Rolando Garcia-Milian

Detection and Typing of Human Papillomavirus DNA in Benign and Malignant Tumours of Laryngeal Epithelium

The role of human papillomaviruses (HPV) in laryngeal squamous cell carcinoma has not yet been established. Thirty-three cases of laryngeal squamous cell carcinoma were analysed for the presence of HPV DNA and compared with 25 cases of normal larynx and 29 cases of laryngeal squamous papilloma in their positivity index. The presence of HPV DNA was analysed by using L1 consensus primers and also by primers specific for the E7 gene of HPV types 16 and 18. Four normal laryngeal samples (16%) were positive for HPV DNA against the 24 samples (82%) (p < 0.001) found for laryngeal papilloma and 16 (48.5%) (p < 0.05) found for laryngeal squamous cell carcinoma. HPV 16 was the type most frequently found in laryngeal carcinoma samples. Our results support an etiologic role for this type of HPV in the pathogenesis of laryngeal carcinoma.

The presence of academic health sciences libraries on Facebook: the relationship between content and library popularity.

Social networks such as Facebook allow libraries to be proactive in reaching their users. While some libraries have popular Facebook pages, it remains unclear what attracts users to these pages. This study evaluates relationships between libraries’ Facebook page content and popularity. An analysis of 72 academic health sciences libraries’ Facebook pages showed positive correlations between number of library fans and number of tabs, photos, events, and wall posts on Facebook. Libraries posting videos had significantly more fans than libraries without them. This study contributes to an understanding of correlations between content and popularity on Facebook, with implications for library outreach.

The use of Research Electronic Data Capture (REDCap) software to create a database of librarian-mediated literature searches.

Expert-mediated literature searching, a keystone service in biomedical librarianship, would benefit significantly from regular methodical review. This article describes the novel use of Research Electronic Data Capture (REDCap) software to create a database of literature searches conducted at a large academic health sciences library. An archive of paper search requests was entered into REDCap, and librarians now prospectively enter records for current searches. Having search data readily available allows librarians to reuse search strategies and track their workload. In aggregate, this data can help guide practice and determine priorities by identifying users’ needs, tracking librarian effort, and focusing librarians’ continuing education.

Librarians as Part of Cross-Disciplinary, Multi-institutional Team Projects: Experiences from the VIVO Collaboration

Cross-disciplinary, team-based collaboration is essential for addressing todays complex research questions, and librarians are increasingly entering into such collaborations. This study identifies skills needed as librarians integrate into cross-disciplinary teams, based on the experiences of librarians involved in the development and implementation of VIVO, a research discovery and collaboration platform. Participants discussed the challenges, skills gained, and lessons learned throughout the project. Their responses were analyzed in the light of the science of team science literature, and factors affecting collaboration on the VIVO team were identified. Skills in inclusive thinking, communication, perseverance, adaptability, and leadership were found to be essential.

Moving beyond the bookshelves

VIRTUAL PROJECTS Moving beyond the bookshelves DOI: http://dx.doi.org/10.3163/1536-5050.101.4.002 Introduction New technologies, the ubiquity of the Internet, and the superabun- dance of available information have given librarians new oppor- tunities to reenvision their roles, service solutions, and collabora- tions in this evolving information environment. More than anything else, digital content and technolo- gy-rich library services are moving the library ‘‘presence’’ outside the physical building to support users in their digital spaces, wherever and whenever. In this virtual li- brary world, librarians are crea- tively distributing services out- ward into communities and to library users on the go. Libraries have responded to this ‘‘digital shift’’ in a wide variety of ways. Today’s library website serves as the virtual front door of the library; a gateway to quality and specialized resources; a mis- sion-critical service point that of- fers assistance, guidance, and in- struction; and a platform for user engagement. Catalogs are becom- ing more ‘‘webby’’ and integrated with other discovery and federated search tools and into clinical work- flow environments. The increasing prevalence of mobile devices and tablet computing in research, pa- tient care, and teaching has given rise to libraries providing mobile- friendly websites, content, and support services to meet the needs of a growing mobile library com- munity. The focus of this first column is to provide concrete examples of virtual projects in health sciences libraries that illustrate this digital shift. All these projects are practi- cal, real-world implementations of a new technology or application in health sciences libraries that ex- tend services beyond the confines of the physical library. Each report provides a brief narrative descrip- tion of the project, technical back- ground information, and a contact person for readers who would like J Med Lib Assoc 101(4) October 2013 to follow up with relevant staff to obtain further information. The list of virtual projects in this year’s column was developed by a small advisory group of MLA members who are technology ex- perts: Kimberly Barker, Claude Moore Health Sciences Library, University of Virginia; Janis F. Brown, AHIP, Norris Medical Li- brary, University of Southern Cal- ifornia; Michelle Kraft, AHIP, Cle- veland Clinic Alumni Library, Cleveland Clinic; Eric Schnell, Pri- or Health Sciences Library, Ohio State University; and Elizabeth C. Whipple, AHIP, Ruth Lilly Medi- cal Library, Indiana University. A special call for projects was made in MLA-FOCUS and sent to vari- ous MLA section email discussion lists at the beginning of 2013 that garnered many suggestions. The virtual projects highlighted in the column were primarily identified through that call. General guide- lines for the column and an au- thor’s guide for contributors have been developed with the helpful assistance of the advisory commit- tee and Journal of the Medical Library Association Editor Susan Starr ,http://www.mlanet.org/ publications/jmla/author_reviewer _info.html.. Future columns will be published on an annual basis that explore a particular theme or topic in conjunction with periodic calls and announcements to encourage sub- missions from all types of libraries. Health sciences librarians are doing amazing things in technolo- gy and innovation, coming up with smart solutions, and finding crea- tive ways of ‘‘blending in’’ to better serve their user communi- ties. Their efforts to create and test new models for information access and delivery are making the li- brary vital and relevant for their communities in the twenty-first century. Please consider sharing your knowledge and experiences with implementing virtual projects in your library to inspire and encourage your peers, partners, and communities. If you have a virtual project that you think has transformed the way your library works, let us know. Questions, submissions, and suggestions should be directed to Susan Les- sick at slessick@uci.edu. Susan Lessick, MA, MLS, AHIP, FMLA, slessick@uci.edu, Librarian Emerita, Grunigen Medical Library, University of California, Irvine, 101 The City Drive South, Orange, CA Responsive web design for an academic health sciences library website Submitted by Eric Rumsey, MA, MLS; Linda Roth; William Shane Wallace, MSLS; University of Iowa Before the iPad came out in 2010, the working assumption was that web pages needed to accommodate only two screen sizes: desktop/ laptop and iPhone/smartphone siz- es. Accordingly, many sites, includ- ing libraries, built separate mobile pages for smartphones. With the iPad, as well as several other tablets with differing screen sizes, it has become increasingly impractical to make separate web page sizes for each screen size. Responsive web design (RWD) is a way of coding web pages so that they look good on any screen. Since it was introduced in 2010, RWD has become popular in business and the dotcom world, although its adoption in the aca- demic and library environments has not yet become widespread. Because the University of Iowa Libraries has experienced and skilled information technology staff who are equipped to handle the complexities of RWD, we were able to begin implementing RWD in May 2011. When we began considering the switch to respon- sive design, we had an existing theme for our site that we needed to modify. In retrospect, it might have been easier to choose an

Replicated risk nicotinic cholinergic receptor genes for nicotine dependence

It has been hypothesized that the nicotinic acetylcholine receptors (nAChRs) play important roles in nicotine dependence (ND) and influence the number of cigarettes smoked per day (CPD) in smokers. We compiled the associations between nicotinic cholinergic receptor genes (CHRNs) and ND/CPD that were replicated across different studies, reviewed the expression of these risk genes in human/mouse brains, and verified their expression using independent samples of both human and mouse brains. The potential functions of the replicated risk variants were examined using cis-eQTL analysis or predicted using a series of bioinformatics analyses. We found replicated and significant associations for ND/CPD at 19 SNPs in six genes in three genomic regions (CHRNB3-A6, CHRNA5-A3-B4 and CHRNA4). These six risk genes are expressed in at least 18 distinct areas of the human/mouse brain, with verification in our independent human and mouse brain samples. The risk variants might influence the transcription, expression and splicing of the risk genes, alter RNA secondary or protein structure. We conclude that the replicated associations between CHRNB3-A6, CHRNA5-A3-B4, CHRNA4 and ND/CPD are very robust. More research is needed to examine how these genetic variants contribute to the risk for ND/CPD.

Data challenges of biomedical researchers in the age of omics

Background High-throughput technologies are rapidly generating large amounts of diverse omics data. Although this offers a great opportunity, it also poses great challenges as data analysis becomes more complex. The purpose of this study was to identify the main challenges researchers face in analyzing data, and how academic libraries can support them in this endeavor. Methods A multimodal needs assessment analysis combined an online survey sent to 860 Yale-affiliated researchers (176 responded) and 15 in-depth one-on-one semi-structured interviews. Interviews were recorded, transcribed, and analyzed using NVivo 10 software according to the thematic analysis approach. Results The survey response rate was 20%. Most respondents (78%) identified lack of adequate data analysis training (e.g., R, Python) as a main challenge, in addition to not having the proper database or software (54%) to expedite analysis. Two main themes emerged from the interviews: personnel and training needs. Researchers feel they could improve data analyses practices by having better access to the appropriate bioinformatics expertise, and/or training in data analyses tools. They also reported lack of time to acquire expertise in using bioinformatics tools and poor understanding of the resources available to facilitate analysis. Conclusions The main challenges identified by our study are: lack of adequate training for data analysis (including need to learn scripting language), need for more personnel at the University to provide data analysis and training, and inadequate communication between bioinformaticians and researchers. The authors identified the positive impact of medical and/or science libraries by establishing bioinformatics support to researchers.

Evaluation of Potential Carcinogenicity of Organic Chemicals in Synthetic Turf Crumb Rubber

Abstract Currently, there are >11,000 synthetic turf athletic fields in the United States and >13,000 in Europe. Concerns have been raised about exposure to carcinogenic chemicals resulting from contact with synthetic turf fields, particularly the infill material (“crumb rubber”), which is commonly fabricated from recycled tires. However, exposure data are scant, and the limited existing exposure studies have focused on a small subset of crumb rubber components. Our objective was to evaluate the carcinogenic potential of a broad range of chemical components of crumb rubber infill using computational toxicology and regulatory agency classifications from the United States Environmental Protection Agency (US EPA) and European Chemicals Agency (ECHA) to inform future exposure studies and risk analyses. Through a literature review, we identified 306 chemical constituents of crumb rubber infill from 20 publications. Utilizing ADMET Predictor™, a computational program to predict carcinogenicity and genotoxicity, 197 of the identified 306 chemicals met our a priori carcinogenicity criteria. Of these, 52 chemicals were also classified as known, presumed or suspected carcinogens by the US EPA and ECHA. Of the remaining 109 chemicals which were not predicted to be carcinogenic by our computational toxicology analysis, only 6 chemicals were classified as presumed or suspected human carcinogens by US EPA or ECHA. Importantly, the majority of crumb rubber constituents were not listed in the US EPA (n = 207) and ECHA (n = 262) databases, likely due to an absence of evaluation or insufficient information for a reliable carcinogenicity classification. By employing a cancer hazard scoring system to the chemicals which were predicted and classified by the computational analysis and government databases, several high priority carcinogens were identified, including benzene, benzidine, benzo(a)pyrene, trichloroethylene and vinyl chloride. Our findings demonstrate that computational toxicology assessment in conjunction with government classifications can be used to prioritize hazardous chemicals for future exposure monitoring studies for users of synthetic turf fields. This approach could be extended to other compounds or toxicity endpoints. Highlights306 crumb rubber infill chemical constituents identified in a literature review.197 (64%) chemicals were predicted to be carcinogenic by ADMET Predictor™.58 (19%) chemicals were classified as carcinogens by government agencies.Most chemicals were not listed in US and European databases respectively.Chemicals were prioritized using both ADMET and government classifications.

Prioritization of reproductive toxicants in unconventional oil and gas operations using a multi-country regulatory data-driven hazard assessment

BACKGROUND Recent trends have witnessed the global growth of unconventional oil and gas (UOG) production. Epidemiologic studies have suggested associations between proximity to UOG operations with increased adverse birth outcomes and cancer, though specific potential etiologic agents have not yet been identified. To perform effective risk assessment of chemicals used in UOG production, the first step of hazard identification followed by prioritization specifically for reproductive toxicity, carcinogenicity and mutagenicity is crucial in an evidence-based risk assessment approach. To date, there is no single hazard classification list based on the United Nations Globally Harmonized System (GHS), with countries applying the GHS standards to generate their own chemical hazard classification lists. A current challenge for chemical prioritization, particularly for a multi-national industry, is inconsistent hazard classification which may result in misjudgment of the potential public health risks. We present a novel approach for hazard identification followed by prioritization of reproductive toxicants found in UOG operations using publicly available regulatory databases. METHODS GHS classification for reproductive toxicity of 157 UOG-related chemicals identified as potential reproductive or developmental toxicants in a previous publication was assessed using eleven governmental regulatory agency databases. If there was discordance in classifications across agencies, the most stringent classification was assigned. Chemicals in the category of known or presumed human reproductive toxicants were further evaluated for carcinogenicity and germ cell mutagenicity based on government classifications. A scoring system was utilized to assign numerical values for reproductive health, cancer and germ cell mutation hazard endpoints. Using a Cytoscape analysis, both qualitative and quantitative results were presented visually to readily identify high priority UOG chemicals with evidence of multiple adverse effects. RESULTS We observed substantial inconsistencies in classification among the 11 databases. By adopting the most stringent classification within and across countries, 43 chemicals were classified as known or presumed human reproductive toxicants (GHS Category 1), while 31 chemicals were classified as suspected human reproductive toxicants (GHS Category 2). The 43 reproductive toxicants were further subjected to analysis for carcinogenic and mutagenic properties. Calculated hazard scores and Cytoscape visualization yielded several high priority chemicals including potassium dichromate, cadmium, benzene and ethylene oxide. CONCLUSIONS Our findings reveal diverging GHS classification outcomes for UOG chemicals across regulatory agencies. Adoption of the most stringent classification with application of hazard scores provides a useful approach to prioritize reproductive toxicants in UOG and other industries for exposure assessments and selection of safer alternatives.

Interinstitutional collaboration for end-user bioinformatics training: Cytoscape as a case study

Background This case study describes the value of and need for interinstitutional collaboration to train biomedical researchers in data visualization, using Cytoscape network analysis software as an example. To provide training on Cytoscape software to Yale University biomedical researchers, a collaboration was formed between the Yale Harvey Cushing/John Hay Whitney Medical Library’s (CWML’s) biomedical sciences research support librarian and the University of Michigan (U-M) Taubman Health Sciences Library’s bioinformationist, who has expertise in Cytoscape software. Case Presentation The U-M bioinformationist offered a webinar to the Yale community, followed by a one-day onsite workshop. This collaboration allowed Yale biomedical researchers and librarians to receive training on Cytoscape software, in addition to giving the Yale librarian a collaborator for answering future questions about the software. Conclusions This collaboration furthered the U-M bioinformationist’s role in the field as an expert in Cytoscape instruction, while also establishing the CWML as a leader in providing support for analyzing and visualizing molecular data at Yale University. The authors found this collaboration to be a successful way for librarians to fill end-user training gaps in rapidly changing fields such as bioinformatics.