Miracle-dz/UniFAR-FTUs huggingface dataset:
AFRL-AFOSR-VA-TR-2015-0387 (MURI-09) DISTRIBUTED LEARNING AND INFORMATION DYNAMICS IN NETWORKED AUTONOMOUS

This project is motivated by the need to enable advanced operations of teams of autonomous vehicles to learn and adapt to uncertain and hostile environments under effective utilization of communications resources. Of particular interest is the interplay between distributed learning and information dynamics. Distributed learning refers to a collection of interacting agents with limited local processing, information, and communications, all seeking to achieve a global objective in an uncertain and possibly hostile environment. Information dynamics refers to the architecture, either inherited or designed, of information flow among the distributed agents. The interplay of distributed learning algorithms and information dynamics can have dramatic effects on the efficiency of the collective. Specific research thrusts include: i) online resource allocation, ii) networked operations, and iii) evolving and uncertain operations. Distribution Statement This is block 12 on the SF298 form. Distribution A Approved for Public Release Explanation for Distribution Statement If this is not approved for public release, please provide a short explanation. E.g., contains proprietary information. SF298 Form Please attach your SF298 form. A blank SF298 can be found here. Please do not password protect or secure the PDF The maximum file size for an SF298 is 50MB. Final_report_cover_page. pdf Upload the Report Document. File must be a PDF. Please do not password protect or secure the PDF . The maximum file size for the Report Document is 50MB. AFOSR Grant FA95500910538.pdf Upload a Report Document, if any. The maximum file size for the Report Document is 50MB. Archival Publications (published) during reporting period:
Effects of Grapefruit Juice on Pharmacokinetic Exposure to Indinavir in HIV‐Positive Subjects

The objective of this study was to determine the effects of double‐strength grapefruit juice on gastric pH and systemic bioavailability of indinavir in HIV‐infected subjects receiving indinavir. Fourteen HIV‐infected subjects took 800 mg of indinavir with 6 ounces (180 ml) of water or double‐strength grapefruit juice. Gastric pH was measured and blood samples were collected for 5 hours after indinavir dosing. Grapefruit juice increased the mean gastric pH (from 1.39 ± 0.4 to 3.20 ± 0.3; p < 0.05) and slightly delayed the absorption of indinavir (tmax increased from 1.12 ± 0.8hto 1.56± 0.6 h; p < 0.05). However, there were no significant differences in indinavir exposure. Cmax was 16.7 ± 7.3 μ with water versus 13.9 ± 4.2 μ with grapefruit juice (p = NS), and AUC0–8 was 37.5 ± 19 with water versus 36.9 ± 15 with grapefruit juice (p = NS). The authors concluded that concomitant administration of grapefruit juice increases gastric pH and delays indinavir absorption but does not uniformly affect the systemic bioavailability of indinavir in HIV‐infected subjects.
Dynamic transitions in RNA polymerase II density profiles during transcription termination

Eukaryotic protein-coding genes are transcribed by RNA polymerase II (RNAPII) through a cycle composed of three main phases: initiation, elongation, and termination. Recent studies using chromatin immunoprecipitation coupled to high-throughput sequencing suggest that the density of RNAPII molecules is higher at the 3′-end relative to the gene body. Here we show that this view is biased due to averaging density profiles for “metagene” analysis. Indeed, the majority of genes exhibit little, if any, detectable accumulation of polymerases during transcription termination. Compared with genes with no enrichment, genes that accumulate RNAPII at the 3′-end are shorter, more frequently contain the canonical polyadenylation [poly(A)] signal AATAAA and G-rich motifs in the downstream sequence element, and have higher levels of expression. In 1% to 4% of actively transcribing genes, the RNAPII enriched at the 3′-end is phosphorylated on Ser5, and we provide evidence suggesting that these genes have their promoter and terminator regions juxtaposed. We also found a striking correlation between RNAPII accumulation and nucleosome organization, suggesting that the presence of nucleosomes after the poly(A) site induces pausing of polymerases, leading to their accumulation. Yet we further observe that nucleosome occupancy at the 3′-end of genes is dynamic and correlates with RNAPII density. Taken together, our results provide novel insight to transcription termination, a fundamental process that remains one of the least understood stages of the transcription cycle.
The Role of Allogenic Amniotic Membrane in Burn Treatment

Amniotic membrane (AM) has been used in burns for nearly 100 years. The purpose of this article is to give a comprehensive review of the English literature published in the last two decades (1987–2007) to present the current state of this therapy form. Three medical databases (PubMed, Medline, The Cochrane Library) and specific burn journals were electronically screened for relevant articles using carefully selected retrieval strategies and keywords (AM, amnion grafts, burns, wound dressing, amnion banking). Bibliographies of relevant articles were analyzed for additional pertinent publications. After exclusion of articles which referred to the use of AM in reconstructive and ophthalmologic surgery, the inquiry yielded 31 relevant articles in English language dealing with AM and burns. There was no publication fulfilling the criteria of evidence level I, 6 articles had evidence level II, 10 had evidence level III, 6 had evidence level IV, and 9 were merely narrative (level V). The review testifies to—in view of good tissue practice—heightened use of processed AM in burns, especially in the last decade. Randomized clinical trials favored the use of amnion in burns in the first place for promotion of wound healing and in the second place for its comfortable and less dressing changes. Antimicrobial effects, pain relief, reduction of fluid, and scar formation were demonstrated additionally.
Entity resolution in disjoint graphs: An application on genealogical data

Entity Resolution (ER) is the process of identifying references referring to the same entity from one or more data sources. In the ER process, most existing approaches exploit the content information of references, categorized as content-based ER, or additionally consider linkage information among references, categorized as context-based ER. However, in new applications of ER, such as in the genealogical domain, the very limited linkage information among references results in a disjoint graph in which the existing content-/context-based ER techniques have very limited applicability. Therefore, in this paper we propose first, to use the homophily principle for augmentation of the original input graph by connecting the potential similar references, and second, to use a Random Walk based approach to consider contextual information available for each reference in the augmented graph. We evaluate the proposed method by applying it to a large genealogical dataset and we succeed to predict 420,000 reference matches with precision 92% and discover six novel and informative patterns among them which can not be detected in the original disjoint graph.
How to Assess Prognostic Models for Survival Data: A Case Study in Oncology

Summary Objectives: A lack of generally applicable tools for the assessment of predictions for survival data has to be recognized. Prediction error curves based on the Brier score that have been suggested as a sensible approach are illustrated by means of a case study. Methods: The concept of predictions made in terms of conditional survival probabilities given the patient’s covariates is introduced. Such predictions are derived from various statistical models for survival data including artificial neural networks. The idea of how the prediction error of a prognostic classification scheme can be followed over time is illustrated with the data of two studies on the prognosis of node positive breast cancer patients, one of them serving as an independent test data set. Results and Conclusions: The Brier score as a function of time is shown to be a valuable tool for assessing the predictive performance of prognostic classification schemes for survival data incorporating censored observations. Comparison with the prediction based on the pooled Kaplan Meier estimator yields a benchmark value for any classification scheme incorporating patient’s covariate measurements. The problem of an overoptimistic assessment of prediction error caused by data-driven modelling as it is, for example, done with artificial neural nets can be circumvented by an assessment in an independent test data set.
Phagocytic and oxidative burst activity of neutrophils in the end stage of liver cirrhosis.

AIM To evaluate the phagocytic activity and neutrophil oxidative burst in liver cirrhosis. METHODS In 45 patients with advanced postalcoholic liver cirrhosis (aged 45+/-14 years) and in 25 healthy volunteers (aged 38+/-5 years), the percentage of phagocytizing cells after in vitro incubation with E. coli (Phagotest Kit), phagocytic activity (mean intensity of fluorescence, MIF) and the percentage of neutrophil oxidative burst (Bursttest Kit), and the level of free oxygen radical production (MIF of Rodamine 123) were analyzed by flow cytometry. The levels of soluble sICAM-1, sVCAM-1, sP-selectin, sE-selectin, sL-selectin, and TNF-alpha were determined in blood serum. RESULTS The percentage of E. coli phagocytizing neutrophils in liver cirrhosis patients was comparable to that in healthy subjects. MIF of neutrophil -- ingested E. coli was higher in patients with liver cirrhosis. The oxidative burst in E. coli phagocytizing neutrophils generated less amount of active oxygen compounds in liver cirrhosis patients (MIF of R123: 24.7+/-7.1 and 29.7+/-6.6 in healthy, P<0.01). Phorbol myristate acetate (PMA) -- stimulated neutrophilsproduced less reactive oxidants in liver cirrhosis patients than in healthy subjects (MIF of R123: 42.7+/-14.6 vs 50.2+/-13.3, P<0.01). A negative correlation was observed between oxidative burst MIF of PMA-stimulated neutrophils and ALT and AST levels (r -0.35, P<0.05; r-0.4, P<0.03). sVCAM-1, sICAM-1, sE-selectin concentrations correlated negatively with the oxygen free radical production (MIF of R123) in neutrophils after PMA stimulation in liver cirrhosis patients (r-0.45, P<0.05; r-0.41, P<0.05; r-0.39, P<0.05, respectively). CONCLUSION Neutrophil metabolic activity diminishes together with the intensification of liver failure. The metabolic potential of phagocytizing neutrophils is significantly lower in liver cirrhosis patients, which can be one of the causes of immune mechanism damage. The evaluation of oxygen metabolism of E. coli-stimulated neutrophils reveals that the amount of released oxygen metabolites is smaller in liver cirrhosis patients than in healthy subjects.
Questioning the Clinical Utility of Exome Sequencing in Developing Countries

The availability of whole‐exome sequencing has revolutionized the study of genetic disease in recent years, particularly in dermatology, where clinical phenotypes are readily recognized. As this technology becomes increasingly affordable and accessible, questions are emerging regarding the clinical and ethical responsibilities of physicians who determine variants underlying disease, especially with regard to children, for whom treatment may be warranted and clinical course improved based on a known genotype. These responsibilities are accentuated in the developing countries, which harbor most consanguineous populations and thus bear the brunt of monogenic genodermatoses. Although many genetic disorders are identified in these populations, limited educational and clinical infrastructure rarely offers opportunities to improve the course of disease. Here we report a genetic study that illustrates these challenges.
Screening for postpartum depression in a private health care network in Chile.

BACKGROUND It has been demonstrated that postpartum depression (PPD) has an impact on infant development with repercussions in the child's cognitive, socioemotional and conduct regulation. Screening for this disorder with the Edinburgh Postnatal Depression Scale (EPDS) has been recommended because this significantly identifies more cases of PPD than usual clinical evaluation. AIM To evaluate the use of the EPDS to screen mothers attending well child care visits with their infants during the first 6 months of age and identifying the factors associated with its use in the largest private health care network in Chile. METHODS Cross-sectional study, conducted by random sampling of the children's medical charts from a universe of 5700 infants aged 1-6 months that attended the health care network during 2009 and 2011. Estimated sample size: 500 medical charts, assuming a recording frequency of the EPDS of 5% (confidence level of 95% and power of 80%). The descriptive data analysis of the variables was carried out using a uni and multivariate analysis. All values of P < 0.05 were considered significant (Software SPSS 17.0). RESULTS A total of 1940 visits, belonging to 503 medical charts of infants under 6 months of age were reviewed. The use of the EPDS to screen mothers was recorded in nine medical charts (1.7% of the infant population). The only variable that was significantly associated with the recording of the EPDS was the background of previous depression in the mother (P < 0.001). CONCLUSION The record of the use of EPDS on mothers of infants seen in the private health care network is much less than what is recommended.
Quorum sensing and signal interference: diverse implications

Quorum sensing (QS) is a community genetic regulation mechanism that controls microbiological functions of medical, agricultural and industrial importance. Discovery of microbial QS signals and the signalling mechanisms led to identification of numerous enzymatic and non‐enzymatic signal interference mechanisms that quench microbial QS signalling. Evidence is accumulating that such signal interference mechanisms can be developed as promising approaches to control microbial infection and biofilm formation. In addition, these mechanisms exist not only in microorganisms but also in the host organisms of bacterial pathogens, highlighting their potential implications in microbial ecology and in host–pathogen interactions. Investigation of QS and signal interference mechanisms might significantly broaden the scope of research in microbiology.
Geographic Information Systems: A Tutorial and Introduction

This tutorial provides a foundation in GIS including its basic structure and concepts, and spatial analysis. Spatial Decision Support Systems are introduced, emphasizing one current model. The links of GIS to related technologies such as GPS, wireless, location-based technologies, and RFID are examined. The tutorial gives an overview of vertical-sector uses of GIS, and concentrates on a few examples in marketing and banking. GIS is a new field in business schools, and presents opportunities for research. It is derivative from about 8 to 10 disciplines, some unfamiliar to most IS researchers. Several conceptual models and research methodologies are discussed.
Pharmacist-Operated Drug Information Centers in the United States: A Directory of Centers that Meet Listed Criteria—1999

Pharmacist-operated drug information centers (DICs) in the United States were surveyed to obtain current information on the availability and scope of their services. Questionnaires were mailed in late 1991 to 179 institutions believed to have organized DICs. Topics covered in the questionnaire included staffing, resources, funding, and services provided. The results were compared with previous survey results to identify trends. Through 1992, 120 usable responses were received. Compared with findings from earlier surveys, DICs' affiliations with medical centers and hospitals have declined and affiliations with pharmacy schools have increased. More personnel work in DICs than ever. Computers are now used by nearly every DIC, there is an increased emphasis on quality-assurance programs for services rendered, and many DICs have increased revenue with new and expanded services. Although DICs are no longer increasing in number, their services are becoming more sophisticated.
Altered integrity of the right arcuate fasciculus as a trait marker of schizophrenia: A sibling study using tractography‐based analysis of the whole brain

Trait markers of schizophrenia aid the dissection of the heterogeneous phenotypes into distinct subtypes and facilitate the genetic underpinning of the disease. The microstructural integrity of the white matter tracts could serve as a trait marker of schizophrenia, and tractography‐based analysis (TBA) is the current method of choice. Manual tractography is time‐consuming and limits the analysis to preselected fiber tracts. Here, we sought to identify a trait marker of schizophrenia from among 74 fiber tracts across the whole brain using a novel automatic TBA method. Thirty‐one patients with schizophrenia, 31 unaffected siblings and 31 healthy controls were recruited to undergo diffusion spectrum magnetic resonance imaging at 3T. Generalized fractional anisotropy (GFA), an index reflecting tract integrity, was computed for each tract and compared among the three groups. Ten tracts were found to exhibit significant differences between the groups with a linear, stepwise order from controls to siblings to patients; they included the right arcuate fasciculus, bilateral fornices, bilateral auditory tracts, left optic radiation, the genu of the corpus callosum, and the corpus callosum to the bilateral dorsolateral prefrontal cortices, bilateral temporal poles, and bilateral hippocampi. Posthoc between‐group analyses revealed that the GFA of the right arcuate fasciculus was significantly decreased in both the patients and unaffected siblings compared to the controls. Furthermore, the GFA of the right arcuate fasciculus exhibited a trend toward positive symptom scores. In conclusion, the right arcuate fasciculus may be a candidate trait marker and deserves further study to verify any genetic association. Hum Brain Mapp 36:1065–1076, 2015. © 2014 Wiley Periodicals, Inc.
The Postcardiac Arrest Consult Team: Impact on Hospital Care Processes for Out-of-Hospital Cardiac Arrest Patients*

Objective:To evaluate whether a Post-Arrest Consult Team improved care and outcomes for patients with out-of-hospital cardiac arrest. Design:Prospective cohort study of Post-Arrest Consult Team implementation at two hospitals, with concurrent controls from 27 others. Setting:Twenty-nine hospitals within the Strategies for Post-Arrest Care Network of Southern Ontario, Canada. Patients:We included comatose adult nontraumatic out-of-hospital cardiac arrest patients surviving more than or equal to 6 hours after emergency department arrival who had no contraindications to targeted temperature management. Intervention:The Post-Arrest Consult Team was an advisory consult service to improve 1) targeted temperature management, 2) assessment for percutaneous coronary intervention, 3) electrophysiology assessment, and 4) appropriately delayed neuroprognostication. Measurements and Main Results:We used generalized linear mixed models to explore the association between Post-Arrest Consult Team implementation and performance of targeted processes. We included 1,006 patients. The Post-Arrest Consult Team was associated with a significant reduction over time in rates of withdrawal of life-sustaining therapy within 72 hours of emergency department arrival on the basis of predictions of poor neurologic prognosis (ratio of odds ratios, 0.13; 95% CI, 0.02–0.98). Post-Arrest Consult Team was not associated with improved successful targeted temperature management (ratio of odds ratios, 0.91; 95% CI, 0.31–2.65), undergoing angiography (ratio of odds ratios, 1.91; 95% CI, 0.17–21.04), receiving electrophysiology consultation (ratio of odds ratios, 0.93; 95% CI, 0.11–8.16), or functional survival (ratio of odds ratios, 0.75; 95% CI, 0.19–2.94). Conclusions:Implementation of a Post-Arrest Consult Team reduced premature withdrawal of life-sustaining therapy but did not improve rates of successful targeted temperature management, coronary angiography, formal electrophysiology assessments, or functional survival for comatose patients after out-of-hospital cardiac arrest.
ASYMMETRIC EFFECTS OF LOSS AND GAIN OF A FLORAL TRAIT ON POLLINATOR PREFERENCE

Shifts in pollination syndromes involve coordinated changes in multiple floral traits. This raises the question of how plants can cope with rapid changes in pollinator availability by the slow process of accumulation of mutations in multiple genes. Here we study the transition from bee to hawkmoth pollination in the genus Petunia. Interspecific crosses followed by single locus introgressions were used to recreate putative intermediate evolutionary stages in the evolution of moth pollination. The effect of the loss/gain of petal color was asymmetric: it had no influence on the established pollinator but enhanced visitation by the new pollinator. Therefore, shifts in pollination syndromes may proceed through intermediate stages of reduced specialization and consequently enhanced reproductive assurance. The loss of petal color in moth‐pollinated Petunia involves null mutations in a single regulatory gene, An2. Such simple genetic changes may be sufficiently rapid and frequent to ensure survival during pollinator failure.
Identification of cellular origin of type I collagen in glomeruli of rats with crescentic glomerulonephritis induced by anti-glomerular basement membrane antibody.

BACKGROUND Type I collagen is an interstitial collagen, which is not present in normal glomeruli. As type I collagen was observed in advanced glomerular lesions, it appears to be associated with deterioration of renal function. However, the origins of cells expressing type I collagen mRNA in glomeruli of diseased kidneys remains controversial. METHODS We examined the expression of type I collagen in glomeruli at protein and mRNA levels in rat crescentic glomerulonephritis induced by anti-glomerular basement membrane (GBM) antibody. In addition, in situ hybridization and immunohistochemical staining of serial sections were performed to identify the cellular origin of type I collagen in glomeruli. RESULTS Semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) in isolated glomeruli showed that mRNA expression of type I collagen was remarkably increased on days 7, 14, and 28 after anti-GBM antibody injection (12.2+/-1.4, 20.2+/-2.1 and 14.6+/-1.0-fold over day 0, respectively). Immunofluorescence for type I collagen demonstrated marked staining in the fibrocellular and fibrous crescents, and weak staining within glomerular mesangial areas. In close association with mRNA levels analysed by RT-PCR, in situ hybridization revealed predominant presence of alpha1(I) collagen mRNA in cells within crescentic areas and Bowman's capsules. Serial section analysis for immunostaining and in situ hybridization showed that some alpha1(I) collagen mRNA-positive cells were also positive for cytokeratin. In contrast, no alpha1(I) collagen mRNA-positive cells were stained by ED-1 and podocalyxin. CONCLUSIONS It appears that increased expression of type I collagen at the protein and mRNA levels in glomeruli is involved in the progression of glomerulonephritis. At least in this crescentic model, parietal epithelial cells (PECs) may partially contribute to the dysregulated production of type I collagen, which leads to glomerulosclerosis.