Improving Human Health by Increasing Access to Natural Areas: Linking Research to Action at Scale

Report of the 2014 Berkley Workshop Held at the Wingspread Conference Center, Johnson Foundation, Racine, Wisconsin - June 201

A geometric approach to visualization of variability in functional data

We propose a new method for the construction and visualization of boxplot-type displays for functional data. We use a recent functional data analysis framework, based on a representation of functions called square-root slope functions, to decompose observed variation in functional data into three main components: amplitude, phase, and vertical translation. We then construct separate displays for each component, using the geometry and metric of each representation space, based on a novel definition of the median, the two quartiles, and extreme observations. The outlyingness of functional data is a very complex concept. Thus, we propose to identify outliers based on any of the three main components after decomposition. We provide a variety of visualization tools for the proposed boxplot-type displays including surface plots. We evaluate the proposed method using extensive simulations and then focus our attention on three real data applications including exploratory data analysis of sea surface temperature functions, electrocardiogram functions and growth curves

Detection of missense mutations by single-strand conformational polymorphism (SSCP) analysis in five dysfunctional variants of coagulation factor VII

Five unrelated subjects with dysfunctional coagulation factor VII (FVII) were studied In order to Identify missense mutations affecting function. Exons 2 to 8 and the Intron-exon Junctions of their FVIl genes were amplified from peripheral white blood cell DNA by PCR and screened by SSCP analysis. DNA fragments showing aberrant mobility were sequenced. The following mutations were Identified: In case 1 (FVII: C <1%, FVIl:Ag 18%) a heterozygous A to G transltion at nucleotlde 8915 In exon 6 results In the amlno acid substitution Lys-137 to Glu near the C-termlnus of the FVlla llght chaln; In case 2 (FVII: C 7%, FVll:Ag 47%) a heterozygous A to G transltion at nucleotide 7834 In exon 5 results in the substitution of Gin-100 by Arg in the second EGF-like domain; In case 3 (FVll:C 20%, FVIl:Ag 76%) a homozygous G to A transition at nucleotide position 6055 in exon 4 was detected resulting in substitution of Arg-79 by Gin in the first EGF-like domain; in case 5 (FVIl:C 10%, FVIl:Ag 52%) a heterozygous C to T transition at nucleotide position 6054 in exon 4 also results in the substitution of Arg79, but in this case it is replaced by Trp; case 4 (FVll:C <1%, FVIl:Ag 100%) was homozygous for a previously reported mutation (G to A) at nucleotide position 10715 in exon 8, substituting Gin for Arg at position 304 in the protease domain. Cases 1,2 and 5 evidently have additional undetected mutation

The microRNA-29 family in cartilage homeostasis and osteoarthritis

MicroRNAs have been shown to function in cartilage development and homeostasis, as well as in progression of osteoarthritis. The objective of the current study was to identify microRNAs involved in the onset or early progression of osteoarthritis and characterise their function in chondrocytes. MicroRNA expression in mouse knee joints post-DMM surgery was measured over 7 days. Expression of miR-29b-3p was increased at day 1 and regulated in the opposite direction to its potential targets. In a mouse model of cartilage injury and in end-stage human OA cartilage, the miR-29 family were also regulated. SOX9 repressed expression of miR-29a-3p and miR-29b-3p via the 29a/b1 promoter. TGFβ1 decreased expression of miR-29a, b and c (3p) in primary chondrocytes, whilst IL-1β increased (but LPS decreased) their expression. The miR-29 family negatively regulated Smad, NFκB and canonical WNT signalling pathways. Expression profiles revealed regulation of new WNT-related genes. Amongst these, FZD3, FZD5, DVL3, FRAT2, CK2A2 were validated as direct targets of the miR-29 family. These data identify the miR-29 family as microRNAs acting across development and progression of OA. They are regulated by factors which are important in OA and impact on relevant signalling pathways

Genetic analysis of haemophilia A in Bulgaria

BACKGROUND: Haemophilias are the most common hereditary severe disorders of blood clotting. In families afflicted with heamophilia, genetic analysis provides opportunities to prevent recurrence of the disease. This study establishes a diagnostical strategy for carriership determination and prenatal diagnostics of haemophilia A in Bulgarian haemophilic population. METHODS: A diagnostical strategy consisting of screening for most common mutations in the factor VIII gene and analysis of a panel of eight linked to the factor VIII gene locus polymorphisms was established. RESULTS: Polymorphic analysis for carrier status determination of haemophilia A was successful in 30 families out of 32 (94%). Carrier status was determined in 25 of a total of 28 women at risk (89%). Fourteen prenatal diagnoses in women at high risk of having a haemophilia A – affected child were performed, resulting in 6 healthy boys and 5 girls. CONCLUSION: The compound approach proves to be a highly informative and cost-effective strategy for prevention of recurrence of haemophilia A in Bulgaria. DNA analysis facilitates carriership determination and subsequent prenatal diagnosis in the majority of Bulgarian families affected by haemophilia A

Community-acquired pneumonia by Legionella pneumophila serogroups 1–6 in Brazil

SummaryA prospective cohort study of adult patients hospitalized due to community-acquired pneumonia was carried out for 1 year in a Brazilian university general hospital to detect the incidence of community-acquired pneumonia by Legionella pneumophila serogroups 1–6. During a whole year, a total of 645 consecutive patients who were hospitalized due to a initial presumptive diagnosis of respiratory disease by ICD-10 (J00–J99), excluding upper respiratory diseases, were screened to detect the patients with community-acquired pneumonia. Fifty-nine consecutive patients hospitalized due to community-acquired pneumonia between July 19, 2000 and July 18, 2001, were included in the study. They had determinations of serum antibodies to L. pneumophila serogroups 1–6 by indirect immunofluorescence antibody test at the Infectious Diseases Laboratory of University of Louisville (KY, USA) and urinary antigen tests for L. pneumophila serogroup 1. Three patients had community-acquired pneumonia by L. pneumophila serogroups 1–6, two patients being diagnosed by seroconversion and positive urinary antigen tests; the other had negative serologies but strongly positive urinary antigen test. The incidence of community-acquired pneumonia by L. pneumophila serogroups 1–6 in our hospital was 5.1%

Discovery of Porcine microRNAs and Profiling from Skeletal Muscle Tissues during Development

MiRNAs (microRNAs) play critical roles in many important biological processes such as growth and development in mammals. In this study, we identified hundreds of porcine miRNA candidates through in silico prediction and analyzed their expression in developing skeletal muscle using microarray. Microarray screening using RNA samples prepared from a 33-day whole embryo and an extra embryo membrane validated 296 of the predicted candidates. Comparative expression profiling across samples of longissimus muscle collected from 33-day and 65-day post-gestation fetuses, as well as adult pigs, identified 140 differentially expressed miRNAs amongst the age groups investigated. The differentially expressed miRNAs showed seven distinctive types of expression patterns, suggesting possible involvement in certain biological processes. Five of the differentially expressed miRNAs were validated using real-time PCR. In silico analysis of the miRNA-mRNA interaction sites suggested that the potential mRNA targets of the differentially expressed miRNAs may play important roles in muscle growth and development

Regulation of the IGFBP-5 and MMP-13 genes by the microRNAs miR-140 and miR-27a in human osteoarthritic chondrocytes

<p>Abstract</p> <p>Background</p> <p>MMP-13 and IGFBP-5 are important factors involved in osteoarthritis (OA). We investigated whether two highly predicted microRNAs (miRNAs), miR-140 and miR-27a, regulate these two genes in human OA chondrocytes.</p> <p>Methods</p> <p>Gene expression was determined by real-time PCR. The effect of each miRNA on IGFBP-5 and MMP-13 expression/production was evaluated by transiently transfecting their precursors (pre-miRNAs) and inhibitors (anti-miRNAs) into human OA chondrocytes. Modulation of IGFBP-5, miR-140 and miR-27a expression was determined upon treatment of OA chondrocytes with cytokines and growth factors.</p> <p>Results</p> <p>IGFBP-5 was expressed in human chondrocytes with its level significantly lower (p < 0.04) in OA. Five computational algorithms identified miR-140 and miR-27a as possible regulators of MMP-13 and IGFBP-5 expression. Data showed that both miRNAs were expressed in chondrocytes. There was a significant reduction (77%, p < 0.01) in miR-140 expression in OA compared to the normal chondrocytes, whereas miR-27a expression was only slightly decreased (23%). Transfection with pre-miR-140 significantly decreased (p = 0.0002) and with anti-miR-140 significantly increased (p = 0.05) IGFBP-5 expression at 24 hours, while pre-miR-27a did not affect either MMP-13 or IGFBP-5. Treatment with anti-miR-27a, but not with anti-miR-140, significantly increased the expression of both MMP-13 (p < 0.05) and IGFBP-5 (p < 0.01) after 72 hours of incubation. MMP-13 and IGFBP-5 protein production followed the same pattern as their expression profile. These data suggest that IGFBP-5 is a direct target of miR-140, whereas miR-27a down-regulates, likely indirectly, both MMP-13 and IGFBP-5.</p> <p>Conclusion</p> <p>This study is the first to show the regulation of these miRNAs in human OA chondrocytes. Their effect on two genes involved in OA pathophysiology adds another level of complexity to gene regulation, which could open up novel avenues in OA therapeutic strategies.</p

Remembering the Sea: Personal and Communal Recollections of Maritime Life in Jizan and the Farasan Islands, Saudi Arabia

This is the final version of the article. Available from the publisher via the DOI in this record.People create narratives of their maritime past through the remembering and forgetting of seafaring experiences, and through the retention and disposal of maritime artefacts that function mnemonically to evoke or suppress those experiences. The sustenance and reproduction of the resulting narratives depends further on effective media of intergenerational transmission; otherwise, they are lost. Rapid socio-economic transformation across Saudi Arabia in the age of oil has disrupted longstanding seafaring economies in the Red Sea archipelago of the Farasan Islands, and the nearby mainland port of Jizan. Vestiges of wooden boatbuilding activity are few; long-distance dhow trade with South Asia, the Arabian-Persian Gulf and East Africa has ceased; and a once substantial pearling and nacre (mother of pearl) collection industry has dwindled to a tiny group of hobbyists: no youth dive today. This widespread withdrawal from seafaring activity among many people in these formerly maritime-oriented communities has diminished the salience of such activity in cultural memory, and has set in motion narrative creation processes, through which memories are filtered and selected, and objects preserved, discarded, or lost. This paper is a product of the encounter of the authors with keepers of maritime memories and objects in the Farasan Islands and Jizan. An older generation of men recall memories of their experiences as boat builders, captains, seafarers, pearl divers and fishermen. Their recounted memories are inscribed, and Arabic seafaring terms recorded. The extent of the retention of maritime material cultural items as memorials is also assessed, and the rôle of individual, communal and state actors in that retention is considered. Through this reflection, it becomes clear that the extra-biological memory and archive of the region’s maritime past is sparse; that intergenerational transmission is failing; that the participation of state agencies in maritime heritage creation is highly limited; and that, as a result, memories current among the older generation have limited prospect of survival. These memories, recorded and interpreted here, identify the Farasan Islands as a former centre of the pearling industry in the Red Sea, and identify them and Jizan as open to far-reaching maritime-mediated cultural influences in an era before the imposition of the attributes of the modern nation-state.This study was funded by the Golden Web Foundation (UK registered charity number 1100608), with additional support from the Seven Pillars of Wisdom Trust (UK registered charity number 208669)