Interactive Data Visualization for HIV Cohorts: Leveraging Data Exchange Standards to Share and Reuse Research Tools

Objective

To develop and disseminate tools for interactive visualization of HIV cohort data.

Design and Methods

If a picture is worth a thousand words, then an interactive video, composed of a long string of pictures, can produce an even richer presentation of HIV population dynamics. We developed an HIV cohort data visualization tool using open-source software (R statistical language). The tool requires that the data structure conform to the HIV Cohort Data Exchange Protocol (HICDEP), and our implementation utilized Caribbean, Central and South America network (CCASAnet) data.

Results

This tool currently presents patient-level data in three classes of plots: (1) Longitudinal plots showing changes in measurements viewed alongside event probability curves allowing for simultaneous inspection of outcomes by relevant patient classes. (2) Bubble plots showing changes in indicators over time allowing for observation of group level dynamics. (3) Heat maps of levels of indicators changing over time allowing for observation of spatial-temporal dynamics. Examples of each class of plot are given using CCASAnet data investigating trends in CD4 count and AIDS at antiretroviral therapy (ART) initiation, CD4 trajectories after ART initiation, and mortality.

Conclusions

We invite researchers interested in this data visualization effort to use these tools and to suggest new classes of data visualization. We aim to contribute additional shareable tools in the spirit of open scientific collaboration and hope that these tools further the participation in open data standards like HICDEP by the HIV research community.     

Uncertainty in identifying local extinctions: the distribution of missing data and its effects on biodiversity measures

Identifying local extinctions is integral to estimating species richness and geographic range changes and informing extinction risk assessments. However, the species occurrence records underpinning these estimates are frequently compromised by a lack of recorded species absences making it impossible to distinguish between local extinction and lack of survey effort—for a rigorously compiled database of European and Asian Galliformes, approximately 40% of half-degree cells contain records from before but not after 1980. We investigate the distribution of these cells, finding differences between the Palaearctic (forests, low mean human influence index (HII), outside protected areas (PAs)) and Indo-Malaya (grassland, high mean HII, outside PAs). Such cells also occur more in less peaceful countries. We show that different interpretations of these cells can lead to large over/under-estimations of species richness and extent of occurrences, potentially misleading prioritization and extinction risk assessment schemes. To avoid mistakes, local extinctions inferred from sightings records need to account for the history of survey effort in a locality.     

Correlation of thrombin-induced glycoprotein V hydrolysis and platelet activation

To assess the possibility that hydrolysis of the platelet surface thrombin substrate, glycoprotein V, is a necessary step in thrombin-induced platelet activation, thrombin-catalyzed hydrolysis of glycoprotein V was correlated with thrombin-induced platelet activation. Hydrolysis of tritium-labeled glycoprotein V on washed human platelets was measured by the appearance of a labeled supernatant fragment, and platelet activation was measured as secretion of ATP. Hydrolysis of glycoprotein V was linear with respect to both thrombin concentration and time of incubation. The extent of platelet activation was correlated with the rate of hydrolysis but not with the amount hydrolyzed. Maximum platelet activation could be obtained with thrombin treatments resulting in hydrolysis of as little as 4% of glycoprotein V per min. Glycoprotein V was partially removed from platelets by pretreatment with either platelet calcium-dependent protease or chymotrypsin. The rate of thrombin-catalyzed hydrolysis of the remaining glycoprotein V from these pretreated platelets was as little as 1.5% the rate from control platelets, but there was no impairment of the extent of platelet activation. Thus, these protease-pretreated platelets compared with control platelets showed a different correlation of glycoprotein V hydrolysis with platelet activation. Glycoprotein V was also partially removed by pretreatment of prostacyclin-inhibited platelets with thrombin. After removal of thrombin and prostacyclin, these platelets were desensitized to subsequent activation by thrombin. Incubation of desensitized platelets with nonsaturating levels of thrombin led to less than 25% of the activation seen with control platelets but to a slightly greater hydrolysis of glycoprotein V. Thus, the desensitization to thrombin was not due to loss of ability of the activating thrombin to hydrolyze glycoprotein V. These results do not exclude a role for glycoprotein V as a component of the platelet thrombin receptor, but they indicate that there is no simple relationship between thrombin-induced hydrolysis of glycoprotein V and platelet activation.     

Regulation of rat ovarian cell growth and steroid secretion

A cultured rat ovarian cell line (31 A-F(2)) was used to study the effect of growth factors (epidermal growth factor [EGF] and fibroblast growth factor [FGF]), a survival factor (ovarian growth factor [OGF]), a hormone (insulin), and an iron-binding protein (transferring) on cell proliferation and steroid production under defined culture conditions. EGF and insulin were shown to be mitogenic (half-maximal response at 0.12 nM and 0.11 muM, respectively) for 31A-F(2) cells incubated in serum-free medium. EGF induced up to three doublings in the cell population, whereas insulin induced an average of one cell population doubling. FGF, OGF, and transferrin were found not to have any prominent effect on cell division when incubated individually with 31A-F(2) cells in serum-free medium. However, a combination of EGF, OGF, insulin, and transferrin stimulated cell division to the same approximate extent as cells incubated in the presence of 5 percent fetal calf serum. EGF or insulin did not significantly affect total cell cholesterol levels (relative to cells incubated in serum-free medium) when incubated individually with 31A-F(2) cells. However, cell cholesterol levels were increased by the addition of OGF (250 percent), FGF (370 percent), or a combination of insulin and EGF (320 percent). Progesterone secretion from 31A-F(2) cells was enhanced by EGF (25 percent), FGF (80 percent), and insulin (115 percent). However, the addition of a mitogenic mixture of EGF, OGF, insulin, and transferrin suppressed progesterone secretion 150 percent) below that of control cultures. These studies have permitted us to determine that EGF and insulin are mitogenic factors that are required for the growth of 31A-F(2) cells and that OGF and transferrin are positive cofactors that enhance growth. Also, additional data suggest that cholesterol and progesterone production in 31A-F(2) cells can be regulated by peptide growth factors and the hormone insulin.     

Effects of culture duration and time of gonadotropin addition on in vitro maturation and fertilization of red deer (Cervus elaphus) oocytes

Immature red deer (Cervus elaphus ) oocytes (n = 1208) were collected from 1 to 4 - mm diameter follicles on ovaries and then cultured for 16, 20, 24 or 28 h (Groups I to IV) in TCM 199 supplemented with 10% FCS, 1 x 10(6) granulosa cells/ml and 1 mug/ml estradiol at 39 degrees C under 5% CO(2) in air. Gonadotropins (10 mug/ml, FSH and LH) were added to the culture medium at the start of culture (0 h) or after 6 h. Approximately one-third of the oocytes were examined for maturation, and the remainder were fertilized in vitro with frozen-thawed semen collected from a stag by electroejaculation. In vitro fertilized oocytes (n = 309) from four of the maturation treatment (Groups II and III in both gonadotropin treatments) were cultured for 7 d and examined for cleavage. Oocytes cultured for 16 h (Group I) had lower (P < 0.001) maturation rates (4.7%) than those in the longer culture durations (Groups II to IV: 68.9%). Culture for 20 (Group II) and 24 h (Group III) resulted in higher (P <0.001) fertilization rates than culture for 16 (Group I) and 28 h (Group IV) (18.3, 20.5, 7.1, 7.8%, respectively). The time of gonadotropin addition did not affect maturation or fertilization rates, but its addition at 6 h increased (P < 0.05) the percentage of oocytes cleaving (5.7 vs 12.5%). Oocytes cultured for 20 h (Group II) and with the delayed addition of gonadotropins cleaved most readily (18.2%). No embryos developed beyond eight-cell stage.     

Depression of follicle stimulating hormone in bulls injected with follicular fluid

Eight bulls were divided into two groups and injected with either charcoal-extracted steer blood serum or charcoal-extracted bovine follicular fluid (bFF). Ten-milliliter injections were given subcutaneous every 12 h for 4 wk. Jugular blood collected before, during and after the injection period was analyzed for follicle-stimulating hormone (FSH) and luteinizing hormone (LH) by radioimmunoassay. All bulls were exposed to restrained, estrual heifers for 15 min every 2 wk for 16 wk starting 4 wk before the first injection. The number of mounts and services by each bull was recorded. Semen was collected with an artificial vagina and evaluated on alternate weeks during the same period. The concentration of FSH in serum decreased (P < 0.05) by 12 h after the first injection and remained 61% lower than that of serum-injected bulls during the injection period. The concentration of FSH increased (P < 0.05) by 3 d after the last injection. Injections of bFF did not affect the concentration of LH in serum. Bovine follicular fluid injections significantly depressed FSH; however, libido, serving capacity, and semen characteristics were unchanged.     

Reciprocal regulation of adult rat hepatocyte growth and functional activities in culture by dimethyl sulfoxide

Hepatocyte DNA synthesis, initiated by epidermal growth factor (EGF), is reversibly inhibited by 2% dimethyl sulfoxide (DMSO). At that concentration, both the survival of the cells in culture and the expression of differentiated functions are prolonged. DMSO does not affect thymidine uptake or EGF receptor binding. Moreover, EGF receptor binding is maintained at 84% of initial 12 hr binding when cells are cultured for several days in the presence of DMSO, whereas specific receptor binding declines to 49% of initial binding under standard culture conditions without DMSO. Studies of hepatocyte functional activity indicate that, during early culture, total cellular export protein synthesis, specific albumin synthesis, and glycogen synthesis are enhanced in the presence of DMSO. Dexamethasone is required for the effect of DMSO on survival, and although dexamethasone alone enhances hepatocyte DNA synthesis in the presence of EGF, it does not reverse the inhibitory effect of 2% DMSO on DNA replication. The correlation of prolonged survival with growth inhibition supports the hypothesis that hepatic growth and differentiated functional activity may be reciprocally regulated.