EnsCat: clustering of categorical data via ensembling

Background: Clustering is a widely used collection of unsupervised learning techniques for identifying natural classes within a data set. It is often used in bioinformatics to infer population substructure. Genomic data are often categorical and high dimensional, e.g., long sequences of nucleotides. This makes inference challenging: The distance metric is often not well-defined on categorical data; running time for computations using high dimensional data can be considerable; and the Curse of Dimensionality often impedes the interpretation of the results. Up to the present, however, the literature and software addressing clustering for categorical data has not yet led to a standard approach. Results: We present software for an ensemble method that performs well in comparison with other methods regardless of the dimensionality of the data. In an ensemble method a variety of instantiations of a statistical object are found and then combined into a consensus value. It has been known for decades that ensembling generally outperforms the components that comprise it in many settings. Here, we apply this ensembling principle to clustering. We begin by generating many hierarchical clusterings with different clustering sizes. When the dimension of the data is high, we also randomly select subspaces also of variable size, to generate clusterings. Then, we combine these clusterings into a single membership matrix and use this to obtain a new, ensembled dissimilarity matrix using Hamming distance. Conclusions: Ensemble clustering, as implemented in R and called EnsCat, gives more clearly separated clusters than other clustering techniques for categorical data. The latest version with manual and examples is available at https://github.com/jlp2duke/EnsCat

Integrated Design of a Telerobotic Workstation

The experiments described in this paper are part of a larger joint MIT/NASA research effort that focuses on the development of a methodology for designing and evaluating integrated interfaces for highly dexterous and multi-functional telerobots. Specifically, a telerobotic workstation is being designed for an Extravehicular Activity (EVA) anthropomorphic space station telerobot. Previous researchers have designed telerobotic workstations based upon performance of discrete subsets of tasks (for example, peg-in-hole, tracking, etc.) without regard for transitions that operators go through between tasks performed sequentially in the context of larger integrated tasks. The exploratory research experiments presented here took an integrated approach and assessed how subjects operating a full-immersion telerobot perform during the transitions between sub-tasks of two common EVA tasks. Preliminary results show that up to 30% of total task time is spent gaining and maintaining Situation Awareness (SA) of their task space and environment during transitions. Although task performance improves over the two trial days, the percentage of time spent on SA remains the same. This method identifies areas where workstation displays and feedback mechanisms are most needed to increase operator performance and decrease operator workload - areas that previous research methods have not been able to address

Space Station Human Factors: Designing a Human-Robot Interface

The experiments described in this paper are part of a larger joint MIT/NASA research effort and focus on the development of a methodology for designing and evaluating integrated interfaces for highly dexterous and multifunctional telerobot. Specifically, a telerobotic workstation is being designed for an Extravehicular Activity (EVA) anthropomorphic space station telerobot called Robonaut. Previous researchers have designed telerobotic workstations based upon performance of discrete subsets of tasks (for example, peg-in-hole, tracking, etc.) without regard for transitions that operators go through between tasks performed sequentially in the context of larger integrated tasks. The experiments presented here took an integrated approach to describing teleoperator performance and assessed how subjects operating a full-immersion telerobot perform during fine position and gross position tasks. In addition, a Robonaut simulation was also developed as part of this research effort, and experimentally tested against Robonaut itself to determine its utility. Results show that subject performance of teleoperated tasks using both Robonaut and the simulation are virtually identical, with no significant difference between the two. These results indicate that the simulation can be utilized as both a Robonaut training tool, and as a powerful design platform for telepresence displays and aids

Cranberries and Cancer: An Update of Preclinical Studies Evaluating the Cancer Inhibitory Potential of Cranberry and Cranberry Derived Constituents

Cranberries are rich in bioactive constituents reported to influence a variety of health benefits, ranging from improved immune function and decreased infections to reduced cardiovascular disease and more recently cancer inhibition. A review of cranberry research targeting cancer revealed positive effects of cranberries or cranberry derived constituents against 17 different cancers utilizing a variety of in vitro techniques, whereas in vivo studies supported the inhibitory action of cranberries toward cancers of the esophagus, stomach, colon, bladder, prostate, glioblastoma and lymphoma. Mechanisms of cranberry-linked cancer inhibition include cellular death induction via apoptosis, necrosis and autophagy; reduction of cellular proliferation; alterations in reactive oxygen species; and modification of cytokine and signal transduction pathways. Given the emerging positive preclinical effects of cranberries, future clinical directions targeting cancer or premalignancy in high risk cohorts should be considered

Small bowel stomas are associated with higher risk of circulating food-specific-IgG than patients with organic gastrointestinal conditions and colostomies

Objective The effects of food sensitivity can easily be masked by other digestive symptoms in ostomates and are unknown. We investigated food-specific- IgG presence in ostomates relative to participants affected by other digestive diseases. Design Food-specific- IgG was evaluated for 198 participants with a panel of 109 foods. Immunocompetency status was also tested. Jejunostomates, ileostomates and colostomates were compared with individuals with digestive tract diseases with inflammatory components (periodontitis, eosinophilic esophagitis, duodenitis, ulcerative colitis, Crohn’s disease and appendicitis), as well as food malabsorption due to intolerance. A logistic regression model with covariates was used to estimate the effect of the experimental data and demographic characteristics on the likelihood of the immune response. Results Jejunostomates and ileostomates had a significant risk of presenting circulating food-specific- IgG in contrast to colostomates (OR 12.70 (p=0.002), 6.19 (p=0.011) and 2.69 (p=0.22), respectively). Crohn’s disease, eosinophilic esophagitis and food malabsorption groups also showed significantly elevated risks (OR 4.67 (p=0.048), 8.16 (p=0.016) and 18.00 (p=0.003), respectively), but not the ulcerative colitis group (OR 2.05 (p=0.36)). Individuals with profoundly or significantly reduced, and mild to moderately reduced, levels of total IgG were protected from the formation of food-specific IgG (OR 0.09 (p=\u3c0.001) and 0.33 (p=0.005), respectively). Males were at higher risk than females. Conclusion The strength of a subject’s immunocompetence plays a role in the intensity to which the humoral system responds via food-specific- IgG. An element of biogeography emerges in which the maintenance of a colonic space might influence the risk of having circulating food-specific- IgG in ostomates. Includes supplementary materials

Hyponatremia : Special Considerations in Older Patients

Acknowledgments Roy L. Soiza is funded by an NRS Career Research Fellowship.Peer reviewedPublisher PD

Cranberry Polyphenols in Esophageal Cancer Inhibition: New Insights

Esophageal adenocarcinoma (EAC) is a cancer characterized by rapidly rising incidence and poor survival, resulting in the need for new prevention and treatment options. We utilized two cranberry polyphenol extracts, one proanthocyanidin enriched (C-PAC) and a combination of anthocyanins, flavonoids, and glycosides (AFG) to assess inhibitory mechanisms utilizing premalignant Barrett’s esophagus (BE) and EAC derived cell lines. We employed reverse phase protein arrays (RPPA) and Western blots to examine cancer-associated pathways and specific signaling cascades modulated by C-PAC or AFG. Viability results show that C-PAC is more potent than AFG at inducing cell death in BE and EAC cell lines. Based on the RPPA results, C-PAC significantly modulated 37 and 69 proteins in JH-EsoAd1 (JHAD1) and OE19 EAC cells, respectively. AFG treatment significantly altered 49 proteins in both JHAD1 and OE19 cells. Bioinformatic analysis of RPPA results revealed many previously unidentified pathways as modulated by cranberry polyphenols including NOTCH signaling, immune response, and epithelial to mesenchymal transition. Collectively, these results provide new insight regarding mechanisms by which cranberry polyphenols exert cancer inhibitory effects targeting EAC, with implications for potential use of cranberry constituents as cancer preventive agents

Development of a Multiplex Real-Time PCR Assay for Predicting Macrolide and Tetracycline Resistance Associated with Bacterial Pathogens of Bovine Respiratory Disease

Antimicrobial resistance (AMR) in bovine respiratory disease (BRD) is an emerging concern that may threaten both animal and public health. Rapid and accurate detection of AMR is essential for prudent drug therapy selection during BRD outbreaks. This study aimed to develop a multiplex quantitative real-time polymerase chain reaction assay (qPCR) to provide culture-independent information regarding the phenotypic AMR status of BRD cases and an alternative to the gold-standard, culture-dependent test. Bovine clinical samples (297 lung and 111 nasal) collected in Nebraska were subjected to qPCR quantification of macrolide (MAC) and tetracycline (TET) resistance genes and gold-standard determinations of AMR of BRD pathogens. Receiver operating characteristic curve analysis was used to classify AMR based on the qPCR results. For lung tissues, the qPCR method showed good agreement with the gold-standard test for both MACs and TETs, with a sensitivity of 67–81% and a specificity higher than 80%. For nasal swabs, qPCR results passed validation criteria only for TET resistance detection, with a sensitivity of 88%, a specificity of 80% and moderate agreement. The culture-independent assay developed here provides the potential for more rapid AMR characterization of BRD cases directly from clinical samples at equivalent accuracy and higher time efficiency compared with the gold-standard, culture-based test