GA4GH: International policies and standards for data sharing across genomic research and healthcare

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.

The use of prophylactic gastroprotective therapy in patients with nonsteroidal anti-inflammatory drug- and aspirin-associated ulcer bleeding: a cross-sectional study

BACKGROUND

Poor adherence to gastroprotective agents (GPAs) is common among users of nonsteroidal anti-inflammatory drugs (NSAIDs) or low-dose aspirin (ASA). There are little data on the utilization of GPAs among NSAID and ASA users complicated by ulcer bleeding.

AIM

To study the utilization of GPA among NSAID and ASA ulcers before the onset of ulcer bleeding.

METHODS

We conducted a cross-sectional study to determine the exposure to NSAIDs, ASA, and GPAs within 4 weeks before endoscopically confirmed ulcer bleeding. Sensitivity analysis was performed to study how improving adherence to GPA use would reduce the risk of ulcer bleeding in high-risk users.

RESULTS

Between 2000 and 2009, 1093 and 2277 patients had NSAID- and ASA-associated ulcer bleeding respectively. The incidence of NSAID-associated ulcer bleeding declined by 40%, whereas that of ASA-associated ulcer bleeding increased by 46%. Thirty-nine per cent of NSAID users and 75% of ASA users belonged to high ulcer risk category. Although GPA prescription rate has increased over time, only 41.6% and 30.6% of high-risk NSAID and ASA users received GPAs before ulcer bleeding respectively. Sensitivity analysis showed that if GPAs could reduce bleeding risk by 50%, improving adherence would prevent up to 35% of ulcer bleeding in high-risk users.

CONCLUSIONS

A substantial proportion of high-risk NSAID and ASA users had not received prophylaxis with gastroprotective agents before ulcer bleeding. These bleeding episodes may be preventable with better adherence to gastroprotective agent use.

Antioxidant Activities and Total Phenolic Content of Aqueous Extract of Pleurotus ostreatus (Cultivated Oyster Mushroom)

Pleurotus ostreatus better known as oyster mushroom is widely cultivated and consumed as food in Malaysia. The present study aims to assess the antioxidative potential and total phenolic content of P. ostreatus aqueous extract. The antioxidant activities were evaluated against DPPH and ABTS radical-scavenging activity, ferric-reducing antioxidant power (FRAP) and β-carotene-linoleate bleaching assay, and the Folin-Ciocalteu method for total phenolic content (TPC). The DPPH and ABTS radical-scavenging activity was found to be 63.20% and 87.29% respectively; antioxidant activity using FRAP at 1.45 mM FE/100g and β-carotenelinoleate bleaching assay was 83.51%, while the TPC was found to be 798.55 mg GAE/100g. These antioxidant activities were compared to synthetic antioxidant, BHA and ascorbic acid. Ascorbic acid showed highest scavenging effects on DPPH and ABTS radical, followed by P. ostreatus and BHA (at maximum safety limit). The ferric reducing power of P. ostreatus was significantly higher than BHA and ascorbic acid. The antioxidant activity as assessed in β-carotene-linoleate bleaching assay was found to be higher in BHA compared to P. ostreatus. The aqueous extract of P. ostreatus was found to respond differently in antioxidant assays. The antioxidative activity of the aqueous extract of P. ostreatus correlated with its total phenolic content. Generally, the antioxidant activities of P. ostreatus' aqueous extract are comparable to that of BHA and ascorbic acid to a certain extent.

Effect of thermal processing of palm sap on the physico-chemical composition of traditional palm sugar

During the production of palm sugar, the palm sap (Arenga pinnata) is heated up to 150 degrees C. Besides the hydrolysis of carbohydrate to generate reducing sugars and degradation of amino acid, many physicochemical changes produced at all these temperatures, having a significant impact on the overall quality of palm sugar. In this study, changes in physico-chemical properties of the palm sap due to heat processing were investigated. Analysis of colour, soluble solid, pH, temperature, sugar and amino acid concentration was determinant. The results showed clearly that the heating process at these high temperatures was necessary to create an environment which was rich in essential precursors for subsequent reactions such as Maillard reaction. Chemical compounds that showed drastic changes in concentration were polar side chain amino acids especially glutamine, asparagine and arginine as well as sucrose and pH value. Other quality characteristics of palm sugar based on colour and soluble solids (Brix) shared an increase in concentration as a function of time.

Nasal CPAP reduces systemic blood pressure in patients with obstructive sleep apnoea and mild sleepiness

BACKGROUND

A randomised controlled study was undertaken to examine the effect of nasal continuous positive airway pressure (CPAP) on 24 hour systemic blood pressure (BP) in patients with obstructive sleep apnoea (OSA).

METHODS

Patients were fitted with an ambulatory BP measuring device as outpatients during normal activities and recorded for 24 hours before starting therapeutic or subtherapeutic (4 cm H(2)O) CPAP treatment. BP monitoring was repeated before completion of 12 weeks of treatment. The primary end point was the change in 24 hour mean BP.

RESULTS

Twenty three of 28 participants in each treatment arm completed the study. There was no significant difference between the two groups in age, body mass index, Epworth Sleepiness Score, apnoea-hypopnoea index, arousal index, and minimum Sao(2). Twenty four patients were hypertensive. The pressure in the therapeutic CPAP group was 10.7 (0.4) cm H(2)O. CPAP usage was 5.1 (0.4) and 2.6 (0.4) hours/night for the therapeutic and subtherapeutic CPAP groups, respectively (p<0.001). After 12 weeks of treatment there were significant differences between the two CPAP groups in mean (SE) changes in 24 hour diastolic BP (-2.4 (1.2) v 1.1 (1.0) mm Hg (95% CI -6.6 to -0.5), p = 0.025); 24 hour mean BP (-2.5 (1.3) v 1.3 (1.1) mm Hg (95% CI -7.2 to -0.2), p = 0.037); sleep time systolic BP (-4.1 (2.1) v 2.2 (1.8) mm Hg (95% CI -11.8 to -0.7), p = 0.028); and sleep time mean BP (-3.6 (1.7) v 1.3 (1.4) mm Hg (95% CI -9.2 to -0.4), p = 0.033).

CONCLUSIONS

Compared with subtherapeutic CPAP, 12 weeks of treatment with therapeutic CPAP leads to reductions in 24 hour mean and diastolic BP by 3.8 mm Hg and 3.5 mm Hg, respectively, in mildly sleepy patients with OSA.

Antisense inhibition of the Nr gene restores normal ripening to the tomato Never-ripe mutant, consistent with the ethylene receptor-inhibition model

The hormone ethylene regulates many aspects of plant growth and development, including fruit ripening. In transgenic tomato (Lycopersicon esculentum) plants, antisense inhibition of ethylene biosynthetic genes results in inhibited or delayed ripening. The dominant tomato mutant, Never-ripe (Nr), is insensitive to ethylene and fruit fail to ripen. The Nr phenotype results from mutation of the ethylene receptor encoded by the NR gene, such that it can no longer bind the hormone. NR has homology to the Arabidopsis ethylene receptors. Studies on ethylene perception in Arabidopsis have demonstrated that receptors operate by a "receptor inhibition" mode of action, in which they actively repress ethylene responses in the absence of the hormone, and are inactive when bound to ethylene. In ripening tomato fruit, expression of NR is highly regulated, increasing in expression at the onset of ripening, coincident with increased ethylene production. This expression suggests a requirement for the NR gene product during the ripening process, and implies that ethylene signaling via the tomato NR receptor might not operate by receptor inhibition. We used antisense inhibition to investigate the role of NR in ripening tomato fruit and determine its mode of action. We demonstrate restoration of normal ripening in Nr fruit by inhibition of the mutant Nr gene, indicating that this receptor is not required for normal ripening, and confirming receptor inhibition as the mode of action of the NR protein.

Radon action level for high-rise buildings

Radon and its progeny are the major contributors to the natural radiation dose received by human beings. Many countries and radiological authorities have recommended radon action levels to limit the indoor radon concentrations and, hence, the annual doses to the general public. Since the sources of indoor radon and the methods for reducing its concentration are different for different types of buildings, social and economic factors have to be considered when setting the action level. But so far no action levels are specifically recommended for cities that have dwellings and offices all housed in high-rise buildings. In this study, an optimization approach was used to determine an action level for high-rise buildings based on data obtained through previous territory-wide radon surveys. A protection cost of HK$0.044 per unit fresh air change rate per unit volume and a detriment cost of HK$120,000 per person-Sv were used, which gave a minimum total cost at an action level of 200 Bq m(-3). The optimization analyses were repeated for different simulated radon distributions and living environment, which resulted in quite significantly different action levels. Finally, an action level of 200 Bq m(-3) was recommended for existing buildings and 150 Bq m(-3) for newly built buildings.

Behavior of 222Rn and its progeny in high-rise buildings

Unlike detached or semi-detached houses, the main source of indoor radon in high-rise buildings is the building material. Radon released from the building material will be removed by ventilation, either forced or natural, so that its concentration, its progeny's concentration, and the equilibrium between the two will be different for different types of buildings and environmental factors. A number of surveys were carried out in buildings throughout the territory to look at the seasonal variation of indoor 222Rn levels; the dependence of indoor 222Rn concentration on the living environment; the indoor gamma dose rate and its relation to indoor 222Rn concentration; and the dependence of 222Rn progeny concentration and equilibrium factor on the environment in high-rise buildings.

Age, fitness, and regional blood flow during exercise in the heat

During dynamic exercise in warm environments, the requisite increase in skin blood flow (SkBF) is supported by an increase in cardiac output (Qc) and decreases in splanchnic (SBF) and renal blood flows (RBF). To examine interactions between age and fitness in determining this integrated response, 24 men, i.e., 6 younger fit (YF), 6 younger sedentary (YS), 6 older fit (OF), and 6 older sedentary (OS) rested for 50 min, then exercised at 35 and 60% maximal O2 consumption (VO2max) at 36 degrees C ambient temperature. YF had a significantly higher Qc and SkBF than any other group during exercise, but fitness level had no significant effect on any measured variable in the older men. At 60% VO2max, younger subjects had significantly greater decreases in SBF and RBF than the older men, regardless of fitness level. Total flow redirected from these two vascular beds (deltaSBF + deltaRBF) followed YF >> YS > OF > OS. A rigorous 4-wk endurance training program increased exercise SkBF in OS, but deltaSBF and deltaRBF were unchanged. Under these conditions, older men distribute Qc differently to regional circulations, i.e., smaller increases in SkBF and smaller decreases in SBF and RBF. In younger subjects, the higher SkBF associated with a higher fitness level is a function of both a higher Qc and a greater redistribution of flow from splanchnic and renal circulations, but the attenuated splanchnic and renal vasoconstriction in older men does not appear to change with enhanced aerobic fitness.

Evidence supporting a signal transduction pathway leading to the radiation-resistant phenotype in human tumor cells

A signal transduction pathway, involving oncogenes and their normal counterparts the proto-oncogenes, analogous to that for cell growth and differentiation has been proposed to lead to the phenotype of cellular radioresistance (RR). In this report we provide evidence demonstrating the existence of such a pathway by using antisense oligonucleotides (ASO) to reverse the RR phenotype. Utilizing ASO directed against the raf-1 gene, a central component of this proposed pathway, we were able to reverse the RR phenotype of human tumor cell lines having elevated HER-2 expression or a mutant form of Ha-ras, two genes upstream of raf-1 in signal transduction. Additionally, anti-ras ASO were able to radiosensitize HER-2 overexpressing cells. These results, which verify the presence of a signaling pathway leading to cellular RR, also have possible clinical implications for the use of ASO as a means to sensitize radioresistant tumors to radiation therapy.

Age alters regional distribution of blood flow during moderate-intensity exercise

During dynamic exercise in warm environments, requisite increases in skin and active muscle blood flows are supported by increasing cardiac output (Qc) and redistributing flow away from splanchnic and renal circulations. To examine the effect of age on these responses, six young (Y; 26 +/- 2 yr) and six older (O; 64 +/- 2 yr) men performed upright cycle exercise at 35 and 60% of peak O2 consumption (VO2peak) in 22 and 36 degrees C environments. To further isolate age, the two age groups were closely matched for VO2peak, weight, surface area, and body composition. Measurements included heart rate, Qc (CO2 rebreathing), skin blood flow (from increases in forearm blood flow (venous occlusion plethysmography), splanchnic blood flow (indocyanine green dilution), renal blood flow (p-amino-hippurate clearance), and plasma norepinephrine concentration. There were no significant age differences in Qc; however, in both environments the O group maintained Qc at a higher stroke volume and lower heart rate. At 60% VO2peak, forearm blood flow was significantly lower in the O subjects in each environment. Splanchnic blood flow fell (by 12-14% in both groups) at the lower intensity, then decreased to a greater extent at 60% VO2peak in Y than in O subjects (e.g., -45 +/- 2 vs. -33 +/- 3% for the hot environment, P < 0.01). Renal blood flow was lower at rest in the O group, remained relatively constant at 35% VO2peak, then decreased by 20-25% in both groups at 60% VO2peak. At 60% VO2peak, 27 and 37% more total blood flow was redistributed away from these two circulations in the Y than in the O group at 22 and 36 degrees, respectively. It was concluded that the greater increase in skin blood flow in Y subjects is partially supported by a greater redistribution of blood flow away from splanchnic and renal vascular beds.

Indocyanine green test is a reliable indicator of postoperative liver function in biliary atresia

In order to evaluate liver function in postoperative biliary atresia (BA) patients, the indocyanine green (ICG) clearance test was performed. Nineteen patients, ranging in age from 2 to 9 years, were classified into three groups. Group I were those who had no jaundice throughout the postoperative period (n = 9), Group II were those who had recurrent or intermittent jaundice (n = 7), and Group III were those who had persistent jaundice after hepatic portojejunostomy (n = 3). Forty-four volunteers of comparative age and sex served as controls to establish a normal range of ICG-K values in infants and children. The normal minimal ICG-K value in those 2-9 years of age was defined as 0.19. ICG-K values in BA patients were 0.262 +/- 0.073 (Group I), 0.150 +/- 0.060 (Group II), and 0.054 +/- 0.011 (Group III). All nine patients with ICG-K below the normal level had esophageal varices, and seven of nine had a history of gastrointestinal hemorrhage. Two patients with ICG-K values within the normal range had esophageal varices, and none had a history of gastrointestinal hemorrhage. Five of nine patients with ICG-K values below normal had low serum albumin levels, and all had low prealbumin levels. Of those with ICG-K within the normal range, none had low serum albumin or prealbumin levels. On the other hand, serum bilirubin and other liver function tests did not accurately reflect clinical findings. In conclusion, the ICG test using the ICG-K value was confirmed to be a reliable indicator of postoperative liver function in BA patients.

Reduction of blood PO2 decrease and PCO2 increase during asphyxia by paramedian reticular nucleus in cats

Effects of activation of paramedian reticular nucleus (PRN) on the systemic arterial blood pressure (SAP), heart rate, renal nerve activity (RNA), and changes of the partial pressure of the arterial blood oxygen (PO2) and carbon dioxide (PCO2) during asphyxia were studied in cats anesthetized with chloralose (40 mg/kg) and urethane (400 mg/kg). During a 35-s period of asphyxial anoxia, SAP and RNA increased while heart rate decreased significantly. The arterial blood PO2 decreased by 64.6 +/- 4.7% while the PCO2 increased by 54.6 +/- 6.3%. Electrical stimulation of PRN produced a mild to moderate decrease of the SAP, heart rate, and RNA, but arterial PO2 and PCO2 did not change significantly. When PRN was stimulated simultaneously with asphyxia, increases of SAP and RNA and changes of blood gases subsequent to asphyxia reduced significantly. Arterial PO2 decreased only 54.0 +/- 4.9% while the PCO2 increased 39.4 +/- 10.5% (p < 0.01). Similar effects were observed in the venous blood from inferior vena cava. In addition, when the arteriovenous difference of PO2 and PCO2 was compared, simultaneous PRN stimulation during asphyxia produced a higher PO2 reserve (66.3%) and less PCO2 production (-7%) than without PRN stimulation; PO2 54.2%, PCO2 (-2.9%). The results suggest that PRN is a structure that can exert inhibition over a wide spectrum of body functions; not only autonomic system but probably also metabolism.

Particle size measuring device in real time for dense particulate systems

The design and performance of a real-time particle size measuring device for dense particulate systems are reported. Based on measuring the ratio of scattered light at two angles, this device, in contrast to particle sizing instruments previously reported, allows more than one particle in the focal volume at any time and selects the scattered light pulses for processing. Size distributions have been determined with an average number of particles in the focal volume of up to 2.5. This represents a potential increase of more than an order of magnitude in particle concentration over single particle sizing devices.