsequent researchers to enhance the scope of research work in particle-reinforced polymer composites.
Care Configurations and Unmet Care Needs in Older Men and Women
Authors: Potter Andrew J.
Published: September 2017

Older adults frequently experience adverse consequences as the result of unmet care needs, including not getting dressed and going without food when hungry. Previous studies have noted that characteristics of the caregiver network may be associated with unmet needs. Using National Health and Aging Trends Study data, I modeled the association between care configurations and unmet needs for men and women. In generalized linear models, formal care was not associated with unmet need among women or men. Compared with recipients of spousal care, men receiving care from one nonspousal caregiver, and men and women receiving care from any other configuration, had higher odds of unmet needs. The level of difficulty with daily tasks was strongly associated with unmet needs. These findings support monitoring older adults not receiving spousal care, increasing access to formal care, and regularly assessing level of difficulty with daily tasks in clinical and research settings.
Novel organosoluble polyarylates based on diphenylamine-fluorene units
Authors: Meng Shiyao , Sun Ningwei , Su Kaixin , Zhao Xiaogang , Wang Daming , Zhou Hongwei , Chen Chunhai
Published: October 2017

Two kinds of polyarylates with diphenylamine-fluorene units were synthesized from the bisphenol monomer “ N, N-di(4-hydroxyphenyl)-2-amino-9,9-dimethylfluorene” with two different benzenedicarbonyl chlorides. These polyarylates were highly soluble in N, N-dimethylacetamide, tetrahydrofuran, and chloroform and could be easily solution-cast into transparent films. Both of the polyarylates exhibited a couple of reversible redox with half-wave potentials in the range of 0.87–0.90 V. During the electrochromic process, the color of the film changed from colorless (neutral state) to grey green (oxidation state) with a high coloration efficiency of 242 cm2 C−1. Compared with the polyarylates prepared from terephthaloyl chloride, the polyarylates prepared from isophthaloyl chloride exhibited enhanced fluorescence because of the reduced charge-transfer effect. Furthermore, its fluorescence could be reversibly switched under the applied potentials.
Dynamic instrumented palpation – a new method for soft tissue quality assessment: application to prostate disease diagnosis
Authors: Yang TH Jimmy , Phipps Simon , Leung Steve KW , Reuben Robert L , Habib Fouad K , McNeill S Alan
Published: September 2017

The objective is to establish the feasibility of using dynamic instrumented palpation, a novel technique of low-frequency mechanical testing, applied here to diagnose soft tissue condition. The technique is applied, in vitro, to samples of excised prostate gland affected by benign prostate hyperplasia and/or prostate cancer. Particular attention is paid to the relationship between the histological structure of the tissue and the dynamic mechanical properties in an attempt to separate patient-specific aspects from histopathological condition (i.e. prostate cancer or benign prostate hyperplasia). The technique is of clinical interest because it is potentially deployable in vivo. Prostate samples were obtained from a total of 36 patients who had undergone transurethral resection of the prostate to relieve prostatic obstruction and 4 patients who had undergone radical cystoprostatectomy for bladder cancer. Specimens (chips) recovered from transurethral resection of the prostate were of nominal size 5 mm × 8 mm and thicknesses between 2 and 4 mm, whereas those from the cystoprostatectomy were in the form of transverse slices of thickness approximately 6 mm. Specimens were mechanically tested by a controlled strain cyclic compression technique, and the resulting dynamic mechanical properties expressed as the amplitude ratio and phase difference between the cyclic stress and cyclic strain. After mechanical testing, the percentage areas of glandular and smooth muscle were measured at each probe point. Good contrast between the dynamic modulus of chips from benign prostate hyperplasia and prostate cancer patients was demonstrated, and absolute values similar to those published by other authors are reported. For the slices, modulus values were considerably higher than for chips, and good in-patient mechanical contrast was revealed for predominantly nodular and predominantly stromal areas. Extending this classification between patients required pattern recognition techniques. Overall, the study has demonstrated that dynamic mechanical properties can potentially be used for diagnosis of prostate condition using in vivo measurements.
The Role of Powerlessness Among Health Care Workers in Tuberculosis Infection Control
Authors: Chapman Helena J. , Veras-Estévez Bienvenido A. , Pomeranz Jamie L. , Pérez-Then Eddy N. , Marcelino Belkys , Lauzardo Michael
Published: September 2017

Due to their occupational exposure in health care settings, health care workers (HCW) have increased risk of Mycobacterium tuberculosis infection. They face challenges to remain up-to-date with evidence-based clinical practices and translate educational information into actions in infection control practices. Our purpose was to examine this “knowledge−action” gap about how HCWs understand their occupational M. tuberculosis risk and use recommended infection control measures in clinical practices in the Dominican Republic (DR). We conducted 10 focus groups with 40 physicians and nurses at two tertiary-level DR institutions. Using grounded theory methods, we developed a theoretical model to describe the decision-making process related to adherence to M. tuberculosis infection control measures in clinical practice. Findings highlight intrinsic and extrinsic factors that influenced the observed knowledge−action gap related to M. tuberculosis infection control practices in two DR health institutions.
Population Pharmacokinetics of Enoxaparin in Pediatric Patients
Authors: Moffett Brady S. , Lee-Kim YoungNa , Galati Marianne , Mahoney Donald , Shah Mona D. , Teruya Jun , Yee Donald
Published: September 2017

Background: There are no studies evaluating the pharmacokinetics of enoxaparin in the hospitalized pediatric patient population. Objective: To characterize the pharmacokinetics of enoxaparin in pediatric patients. Methods: A retrospective review of inpatients 1 to 18 years of age admitted to our institution who received enoxaparin with anti–factor Xa activity level monitoring was performed. Demographic variables, enoxaparin dosing, and anti–factor Xa activity levels were collected. Population pharmacokinetic analysis was performed with bootstrap analysis. Simulation (n = 10 000) was performed to determine the percentage who achieved targeted anti-Xa levels at various doses. Results: A total of 853 patients (male 52.1%, median age = 12.2 years; interquartile range [IQR] = 4.6-15.8 years) received a mean enoxaparin dose of 0.86 ± 0.31 mg/kg/dose. A median of 3 (IQR = 1-5) anti–factor Xa levels were sampled at 4.4 ± 1.3 hours after a dose, with a mean anti–factor Xa level of 0.52 ± 0.23 U/mL. A 1-compartment model best fit the data, and significant covariates included allometrically scaled weight, serum creatinine, and hematocrit on clearance, and platelets on volume of distribution. Simulations were run for patients both without and with reduced kidney function (creatinine clearance of ≤30 mL/min/1.73 m2). A dose of 1 mg/kg/dose every 12 hours had the highest probability (72.3%) of achieving an anti-Xa level within the target range (0.5-1 U/mL), whereas a dose reduction of ~30% achieved the same result in patients with reduced kidney function. Conclusions: Pediatric patients should initially be dosed at 1-mg/kg/dose subcutaneously every 12 hours for treatment of thromboembolism followed by anti-Xa activity monitoring. Dose reductions of ~30% for creatinine clearance ≤30 mL/min/1.73 m2 are required.
Open Reduction Assisted With an External Fixator and Internal Fixation With Calcaneal Locking Plate for Intra-articular Calcaneal Fractures
Authors: Yao Hui , Lu Huading , Zhao Huiqing , Lv Lulu , Hou Gang
Published: September 2017

Background:

The extensile lateral approach (ELA) has been considered to be a standard approach for displaced intra-articular calcaneal fractures (DICF) because it provides excellent exposure and allows direct reduction of the depressed posterior facet fragment. But continuous retraction during surgery needs sufficient manpower and may cause ischemia. Failure of rigid fixation of DICF will not allow for early weight bearing and may lead to a loss of reduction. To avoid these disadvantages, this study presents open reduction assisted with an external fixator and internal fixation with a calcaneal locking plate.

Methods:

A series of 58 patients with 62 DICFs were treated over a period of 49 months. All patients were clinically and radiologically followed up with a mean follow-up of 35 (range 29-42) months. Clinical follow-up included visual analog scale (VAS), the American Orthopaedic Foot & Ankle Society (AOFAS) hindfoot score, and ability to work. Radiologic follow-up included axial and lateral radiographs and measurements of the Bohler angle and Gissane angle.

Results:

At the final follow-up, all fractures had healed. The mean VAS score was 2.9 (range 0 to 8, SD 1.9) and the average AOFAS score was 71 (range 55-85, SD 8.1). The mean postoperative Bohler angle immediately after the surgery was 28.3 degrees (range 13.0-44.6, SD 7.0), which decreased to 27.5 degrees (range 12.2-43.3, SD 7.0) at the final follow-up, and the mean postoperative Gissane angle after the surgery was 116.3 degrees (range 94.9-131.5, SD 9.0) which finally increased to 118.4 degrees (range 94.5-135.8, SD 9.3). No statistically significant differences regarding Bohler and Gissane angles were found between different Sanders fracture types ( P>.05).

Conclusion:

The presented operative technique was found to provide comparable reduction of Sanders type II-IV injuries.

Level of Evidence:

Level III, case control study.
Evaluation of Specific Administering Devices for Antineoplastic Drugs Compounded in Syringes in Paediatry: Methodology Proposal
Authors: Lefebvre Maximilien , Simon Nicolas , Vasseur Michèle , Sidikou Ousseini , Barthélémy Christine , Décaudin Bertrand , Odou Pascal
Published: October 2017

Purpose

The aims of this study were to propose a simple methodology to assess the rinsing volume of syringe extension sets and to compare several marketed devices.

Methods

A UV-spectrophotometry assay using quinine hydrochloride as drug substitute was developed. Quinine concentration ranged from 20 to 200 µg/ml. The assay was validated with the accuracy profile method and tested on five different assemblies (device+extension sets) with different dead-space volumes (1.28–2.80 ml) and at two different quinine concentrations (0.3 and 8.0 mg/ml). Rinsing was performed stepwise with water for injection until reaching an undetectable quinine concentration. After fitting the data with a Weibull model, assemblies were compared with an ANOVA performed on ranks (GraphPad, La Jolla, USA).

Results

The within-day and between-day precision ranges were 0.39–0.81 and 0.48–0.84%, respectively. The lower limit of quantification was 4.26 µg/ml. The volume required to completely rinse the infusion line was different according to the initial drug concentration and to the device assessed: from 6 to 10 ml for a low quinine concentration and from 7 to 17 ml for a high quinine concentration.

Conclusion

This study shows that a simple, cheap and easy-to-use methodology may be used to assess the rinsing volume of syringe extension sets. The rinsing volume is different according to the tested device.
Am I a Qualified Literacy Researcher and Educator? A Counter-Story of a Professional Journey of One Asian Male Literacy Scholar in the United States
Authors: Jang Bong Gee
Published: October 2017

Although there has been a significant increase in the number of minority faculty members in higher education, little is known about potential barriers and challenges we face during their early career development. In this counter-story article, I share my own professional experiences regarding the choices I made and obstacles I faced in developing my own career including both teaching and research. Compared with mainstream early career scholars, I realized that there are certain areas or methods that I was expected to teach or research. I hope that my counter-story presented in this article can contribute to understanding the conflicts and labels that international faculty may face and reframing them as potential assets that we can develop and bring into meaningful literacy practice.
Promoting the Accessibility of SWPBIS for Students With Severe Disabilities
Authors: Loman Sheldon L. , Strickland-Cohen M. Kathleen , Walker Virginia L.
Published: October 2017

This study heeds a decade-long call to action to examine the accessibility of Schoolwide Positive Behavioral Interventions and Supports (SWPBIS) for students with severe disabilities. To improve the accessibility of SWPBIS, Universal Design for Learning (UDL) and evidence-based practices were used to teach three students with severe disabilities schoolwide behavior expectations in inclusive schoolwide settings. Special education teachers from three different elementary schools adapted their campus SWPBIS Tier 1 lesson plans with additional visual supports, social narratives, and systematic instructional procedures. All participants showed improvement as evidenced by a reduction in the duration of their problem behavior in schoolwide settings. Implementing teachers found the intervention and corresponding materials to be socially valid.
Proteomics: Analysis of Spectral Data
Authors: Burke Harry B
Published: October 2017

The goal of disease-related proteogenomic research is a complete description of the unfolding of the disease process from its origin to its cure. With a properly selected patient cohort and correctly collected, processed, analyzed data, large scale proteomic spectra may be able to provide much of the information necessary for achieving this goal. Protein spectra, which are one way of representing protein expression, can be extremely useful clinically since they can be generated from blood rather than from diseased tissue. At the same time, the analysis of circulating proteins in blood presents unique challenges because of their heterogeneity, blood contains a large number of different abundance proteins generated by tissues throughout the body. Another challenge is that protein spectra are massively parallel information. One can choose to perform top-down analysis, where the entire spectra is examined and candidate peaks are selected for further assessment. Or one can choose a bottom-up analysis, where, via hypothesis testing, individual proteins are identified in the spectra and related to the disease process. Each approach has advantages and disadvantages that must be understood if protein spectral data are to be properly analyzed. With either approach, several levels of information must be in tegrated into a predictive model. This model will allow us to detect disease and it will allow us to discover therapeutic interventions that reduce the risk of disease in at-risk individuals and effectively treat newly diagnosed disease.
Databases and QSAR for Cancer Research
Authors: Malik Adeel , Singh Hemajit , Andrabi Munazah , Husain Syed Akhtar , Ahmad Shandar
Published: October 2017

In this review, we take a survey of bioinformatics databases and quantitative structure-activity relationship studies reported in published literature. Databases from the most general to special cancer-related ones have been included. Most commonly used methods of structure-based analysis of molecules have been reviewed, along with some case studies where they have been used in cancer research. This article is expected to be of use for general bioinformatics researchers interested in cancer and will also provide an update to those who have been actively pursuing this field of research.
Cancer Informatics in the U.K.: The NCRI Informatics Initiative
Authors: Reddington Fiona , Wilkinson J. Max , Clark Robin , Parkinson Helen , Kerr Peter , Begent Richard
Published: October 2017

The arrival of high-throughput technologies in cancer science and medicine has made the possibility for knowledge generation greater than ever before. However, this has brought with it real challenges as researchers struggle to analyse the avalanche of information available to them. A unique U.K.-based initiative has been established to promote data sharing in cancer science and medicine and to address the technical and cultural issues needed to support this.
Tumor Genome Wide DNA Alterations Assessed by Array CGH in Patients with Poor and Excellent Survival following Operation for Colorectal Cancer
Authors: Lagerstedt Kristina K. , Staaf Johan , Jönsson Göran , Hansson Elisabeth , Lönnroth Christina , Kressner Ulf , Lindström Lars , Nordgren Svante , Borg Åke , Lundholm Kent
Published: October 2017

Genome wide DNA alterations were evaluated by array CGH in addition to RNA expression profiling in colorectal cancer from patients with excellent and poor survival following primary operations.

DNA was used for CGH in BAC and cDNA arrays. Global RNA expression was determined by 44K arrays. DNA and RNA from tumor and normal colon were used from cancer patients grouped according to death, survival or Dukes A, B, C and D tumor stage. Confirmed DNA alterations in all Dukes A – D were judged relevant for carcinogenesis, while changes in Dukes C and D only were regarded relevant for tumor progression.

Copy number gain was more common than loss in tumor tissue (p < 0.01). Major tumor DNA alterations occurred in chromosome 8, 13, 18 and 20, where short survival included gain in 8q and loss in 8p. Copy number gains related to tumor progression were most common on chromosome 7, 8, 19, 20, while corresponding major losses appeared in chromosome 8. Losses at chromosome 18 occurred in all Dukes stages. Normal colon tissue from cancer patients displayed gains in chromosome 19 and 20. Mathematical Vector analysis implied a number of BAC-clones in tumor DNA with genes of potential importance for death or survival.

The genomic variation in colorectal cancer cells is tremendous and emphasizes that BAC array CGH is presently more powerful than available statistical models to discriminate DNA sequence information related to outcome. Present results suggest that a majority of DNA alterations observed in colorectal cancer are secondary to tumor progression. Therefore, it would require an immense work to distinguish primary from secondary DNA alterations behind colorectal cancer.
Simultaneous EGFR and VEGF Alterations in Non-Small Cell Lung Carcinoma Based on Tissue Microarrays
Authors: Tsiambas Evangelos , Stamatelopoulos Athanasios , Karameris Andreas , Panagiotou Ioannis , Rigopoulos Dimitrios , Chatzimichalis Antonios , Bouros Demosthenes , Patsouris Efstratios
Published: October 2017

Background

Epidermal growth factor receptor (EGFR) overexpression is observed in significant proportions of non-small cell lung carcinomas (NSCLC). Furthermore, overactivation of vascular endothelial growth factor (VEGF) leads to increased angiogenesis implicated as an important factor in vascularization of those tumors.

Patients and Methods

Using tissue microarray technology, forty-paraffin ( n = 40) embedded, histologically confirmed primary NSCLCs were cored and re-embedded into a recipient block. Immunohistochemistry was performed for the determination of EGFR and VEGF protein levels which were evaluated by the performance of computerized image analysis. EGFR gene amplification was studied by chromogenic in situ hybridization based on the use of EGFR gene and chromosome 7 centromeric probes.

Results

EGFR overexpression was observed in 23/40 (57.5%) cases and was correlated to the stage of the tumors ( p = 0.001), whereas VEGF was overexpressed in 35/40 (87.5%) cases and was correlated to the stage of the tumors ( p = 0.005) and to the smoking history of the patients ( p = 0.016). Statistical significance was assessed comparing the protein levels of EGFR and VEGF ( p = 0.043, k = 0.846). EGFR gene amplification was identified in 2/40 (5%) cases demonstrating no association to its overall protein levels ( p = 0.241), whereas chromosome 7 aneuploidy was detected in 7/40 (17.5%) cases correlating to smoking history of the patients ( p = 0.013).

Conclusions

A significant subset of NSCLC is characterized by EGFR and VEGF simultaneous overexpression and maybe this is the eligible target group for the application of combined anti-EGFR/VEGF targeted therapies at the basis of genetic deregulation (especially gene amplification for EGFR).
Common Peak Approach Using Mass Spectrometry Data Sets for Predicting the Effects of Anticancer Drugs on Breast Cancer
Authors: Ushijima Masaru , Miyata Satoshi , Eguchi Shinto , Kawakita Masanori , Yoshimoto Masataka , Iwase Takuji , Akiyama Futoshi , Sakamoto Goi , Nagasaki Koichi , Miki Yoshio , Noda Tetsuo , Hoshikawa Yutaka , Matsuura Masaaki
Published: October 2017

We propose a method for biomarker discovery from mass spectrometry data, improving the common peak approach developed by Fushiki et al. ( BMC Bioinformatics, 7:358, 2006). The common peak method is a simple way to select the sensible peaks that are shared with many subjects among all detected peaks by combining a standard spectrum alignment and kernel density estimates. The key idea of our proposed method is to apply the common peak approach to each class label separately. Hence, the proposed method gains more informative peaks for predicting class labels, while minor peaks associated with specific subjects are deleted correctly. We used a SELDI-TOF MS data set from laser microdissected cancer tissues for predicting the treatment effects of neoadjuvant therapy using an anticancer drug on breast cancer patients. The AdaBoost algorithm is adopted for pattern recognition, based on the set of candidate peaks selected by the proposed method. The analysis gives good performance in the sense of test errors for classifying the class labels for a given feature vector of selected peak values.
A Practical Multifaceted Approach to Selecting Differentially Expressed Genes
Authors: Zheng Yingye , Pepe Margaret
Published: October 2017

Consider a gene expression array study comparing two groups of subjects where the goal is to explore a large number of genes in order to select for further investigation a subset that appear to be differently expressed. There has been much statistical research into the development of formal methods for designating genes as differentially expressed. These procedures control error rates such as the false detection rate or family wise error rate. We contend however that other statistical considerations are also relevant to the task of gene selection. These include the extent of differential expression and the strength of evidence for differential expression at a gene. Using real and simulated data we first demonstrate that a proper exploratory analysis should evaluate these aspects as well as decision rules that control error rates. We propose a new measure called the mp-value that quantifies strength of evidence for differential expression. The mp-values are calculated with a resampling based algorithm taking into account the multiplicity and dependence encountered in microarray data. In contrast to traditional p-values our mp-values do not depend on specification of a decision rule for their definition. They are simply descriptive in nature. We contrast the mp-values with multiple testing p-values in the context of data from a breast cancer prognosis study and from a simulation model.
Change Detection & Characterization: A New Tool for Imaging Informatics and Cancer Research
Authors: Patriarche Julia W. , Erickson Bradley J.
Published: October 2017

Modern imaging systems are able to produce a rich and diverse array of information, regarding various facets of anatomy and function. The quantity of information produced by these systems is so bountiful, however, as to have the potential to become a hindrance to clinical assessment. In the context of serial image evaluation, computer-based change detection and characterization is one important mechanism to process the information produced by imaging systems, so as to reduce the quantity of data, direct the attention of the physician to regions of the data which are the most informative for their purposes, and present the data in the form in which it will be the most useful. Change detection and characterization algorithms may serve as a basis for the creation of an objective definition of progression, which will reduce inter and intra-observer variability, and facilitate earlier detection of disease and recurrence, which in turn may lead to improved outcomes. Decreased observer variability combined with increased acuity should make it easier to discover promising therapies. Quantitative measures of the response to these therapies should provide a means to compare the effectiveness of treatments under investigation. Change detection may be applicable to a broad range of cancers, in essentially all anatomical regions. The source of information upon which change detection comparisons may be based is likewise broad. Validation of algorithms for the longitudinal assessment of cancer patients is expected to be challenging, though not insurmountable, as the many facets of the problem mean that validation will likely need to be approached from a variety of vantage points. Change detection and characterization is quickly becoming a very active field of investigation, and it is expected that this burgeoning field will help to facilitate cancer care both in the clinic and research.
Exploratory Visual Analysis of Statistical Results from Microarray Experiments Comparing High and Low Grade Glioma
Authors: Reif David M. , Israel Mark A. , Moore Jason H.
Published: October 2017

The biological interpretation of gene expression microarray results is a daunting challenge. For complex diseases such as cancer, wherein the body of published research is extensive, the incorporation of expert knowledge provides a useful analytical framework. We have previously developed the Exploratory Visual Analysis (EVA) software for exploring data analysis results in the context of annotation information about each gene, as well as biologically relevant groups of genes. We present EVA as a flexible combination of statistics and biological annotation that provides a straightforward visual interface for the interpretation of microarray analyses of gene expression in the most commonly occuring class of brain tumors, glioma. We demonstrate the utility of EVA for the biological interpretation of statistical results by analyzing publicly available gene expression profiles of two important glial tumors. The results of a statistical comparison between 21 malignant, high-grade glioblastoma multiforme (GBM) tumors and 19 indolent, low-grade pilocytic astrocytomas were analyzed using EVA. By using EVA to examine the results of a relatively simple statistical analysis, we were able to identify tumor class-specific gene expression patterns having both statistical and biological significance. Our interactive analysis highlighted the potential importance of genes involved in cell cycle progression, proliferation, signaling, adhesion, migration, motility, and structure, as well as candidate gene loci on a region of Chromosome 7 that has been implicated in glioma. Because EVA does not require statistical or computational expertise and has the flexibility to accommodate any type of statistical analysis, we anticipate EVA will prove a useful addition to the repertoire of computational methods used for microarray data analysis. EVA is available at no charge to academic users and can be found at http://www.epistasis.org .
GSMA: Gene Set Matrix Analysis, An Automated Method for Rapid Hypothesis Testing of Gene Expression Data
Authors: Cheadle Chris , Watkins Tonya , Fan Jinshui , Williams Marc A. , Georas Steven , Hall John , Rosen Antony , Barnes Kathleen C.
Published: October 2017

Background

Microarray technology has become highly valuable for identifying complex global changes in gene expression patterns. The assignment of functional information to these complex patterns remains a challenging task in effectively interpreting data and correlating results from across experiments, projects and laboratories. Methods which allow the rapid and robust evaluation of multiple functional hypotheses increase the power of individual researchers to data mine gene expression data more efficiently.

Results

We have developed (gene set matrix analysis) GSMA as a useful method for the rapid testing of group-wise up- or down-regulation of gene expression simultaneously for multiple lists of genes (gene sets) against entire distributions of gene expression changes (datasets) for single or multiple experiments. The utility of GSMA lies in its flexibility to rapidly poll gene sets related by known biological function or as designated solely by the end-user against large numbers of datasets simultaneously.

Conclusions

GSMA provides a simple and straightforward method for hypothesis testing in which genes are tested by groups across multiple datasets for patterns of expression enrichment.
Buprenorphine/Naloxone Maintenance Therapy: an Observational Retrospective Report on the Effect of Dose on 18 months Retention in an Office-Based Treatment Program
Authors: Parran Theodore V , Mace AG , Dahan Yael J , Adelman Christopher A , Kolganov Mykola
Published: October 2017

Context and objective:

Buprenorphine has been available with few reports of the dose range necessary to adequately maintain patients. We report on the effect of 8 mg/d versus 16 mg/d of buprenorphine on long-term patient retention in office-based opioid maintenance (OBOMT).

Design, setting, and participants:

Case series, at an urban hospital-based primary care clinic providing OBOMT to 157 opiate-dependent, low socioeconomic status, uninsured, nonhomeless patients.

Intervention:

The OBOMT program operated by a comprehensive sobriety treatment program experienced State funding cuts. Thus, after 2 years, the program was required by the State funder to decrease the buprenorphine maintenance dose from 16 to 8 mg/d for all new admissions. We report on patient retention before and after dose reduction.

Main outcome measures:

The primary outcomes of this study were to measure and compare patient retention in the 2 cohorts at each point of treatment transition over the 18 months following OBOMT initiation.

Results:

No significant differences in patient retention were observed between the 16 and 8 mg/d patient cohorts. Lower dose buprenorphine maintenance (8 mg/d) in uninsured patients enrolled in publicly funded long-term OBOMT combined with comprehensive sobriety counseling was as effective as higher dose therapy (16 mg/d) in promoting patient retention throughout the study period. This lower dose resulted in a substantial saving to the public funding agency.

Conclusions:

In an observational retrospective report, retention in treatment of opiate-addicted patients was the same at 8 and 16 mg/d buprenorphine doses after 18 months. These data have implications for public and managed care funding of OBOMT, for the general prescribing of buprenorphine in outpatient care, and may be instructive in the ongoing debate about the relationship between buprenorphine dose.
Tagging as Lazy Technique: On the Politics of Art as Work
Authors: Russell Francis
Published: October 2017

This article looks at the graffiti practice known as “tagging”—and, more specifically, “scratching” or “scratch tagging”—as a social phenomenon that can aid the thinking through of potential resistance to the hegemony of what is sometimes referred to as entrepreneurial subjectivity. While much interesting work has been produced on more “artistic” forms of graffiti—as have been made famous by stencil artists such as Banksy—there is very little work that looks to read scratch tagging as a form of political artistic practice, albeit one that emerges unconsciously and outside of what is commonly designated as the “art world.” Given that the figure of the contemporary artist is so wedded to the flows of international capital, it is worthwhile considering how the scratch tagger unconsciously engages in what the contemporary theorist Maurizio Lazzarato has referred to as “lazy techniques:” that is, forms of practice that are not circumscribed within the dominant logics of utility and productivity and are, accordingly, potentially resistant to the logics underpinning neoliberal capital.