Institute Website Research Articles

A FreeSurfer view of the cortical transcriptome generated from the Allen Human Brain Atlas.

The Allen Human Brain Atlas provides an anatomically comprehensive view of gene expression in the brain (Hawrylycz et al., 2012). The complete transcriptome dataset consists of 58,692 measurements of gene expression in 3702 brain samples obtained from 6 individuals. The resulting product, over 200 million gene expression values, can be overwhelming for neuroscientists seeking to use the data. For example, data for a single gene consist of three interlinked files when downloaded from the Allen Institute website. The local expression values are associated with X, Y, and Z coordinates in the MNI152 atlas (Mazziotta et al., 2001), thus allowing one to map these values to other brain atlases. To reduce the complexity of the Allen data, we have summarized the data into the Desikan–Killiany cortical atlas built into the FreeSurfer software for automatic labeling of regions of interest (Desikan et al., 2006). FreeSurfer allows one to segment magnetic resonance images (MRIs) into 68 cortical regions and to estimate their cortical thickness, surface area and volume (http://surfer.nmr.mgh.harvard.edu/). These cortical measurements are stable and agree with past histological studies (Fischl and Dale, 2000; Han et al., 2006; Scholtens et al., 2015). FreeSurfer has been used widely, with over 600 reports covering a broad range of topics that include brain development, aging and a variety of brain disorders (PubMed, May 2015). Adding the perspective of gene expression could facilitate interpretation of these reports. For example, we recently found that the magnitude of group differences in cortical thickness between cannabis users and non-users correlates with regional variations in expression levels of cannabis receptor 1 (CNR1) (French et al., 2015).

Assessing the Spectrum of Primate Behaviors To Produce a Path for Business Conflict Resolution

Editor's note: Longtime Alternatives columnist Bob Creo, a veteran Pittsburgh neutral, is revisiting his classic CPR Institute website columns of a decade ago in a Back to Basics Series that he has subtitled “Human Problems, Human Solutions.” These updated and expanded columns, in print for the first time, began late last year. He has revisited and re‐examined mediation‐room techniques and practice issues. Last month, he focused on the science behind the behaviors common to primates, and how humans can learn about addressing conflict from their ape, chimp, and monkey cousins. In this column, he turns to placing these behaviors against mediation process points, and translates them into a 10‐point checklist for ADR success. He also provides a comprehensive resource list.

The board of directors and corporate reputation: an empirical analysis

PurposeThe purpose of this paper is to test the association between board of director characteristics and corporate reputation.Design/methodology/approachLogistic and multivariate regressions are performed to analyse whether the board of director characteristics are associated with the level of corporate reputation. The sample is composed of listed companies in the Madrid Stock Exchange (Índice General de la Bolsa de Madrid) at least once during the period 2004-2010. Corporate governance data were manually extracted from governance reports released by Spanish companies. The data for the design of a corporate reputation measure were obtained from the Monitor Español de Reputación Corporativa (MERCO) institute web site.FindingsResults from the empirical analysis show that Spanish companies that appear high up in terms of ranking in the reputation index provided by MERCO tend to have a higher percentage of independent directors as well as more female directors on their board. Firm size and the image of the president of a firm are also linked to corporate reputation.Originality/valueThe results have direct implications for the management of corporate governance mechanisms by shareholders who should take into account their role in the creation and maintenance of corporate reputation.

Patterns of access to information on protection against UV during the Brazilian summer: is there such a thing as the "summer effect"?

Internet search patterns associated with "windows" of collective interest have been increasingly investigated in the field of public health. This article sets out to identify search patterns relating to the quest for information on skin protection after the perception of excessive exposure to UV radiation - the so-called "summer effect" as it is commonly referred to in Brazil. To calculate the number of hits on the Brazilian National Cancer Institute website - a renowned source of information resources on prevention - log analyzer software was used to measure the volume of hits on specific content pages. The pages on skin protection and self-examination (pages of interest) were monitored over a 48-month period. It was seen that, although the monthly average of hits on pages of interest revealed statistically significant annual growth, the results for the analysis of variance showed no significant differences between the number of hits in the summer compared with other months (p = 0.7491). In short, the perception of intense exposure to the summer sun did not encourage further interest to search for information on prevention.

Back to Basics: Primates and Me

Editor's note: Longtime Alternatives columnist Bob Creo, a veteran Pittsburgh neutral, is revisiting his classic CPR Institute website columns of a decade ago in a Back to Basics Series that he has subtitled “Human Problems, Human Solutions.” These updated and expanded columns, in print for the first time, began in November. He has revisited and re‐examined mediation‐room techniques and practice issues. This month, the focus is on behavior common to primates, and how humans can learn from their ape, chimp, and monkey cousins.

Back to Basics: Moscow Rules!

Editor's note: Longtime Alternatives columnist Bob Creo, a veteran Pittsburgh neutral, is revisiting his classic CPR Institute website columns of a decade ago in a Back to Basics Series that he has subtitled “Human Problems, Human Solutions.” In his more‐recent Master Mediator columns, Creo has focused on neuroscience, psychological factors and cognitive biases that affect dispute resolution. These updated Back to Basics columns, in print for the first time, began in November, revisiting mediation‐room techniques and practice issues. This month, the focus is on.

Back To Basics: I Mediate, Therefore I Am?

Editor's note: Longtime Alternatives columnist Bob Creo, a veteran Pittsburgh neutral, is revisiting his classic CPR Institute website columns of a decade ago in a Back to Basics Series that he has subtitled “Human Problems, Human Solutions.” In his recent Master Mediators columns, Creo has focused on neuroscience, psychological factors and cognitive biases that affect dispute resolution. These updated Back to Basics columns, in print for the first time, began in November, revisiting mediation‐room techniques and practice issues. This month, the focus is on how the humanity and values of the mediator align with the process and the participants.

Tutorial dialogues and gist explanations of genetic breast cancer risk.

The intelligent tutoring system (ITS) BRCA Gist is a Web-based tutor developed using the Shareable Knowledge Objects (SKO) platform that uses latent semantic analysis to engage women in natural-language dialogues to teach about breast cancer risk. BRCA Gist appears to be the first ITS designed to assist patients' health decision making. Two studies provide fine-grained analyses of the verbal interactions between BRCA Gist and women responding to five questions pertaining to breast cancer and genetic risk. We examined how "gist explanations" generated by participants during natural-language dialogues related to outcomes. Using reliable rubrics, scripts of the participants' verbal interactions with BRCA Gist were rated for content and for the appropriateness of the tutor's responses. Human researchers' scores for the content covered by the participants were strongly correlated with the coverage scores generated by BRCA Gist, indicating that BRCA Gist accurately assesses the extent to which people respond appropriately. In Study 1, participants' performance during the dialogues was consistently associated with learning outcomes about breast cancer risk. Study 2 was a field study with a more diverse population. Participants with an undergraduate degree or less education who were randomly assigned to BRCA Gist scored higher on tests of knowledge than those assigned to the National Cancer Institute website or than a control group. We replicated findings that the more expected content that participants included in their gist explanations, the better they performed on outcome measures. As fuzzy-trace theory suggests, encouraging people to develop and elaborate upon gist explanations appears to improve learning, comprehension, and decision making.

Back To Basics: Rags and Me!

Editor's note: Veteran Alternatives columnist Bob Creo, a Pittsburgh neutral, is revisiting his classic CPR Institute website columns of a decade ago in a Back to Basics Series that he has subtitled “Human Problems, Human Solutions.” In his recent Master Mediators columns, Creo has focused on neuroscience, psychological factors and cognitive biases that affect dispute resolution. These updated Back to Basics columns, in print for the first time, began in November, revisiting mediation‐room techniques and practice issues. This month, the focus is on getting to closure.

Back to Basics: An ADR Intervention that Converts a Legal Problem to a Human Solution

Editor's note: Longtime Alternatives columnist Bob Creo, a veteran Pittsburgh neutral, is revisiting his classic CPR Institute website columns of a decade ago in a Back to Basics Series that he has subtitled “Human Problems, Human Solutions.” In his recent Master Mediators columns, Creo has focused on neuroscience, psychological factors and cognitive biases that affect dispute resolution. These updated Back to Basics columns, in print for the first time, began in November, revisiting mediation‐room techniques and practice issues. This month, the focus is on getting to closure.

Back To Basics: The Playing Field

Editor's note: Longtime Alternatives columnist Bob Creo, a veteran Pittsburgh neutral, is revisiting his classic CPR Institute website columns of a decade ago in a Back to Basics Series that he has subtitled “Human Problems, Human Solutions.” In his recent Master Mediators columns, Creo has focused on neuroscience, psychological factors and cognitive biases that affect dispute resolution. These updated Back to Basics columns, in print for the first time, began in November, revisiting mediation‐room techniques and practice issues. Still to come is an examination of the issues involved in getting to closure.

Exceptional responses in patients with metastatic colorectal cancer enrolled in first-in-man studies from 2002 through 2012.

687 Background: Understanding exceptional responses to therapy at the molecular level may open new venues for the treatment of patients with metastatic colorectal cancer (mCRC). Responses in first-in-man (FIM) studies with targeted therapies are rare and may indicate that actionable genetic aberrations are present in these patients. Methods: We utilized Scopus using the search term “phase 1 and solid tumors” to collect all FIM studies published between 2002 and 2012. We identified patients with mCRC who attained an exceptional response to therapy defined as a complete response (CR) or a partial response (PR) lasting > 6 months (m). Results: We identified 118 FIM studies enrolling 5,369 patients with advanced malignancies. mCRC was the most common tumor type, totaling 1,055 (19.6%) patients. Of these, two patients enrolled in protocols with MDX-1106 (anti PD-1) and RG7180 (mAb EGFR) attained a complete response (CR). Five patients had PR lasting > 6 m. These patients were treated with RG7180 (time on study 7.8 m), Apatinib, a VEGFR tyrosine kinase inhibitor (8.5 and 7.1 m), PV701, a replication-competent oncolytic virus (10 m) and RO4929097, a gamma-secretase inhibitor (7 m). In addition two patients had PR lasting < 6 m with regorafenib (5.3 m) and RG7180 (5.6 m). This database of exceptional responders to therapy will be publicly available at Huntsman Cancer Institute website. Currently, regorafenib and EGFR mAbs (cetuximab and panitumumab) are approved for use in mCRC. EGFR mAbs have shown improvement in survival in RAS wild-type mCRC. Clinical trials are underway evaluating apatinib. Anti-PD1s have shown limited activity as single agents in mCRC and are currently undergoing testing in combination with chemotherapy. Conclusions: We identified exceptional responses among patients with mCRC enrolled in FIM in the last decade. Ongoing efforts are directed to conduct next generation sequencing (NGS) in archived tissue from these patients. Ultimately, this initiative may facilitate the identification of biomarkers of response to be tested in clinical trials with these or novel drugs sharing similar mechanisms of action.

Efficacy of a web-based intelligent tutoring system for communicating genetic risk of breast cancer: a fuzzy-trace theory approach.

. Many healthy women consider genetic testing for breast cancer risk, yet BRCA testing issues are complex. . To determine whether an intelligent tutor, BRCA Gist, grounded in fuzzy-trace theory (FTT), increases gist comprehension and knowledge about genetic testing for breast cancer risk, improving decision making. . In 2 experiments, 410 healthy undergraduate women were randomly assigned to 1 of 3 groups: an online module using a Web-based tutoring system (BRCA Gist) that uses artificial intelligence technology, a second group read highly similar content from the National Cancer Institute (NCI) Web site, and a third that completed an unrelated tutorial. . BRCA Gist applied FTT and was designed to help participants develop gist comprehension of topics relevant to decisions about BRCA genetic testing, including how breast cancer spreads, inherited genetic mutations, and base rates. . We measured content knowledge, gist comprehension of decision-relevant information, interest in testing, and genetic risk and testing judgments. . Control knowledge scores ranged from 54% to 56%, NCI improved significantly to 65% and 70%, and BRCA Gist improved significantly more to 75% and 77%, P < 0.0001. BRCA Gist scored higher on gist comprehension than NCI and control, P < 0.0001. Control genetic risk-assessment mean was 48% correct; BRCA Gist (61%) and NCI (56%) were significantly higher, P < 0.0001. BRCA Gist participants recommended less testing for women without risk factors (not good candidates; 24% and 19%) than controls (50%, both experiments) and NCI (32%), experiment 2, P < 0.0001. BRCA Gist testing interest was lower than in controls, P < 0.0001. . BRCA Gist has not been tested with older women from diverse groups. . Intelligent tutors, such as BRCA Gist, are scalable, cost-effective ways of helping people understand complex issues, improving decision making.

Identification of transition bias in oxidized low density lipoprotein receptor 1 gene in buffalo

Background and aim: Though transition bias has been previously demonstrated in cattle, however, there has not been any study that has explored transition bias in buffalo nuclear genome. The aim of the present study was to evaluate the nucleotide substitution pattern in the Intron I of Oxidised Low Density Lipoprotein Receptor 1 (OLR1) gene in four breeds of Indian buffalo using 24 different nucleotide substitution models and evaluate their association with DNA methylation. Materials and Methods: Transition/transversion bias (R) was estimated by 24 different nucleotide substitution models available in MEGA 5.0. The transition/transversion bias (R) was estimated under the Kimura 2-parameter model. Substitution patterns and the transitions/transversions rates (r) were then estimated by Tamura-Nei-I and Tamura-Nei-II models. The CpG Island search was done by using CpG Plot Island online Software available at European Bioinformatics Institute (EBI) website. Results: The frequency of transition was found to be 3.5 times higher than that of the transversion mutation frequency. Out of 9 nucleotide substitutions, 7 transitions and 2 transversions were found. Among all the nucleotide substitutions, thymine to cytosine substitutions was observed to be very high. CpG Island search tool revealed that IntronI of OLR1 genes is a CpG rich region, thus prone to methylation. Conclusions: Higher transition frequency was found in the intronI of OLR1 gene, however due to the richness of methylated CpGs in the evaluated stretch of genome, the higher T↔C transitions could likely be a result of frequent deaminations of the methylated cytosines into thymines during the evolution of four buffalo breeds.

Book Reviews: Climate Change and Agriculture in sub-Saharan Africa

Both books are available as free downloads from the International Food Policy Research Institute (IFPRI) website at: http://www.ifpri.org/publication/west-africanagriculture-and-climate-change. These volumes are primarily concerned with the potential impact of climate change on agriculture in West and Southern Africa, respectively, and how this may be minimized through careful planning based on accurate foresight analysis. A third volume, dealing with East Africa, is due to be published on 3rd December 2013 (also available from the IFPRI website [see above]; ISBN 978-0-89629-205-5). Climate change, it may be argued, is the most significant threat to agriculture and, therefore, food security, worldwide. Drought, one of the most important consequences of climate change, already places severe constraints on agricultural productivity throughout Sub-Saharan Africa and in some countries of the region the effects have already reached crisis point, notably in the Horn of Africa, to be dealt with in the third volume. The greenhouse effect, it is predicted, will raise temperatures yet further and this, together with other factors, will lead to longer and even more severe periods of drought, imposing ever-increasing pressures on the already scarce supplies of that most precious of all commodities in the region, fresh water (see Grayson, 2013 for an excellent recent analysis of the global situation). Sub-Saharan Africa as a whole is climatologically extremely diverse, however, and although drought is the most significant issue for many of its constituent nations, other predicted consequences of climate change are likely to be of overwhelming importance to the agricultural productivity of others, especially the likelihood of more extreme weather events in general, higher temperatures and increased variation in precipitation patterns in both wet and dry areas. All these, like drought, impact most severely on the poorest members of any society; in other words, those least able and least well equipped to adapt to them rapidly and effectively. The two books reviewed here, together with the as yet unpublished third volume, must therefore be seen as being of the very greatest relevance to all concerned with both food security and the alleviation of poverty south of the Sahara. Given the current debates surrounding climate change issues, it is important to establish first the credentials of The International Food Policy Research, Institute (IFPRI), the organization responsible for the volumes. The institute is a member of the CGIAR (formerly Consultative Group on International Agricultural Research) Consortium. It was established in 1975 to ‘identify and analyze alternative national and international 1 Benin, Burkina Faso, Cote d’Ivoire, Ghana, Guinea, Liberia, Niger, Nigeria, Senegal, Sierra Leone and Togo. 2 Botswana, Lesotho, Malawi, Mozambique, South Africa, Swaziland, Zambia and Zimbabwe. 3 Burundi, Democratic Republic of Congo, Eritrea, Ethiopia, Kenya, Madagascar, Rwanda, Sudan (analyses of the data were completed before South Sudan separated from Sudan), Tanzania and Uganda.

Authorship Pattern, Degree of Collaboration and Research Publication Trend among Scientists/Researchers of CSIR-IMTECH, India 1991–2010: A Bibliometric Study

The Council of Scientific and Industrial Research-Institute of Microbial Technology (IMTECH), India, is the youngest and one of the productive research laboratories in India. It plays an important role in research in the fields of microbiology and biotechnology in India. Due to the importance of IMTECH, we decided to study its academic scientific output in the Web of Science during the years 1991–2010. This paper is an informetric analysis of 902 papers published by the scientists and researchers at the CSIR-IMTECH, Chandigarh, from 1991 to 2010, downloaded from the institute's website as well from science citation index-extended version (Web of Science) of the Thomson Scientific. There is no doubt that collaboration is a common phenomenon in research. This paper examined the collaborative strength and patterns of authorship among the CSIR-IMTECH scientists/researchers, covering a period of 20 years. The results of the data were analysed based on the number of articles published per year, pattern of authorship and the collaborative degree and strength of authors. The study shows that majority of the scientists preferred to publish research papers in joint authorship. Out of 902 articles, 753 (83.48%) were joint works, while only 149 (16.51%) were single-author works. The degree of author's collaboration was also calculated to be 0.83, while the mean numbers of single-author and joint authored articles were 7.45 and 37.65, respectively.

LIt.search: fast tracking access to Aboriginal and Torres Strait Islander health literature.

To develop and validate a PubMed search filter, LIt.search, that automatically retrieves Aboriginal and Torres Strait Islander health literature and to make it publicly accessible through the Lowitja Institute website. Search filter development phases included: (1) scoping of the publication characteristics of Aboriginal and Torres Start Islander literature; (2) advisory group input and review; (3) systematic identification and testing of MeSH and text word terms; (4) relevance assessment of the search filter's retrieved items; and (5) translation for use in PubMed through the web. Scoping study analyses demonstrated complexity in the nature and use of possible search terms and publication characteristics. The search filter achieved a recall rate of 84.8% in the full gold standard test set. To determine real-world performance, post-hoc assessment of items retrieved by the search filter in PubMed was undertaken with 87.2% of articles deemed as relevant. The search filter was constructed as a series of URL hyperlinks to enable one-click searching. LIt.search is a search tool that facilitates research into practice for improving outcomes in Aboriginal and Torres Strait Islander health and is publicly available on the Lowitja Institute website. WHAT IS KNOWN ABOUT THIS TOPIC?: Health professionals, researchers and decision makers can find it difficult to retrieve published literature on Aboriginal and Torres Strait Islander health easily, effectively and in a timely way. WHAT DOES THIS PAPER ADD?: This paper describes a new web-based searching tool, LIt.search, which facilitates access to the relevant literature. WHAT ARE THE IMPLICATIONS FOR PRACTICE?: Ready access to published literature on Aboriginal and Torres Strait Islander health reduces a barrier to the use of this evidence in practice. LIt.search encourages the use of this evidence to inform clinical judgement and policy and service decision-making as well as reducing the burdens associated with searching for community practitioners, academics and policy makers.

Success Rate and Risk Factors for Failure of Empirical Antifungal Therapy with Itraconazole in Patients with Hematological Malignancies: A Multicenter, Prospective, Open-Label, Observational Study in Korea

We assessed the success rate of empirical antifungal therapy with itraconazole and evaluated risk factors for predicting the failure of empirical antifungal therapy. A multicenter, prospective, observational study was performed in patients with hematological malignancies who had neutropenic fever and received empirical antifungal therapy with itraconazole at 22 centers. A total of 391 patients who had abnormal findings on chest imaging tests (31.0%) or a positive result of enzyme immunoassay for serum galactomannan (17.6%) showed a 56.5% overall success rate. Positive galactomannan tests before the initiation of the empirical antifungal therapy (P=0.026, hazard ratio [HR], 2.28; 95% confidence interval [CI], 1.10-4.69) and abnormal findings on the chest imaging tests before initiation of the empirical antifungal therapy (P=0.022, HR, 2.03; 95% CI, 1.11-3.71) were significantly associated with poor outcomes for the empirical antifungal therapy. Eight patients (2.0%) had premature discontinuation of itraconazole therapy due to toxicity. It is suggested that positive galactomannan tests and abnormal findings on the chest imaging tests at the time of initiation of the empirical antifungal therapy are risk factors for predicting the failure of the empirical antifungal therapy with itraconazole. (Clinical Trial Registration on National Cancer Institute website, NCT01060462)

A New Web-Based Tool for Group Audiologic Rehabilitation

The Group Rehabilitation Online Utility Pack (GROUP) was developed to encourage hearing health care professionals to offer group audiologic rehabilitation (GAR) as an integral part of adult hearing rehabilitation and to provide these professionals with the necessary tools to develop and offer GAR in their clinical practice. The GROUP is a dynamic interactive web-based program that allows visitors to craft and create GAR for their professional use. The tool includes the evidence for implementing GAR, content for preparation and planning, instruction for facilitating groups, and actual GAR activities. Each section includes ethnographic videos, allowing professionals to observe GAR in action. The GROUP program available on the Ida Institute website was developed with the intent to provide clinicians, academicians, researchers, and students a resource to facilitate the development and implementation of GAR programs throughout the world.

Inaccuracy and Testimonial Literature: The Case of Loung Ung's First They Killed My Father: A Daughter of Cambodia Remembers

In his 2001 review essay of three survivor accounts of the Cambodian genocide (1975-79), Sody Lay criticizes Loung Ung’s First They Killed My Father: A Daughter of Cambodia Remembers (2000) for historical and cultural inaccuracies, calling Ung’s testimonial text “a sensationalization and over-dramatization of the Killing Fields experience” (“Cambodian” 173). Lay not only accuses Ung of consciously manipulating her story for “the sake of making a buck,” but he also questions her status as a Cambodian: “Given Ung’s lack of memory and her apparent disdain for everything Khmer, it is not only ironic but misrepresentative for her book to be subtitled ‘a daughter of Cambodia remembers’” (181). The Khmer Institute Web site, which Lay co-founded and for which he serves as Executive Director, has published scathing reviews of Ung’s book with similar accusations regarding historical inaccuracies and cultural inauthenticity. One group of reviewers examines a section in First They Killed My Father in which the Ung family takes a trip in the early 1970s to Angkor Wat, pointing out that such a trip was impossible because the area was a battle zone at that time. The reviewers then note that Ung miscalculates Cambodia’s Angkorian period (from approximately the ninth to the fifteenth centuries) when she wrote that “Angkor Wat was built by powerful Khmer kings as monuments of self-glorification in the ninth century and completed three hundred years later” (Ung 67), reducing this seven-hundred-year period to half of its length. The reviewers conclude: “A true ‘daughter of Cambodia’ would not be so careless as to provide such blatantly incorrect information about these [Angkor Wat] temples, as they are an integral part of Khmer heritage and pride” (Hor, Lay, and Quinn). However, such harsh criticism does not take into account the impact on survivors such as Ung of losing family members, being separated from their homeland, and struggling with a new language and culture in an attempt to build a new home thousands of miles away from Cambodia, in a place with unfamiliar customs and rituals. Furthermore, not every Cambodian American has had identical experiences. In attempting to make sense of this controversy, we must explore how to take Lay’s charges into account while still valuing Ung’s memoir. This essay begins with a discussion of the Lay-Ung controversy in the context of the Cambodian diasporic community, paying close attention to the politics of representation and our need for multiple and diverse representations. Teri Shaffer Yamada’s work on Cambodian American autobiography informs the discussion of Ung’s First They Killed