On-line Metasearch, Pooling, and System Evaluation

This thesis presents a unified method for simultaneous solution of three problems in Information Retrieval--- metasearch (the fusion of ranked lists returned by retrieval systems to elicit improved performance), efficient system evaluation (the accurate evaluation of retrieval systems with small numbers of relevance judgements), and pooling or ``active sample selection (the selection of documents for manual judgement in order to develop sample pools of high precision or pools suitable for assessing system quality). The thesis establishes a unified theoretical framework for addressing these three problems and naturally generalizes their solution to the on-line context by incorporating feedback in the form of relevance judgements. The algorithm--- Rankhedge for on-line retrieval, metasearch and system evaluation--- is the first to address these three problems simultaneously and also to generalize their solution to the on-line context. Optimality of the Rankhedge algorithm is developed via Bayesian and maximum entropy interpretations. Results of the algorithm prove to be significantly superior to previous methods when tested over a range of TREC (Text REtrieval Conference) data. In the absence of feedback, the technique equals or exceeds the performance of benchmark metasearch algorithms such as CombMNZ and Condorcet. The technique then dramatically improves on this performance during the on-line metasearch process. In addition, the technique generates pools of documents which include more relevant documents and produce more accurate system evaluations than previous techniques. The thesis includes an information-theoretic examination of the original Hedge algorithm as well as its adaptation to the context of ranked lists. The work also addresses the concept of information-theoretic similarity within the Rankhedge context and presents a method for decorrelating the predictor set to improve worst case performance. Finally, an information-theoretically optimal method for probabilistic ``active sampling is presented with possible application to a broad range of practical and theoretical contexts

easySTORM: a robust, lower-cost approach to localisation and TIRF microscopy

TIRF and STORM microscopy are super-resolving fluorescence imaging modalities for which current implementations on standard microscopes can present significant complexity and cost. We present a straightforward and low-cost approach to implement STORM and TIRF taking advantage of multimode optical fibres and multimode diode lasers to provide the required excitation light. Combined with open source software and relatively simple protocols to prepare samples for STORM, including the use of Vectashield for non-TIRF imaging, this approach enables TIRF and STORM imaging of cells labelled with appropriate dyes or expressing suitable fluorescent proteins to become widely accessible at low cost

Scholars@TAMU Texas A&M University Libraries’

Texas A&M University Libraries has been using VIVO in production since 2015. In that time, we have come up with many creative solutions to meet the needs of our users. In early 2019, we began developing a replacement front end for the VIVO interface to formally address campus demands here at Texas A&M University. Initial requirements: * Align the technology stack as much as possible with the existing VIVO stack to assist with implementation by others if they choose especially smaller libraries. * The majority of the front end is customizable by others. * Read only UI. No updating back to the triple store. * All data is retrieved via a REST API endpoint using Spring Data for Apache Solr. * 100% Search Engine Optimization. IE: A person / crawler can disable JavaScript and still have the same experience. Server side, and Client side rendering if needed

Steer Temperament Influences Stress Responsiveness to Handling Typical In BeefCattle Management

Last updated: 6/1/200

Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces

Due to the spread of resistance, antibiotic exposure receives increasing attention. Ecological consequences for the different niches of individual microbiomes are, however, largely ignored. Here, we report the effects of widely used antibiotics (clindamycin, ciprofloxacin, amoxicillin, and minocycline) with different modes of action on the ecology of both the gut and the oral microbiomes in 66 healthy adults from the United Kingdom and Sweden in a two-center randomized placebo-controlled clinical trial. Feces and saliva were collected at baseline, immediately after exposure, and 1, 2, 4, and 12 months after administration of antibiotics or placebo. Sequences of 16S rRNA gene amplicons from all samples and metagenomic shotgun sequences from selected baseline and post-antibiotic-treatment sample pairs were analyzed. Additionally, metagenomic predictions based on 16S rRNA gene amplicon data were performed using PICRUSt. The salivary microbiome was found to be significantly more robust, whereas the antibiotics negatively affected the fecal microbiome: in particular, health-associated butyrate-producing species became strongly underrepresented. Additionally, exposure to different antibiotics enriched genes associated with antibiotic resistance. In conclusion, healthy individuals, exposed to a single antibiotic treatment, undergo considerable microbial shifts and enrichment in antibiotic resistance in their feces, while their salivary microbiome composition remains unexpectedly stable. The health-related consequences for the gut microbiome should increase the awareness of the individual risks involved with antibiotic use, especially in a (diseased) population with an already dysregulated microbiome. On the other hand, understanding the mechanisms behind the resilience of the oral microbiome toward ecological collapse might prove useful in combating microbial dysbiosis elsewhere in the body. IMPORTANCE Many health care professionals use antibiotic prophylaxis strategies to prevent infection after surgery. This practice is under debate since it enhances the spread of antibiotic resistance. Another important reason to avoid nonessential use of antibiotics, the impact on our microbiome, has hardly received attention. In this study, we assessed the impact of antibiotics on the human microbial ecology at two niches. We followed the oral and gut microbiomes in 66 individuals from before, immediately after, and up to 12 months after exposure to different antibiotic classes. The salivary microbiome recovered quickly and was surprisingly robust toward antibiotic-induced disturbance. The fecal microbiome was severely affected by most antibiotics: for months, health-associated butyrate-producing species became strongly underrepresented. Additionally, there was an enrichment of genes associated with antibiotic resistance. Clearly, even a single antibiotic treatment in healthy individuals contributes to the risk of resistance development and leads to long-lasting detrimental shifts in the gut microbiome

Newsprint coverage of smoking in cars carrying children : a case study of public and scientific opinion driving the policy debate

Acknowledgements Date of Acceptance:17/10/2014 Acknowledgements: This project was funded by Cancer Research UK (MC_U130085862) and the Scottish School of Public Health Research. Cancer Research UK and the Scottish School of Public Health Research was not involved in the collection, analysis, and interpretation of data, writing of the manuscript or the decision to submit the manuscript for publication. Shona Hilton, Karen Wood, Josh Bain and Chris Patterson are funded by the UK Medical Research Council as part of the Understandings and Uses of Public Health Research programme (MC_UU_12017/6) at the MRC/CSO Social and Public Health Sciences Unit, University of Glasgow. We thank Alan Pollock who provided assistance with coding.Peer reviewedPublisher PD

Scholars@TAMU Texas A&M University Libraries’

Texas A&M University Libraries has been using VIVO in production since 2015. In that time, we have come up with many creative solutions to meet the needs of our users. In early 2019, we began developing a replacement front end for the VIVO interface to formally address campus demands here at Texas A&M University. Initial requirements: * Align the technology stack as much as possible with the existing VIVO stack to assist with implementation by others if they choose especially smaller libraries. * The majority of the front end is customizable by others. * Read only UI. No updating back to the triple store. * All data is retrieved via a REST API endpoint using Spring Data for Apache Solr. * 100% Search Engine Optimization. IE: A person / crawler can disable JavaScript and still have the same experience. Server side, and Client side rendering if needed

Analysis of the corporate political activity of major food industry actors in Fiji

BACKGROUND: Non-communicable diseases (NCDs) are the leading cause of mortality in Fiji, a middle-income country in the Pacific. Some food products processed sold and marketed by the food industry are major contributors to the NCD epidemic, and the food industry is widely identified as having strong economic and political power. However, little research has been undertaken on the attempts by the food industry to influence public health-related policies and programs in its favour. The "corporate political activity" (CPA) of the food industry includes six strategies (information and messaging; financial incentives; constituency building; legal strategies; policy substitution; opposition fragmentation and destabilisation). For this study, we aimed to gain a detailed understanding of the CPA strategies and practices of major food industry actors in Fiji, interpreted through a public health lens. METHODS AND RESULTS: We implemented a systematic approach to monitor the CPA of the food industry in Fiji for three months. It consisted of document analysis of relevant publicly available information. In parallel, we conducted semi-structured interviews with 10 stakeholders involved in diet- and/or public health-related issues in Fiji. Both components of the study were thematically analysed. We found evidence that the food industry adopted a diverse range of strategies in an attempt to influence public policy in Fiji, with all six CPA strategies identified. Participants identified that there is a substantial risk that the widespread CPA of the food industry could undermine efforts to address NCDs in Fiji. CONCLUSIONS: Despite limited public disclosure of information, such as data related to food industry donations to political parties and lobbying, we were able to identify many CPA practices used by the food industry in Fiji. Greater transparency from the food industry and the government would help strengthen efforts to increase their accountability and support NCD prevention. In other low- and middle-income countries, it is likely that a systematic document analysis approach would also need to be supplemented with key informant interviews to gain insight into this important influence on NCD prevention

Perceptions and Experiences of Research Participants on Gender-Based Violence Community Based Survey: Implications for Ethical Guidelines

OBJECTIVE: To explore how survey respondents perceived their experiences and the impact of participating in a survey, and to assess adverse consequences resulting from participation. DESIGN: Qualitative study involving purposefully selected participants who had participated in a household-based survey. METHODS: This qualitative study was nested within a survey that investigated the prevalence of gender-based violence perpetration and victimization with adult men and women in South Africa. 13 male- and 10 female-in-depth interviews were conducted with survey respondents. RESULTS: A majority of informants, without gender-differences, perceived the survey interview as a rare opportunity to share their adverse and or personal experiences in a 'safe' space. Gender-differences were noted in reporting perceptions of risks involved with survey participation. Some women remained fearful after completing the survey, that should breach of confidentiality or full survey content disclosure occur, they may be victimized by partners as a punishment for survey participation without men's approval. A number of informants generally discussed their survey participation with others. However, among women with interpersonal violence history or currently in abusive relationships, full survey content disclosure was done with fear; the partner responses were negative, and few women reported receiving threatening remarks but none reported being assaulted. In contrast no man reported adverse reaction by others. Informants with major life adversities reported that the survey had made them to relive the experiences causing them sadness and pain at the time. No informant perceived the survey as emotionally harmful or needed professional support because of survey questions. Rather the vast majority perceived benefit from survey participation. CONCLUSION: Whilst no informant felt answering the survey questions had caused them emotional or physical harm, some were distressed and anxious, albeit temporarily. Research protocols need to put in place safeguards where appropriate so that this group receives support and protection

National Beef Quality Audit-2016: Transportation, mobility, and harvest-floor assessments of targeted characteristics that affect quality and value of cattle, carcasses, and by-products

The National Beef Quality Audit-2016 (NBQA-2016) was conducted to assess current transportation, mobility, and quality characteristics of U.S. fed steers and heifers. Data were collected at 17 beef processing facilities between March and November 2016. About 8,000 live cattle were evaluated for transportation and mobility, and about 25,000 carcasses were evaluated on the slaughter floor. Cattle were in transit to the slaughter facility for a mean duration of 2.7 h from a mean distance of 218.5 km using trailers with dimensions ranging from 17.84 m2 to 59.09 m2. Area allotted per animal averaged 1.13 m2 and ranged from 0.85 m2 to 2.28 m2. A total of 96.8% of cattle received a mobility score of 1 (walks easily, no apparent lameness). Identification types (35.1% had multiple) were lot visual tags (61.5%), individual tags (55.0%), electronic tags (16.9%), metal-clip tags (9.2%), bar-coded tags (0.05%), wattles (0.01%), and other (2.6%). Cattle were black-hided (57.8%), Holstein (20.4%), red-hided (10.5%), yellow-hided (4.8%), gray-hided (2.9%), brown-hided (1.3%), and white-hided (1.1%). Unbranded hides were observed on 74.3% of cattle; 18.6% had brands located on the butt, 6.3% on the side, and 1.3% on the shoulder (values exceed 100% due to multiple brands). For hide-on carcasses, 37.7% displayed no mud or manure; specific locations for mud or manure were legs (40.8%), belly (33.0%), tail region (15.5%), side (6.8%), and top-line (3.9%). Cattle without horns represented 83.3% of the sample, and cattle that did have horns measured: \u3c 2.54 cm (5.5%), 2.54 to 12.7 cm (8.3%), and \u3e 12.7 cm (2.9%). Carcasses without bruises represented 61.1% of those sampled, whereas 28.2% had 1, 8.2% had 2, 2.1% had 3, and 0.3% had 4 bruises. Of those carcasses with a bruise, the bruise was located on the loin (29.7%), round (27.8%), chuck (16.4%), rib (14.4%), and brisket/plate/flank (11.6%). Frequencies of offal condemnations were livers (30.8%), lungs (18.2%), viscera (16.3%), hearts (11.1%), heads (2.7%), and tongues (2.0%). Compared to NBQA-2011, fewer cattle were identified for traceability, fewer were black-hided, a greater number were Holstein cattle, more with no brand and no horns, fewer without bruises, more liver, lung, and viscera condemnations, and fewer heads and tongues were condemned. The NBQA remains an influential survey for the U.S. beef industry to provide benchmarks and strategic plans for continued improvement of beef quality and consistency