Experience Sharing and Evaluation Results of Adaptation Technologies Due to Global Climate Change in Water Shortage Irrigation Zone of Taiwan

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchive

Prodigal: prokaryotic gene recognition and translation initiation site identification

<p>Abstract</p> <p>Background</p> <p>The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals.</p> <p>Results</p> <p>With our years of experience in manually curating genomes for the Joint Genome Institute, we developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm). With Prodigal, we focused specifically on the three goals of improved gene structure prediction, improved translation initiation site recognition, and reduced false positives. We compared the results of Prodigal to existing gene-finding methods to demonstrate that it met each of these objectives.</p> <p>Conclusion</p> <p>We built a fast, lightweight, open source gene prediction program called Prodigal <url>http://compbio.ornl.gov/prodigal/</url>. Prodigal achieved good results compared to existing methods, and we believe it will be a valuable asset to automated microbial annotation pipelines.</p

Genome-Wide Gene Expression Analysis Implicates the Immune Response and Lymphangiogenesis in the Pathogenesis of Fetal Chylothorax

Fetal chylothorax (FC) is a rare condition characterized by lymphocyte-rich pleural effusion. Although its pathogenesis remains elusive, it may involve inflammation, since there are increased concentrations of proinflammatory mediators in pleural fluids. Only a few hereditary lymphedema-associated gene loci, e.g. VEGFR3, ITGA9 and PTPN11, were detected in human fetuses with this condition; these cases had a poorer prognosis, due to defective lymphangiogenesis. In the present study, genome-wide gene expression analysis was conducted, comparing pleural and ascitic fluids in three hydropic fetuses, one with and two without the ITGA9 mutation. One fetus (the index case), from a dizygotic pregnancy (the cotwin was unaffected), received antenatal OK-432 pleurodesis and survived beyond the neonatal stage, despite having the ITGA9 mutation. Genes and pathways involved in the immune response were universally up-regulated in fetal pleural fluids compared to those in ascitic fluids. Furthermore, genes involved in the lymphangiogenesis pathway were down-regulated in fetal pleural fluids (compared to ascitic fluid), but following OK-432 pleurodesis, they were up-regulated. Expression of ITGA9 was concordant with overall trends of lymphangiogenesis. In conclusion, we inferred that both the immune response and lymphangiogenesis were implicated in the pathogenesis of fetal chylothorax. Furthermore, genome-wide gene expression microarray analysis may facilitate personalized medicine by selecting the most appropriate treatment, according to the specific circumstances of the patient, for this rare, but heterogeneous disease

The Effect of Porosity Change in Bentonite Caused by Decay Heat on Radionuclide Transport through Buffer Material

Bentonite is used as a buffer material in most high-level radioactive waste (HLW) repository designs. Smectite clay is the main mineral component of bentonite and plays a key role in controlling the buffer’s physical and chemical behaviors. Moreover, the long-term functions of buffer clay could be lost through smectite dehydration under the prevailing temperature stemming from the heat of waste decay. Therefore, the influence of waste decay temperatures on bentonite performance needs to be studied. However, seldom addressed is the influence of the thermo-hydro-chemical (T-H-C) processes on buffer material degradation in the engineered barrier system (EBS) of HLW disposal repositories as related to smectite clay dehydration. Therefore, we adopted the chemical kinetic model of smectite dehydration to calculate the amount of water expelled from smectite clay minerals caused by the higher temperatures of waste decay heat. We determined that the temperature peak of about 91.3 °C occurred at the junction of the canister and buffer material in the sixth year. After approximately 20,000 years, the thermal caused by the release of the canister had dispersed and the temperature had reduced close to the geothermal background level. The modified porosity of bentonite due to the temperature evolution in the buffer zone between 0 and 0.01 m near the canister was 0.321 (1–2 years), 0.435 (3–10 years), and 0.321 (11–20,000 years). In the buffer zone of 0.01–0.35 m, the porosity was 0.321 (1–20,000 years). In the simulation results of near-field radionuclide transport, we determined that the concentration of radionuclides released from the buffer material for the porosity of 0.321 was higher than that for the unmodified porosity of 0.435. It occurs after 1, 1671, 63, and 172 years for the I-129, Ni-59, Sr-90, and Cs137 radionuclides, respectively. The porosity correction model proposed herein can afford a more conservative concentration and approach to the real release concentration of radionuclides, which can be used for the safety assessment of the repository. Smectite clay could cause volume shrinkage because of the interlayer water loss in smectite and cause bentonite buffer compression. Investigation of the expansion pressure of smectite and the confining stress of the surrounding host rock can further elucidate the compression and volume expansion of bentonite. Within 10,000 years, the proportion of smectite transformed to illite is less than 0.05%. The decay heat temperature in the buffer material should be lower than 100 °C, which is a very important EBS design condition for radioactive waste disposal. The results of this study may be used in advanced research on the evolution of bentonite degradation for both performance assessments and safety analyses of final HLW disposal

Particle size concentration distribution and influences on exhaled breath particles in mechanically ventilated patients.

Humans produce exhaled breath particles (EBPs) during various breath activities, such as normal breathing, coughing, talking, and sneezing. Airborne transmission risk exists when EBPs have attached pathogens. Until recently, few investigations had evaluated the size and concentration distributions of EBPs from mechanically ventilated patients with different ventilation mode settings. This study thus broke new ground by not only evaluating the size concentration distributions of EBPs in mechanically ventilated patients, but also investigating the relationship between EBP level and positive expiratory end airway pressure (PEEP), tidal volume, and pneumonia. This investigation recruited mechanically ventilated patients, with and without pneumonia, aged 20 years old and above, from the respiratory intensive care unit of a medical center. Concentration distributions of EBPs from mechanically ventilated patients were analyzed with an optical particle analyzer. This study finds that EBP concentrations from mechanically ventilated patients during normal breathing were in the range 0.47-2,554.04 particles/breath (0.001-4.644 particles/mL). EBP concentrations did not differ significantly between the volume control and pressure control modes of the ventilation settings in the mechanically ventilated patients. The patient EBPs were sized below 5 µm, and 80% of them ranged from 0.3 to 1.0 µm. The EBPs concentrations in patients with high PEEP (> 5 cmH₂O) clearly exceeded those in patients with low PEEP (≤ 5 cmH₂O). Additionally, a significant negative association existed between pneumonia duration and EBPs concentration. However, tidal volume was not related to EBPs concentration

Comparative Analysis of Energy Consumption, Indoor Thermal–Hygrometric Conditions, and Air Quality for HVAC, LDAC, and RDAC Systems Used in Operating Rooms

As controlling temperature and humidity is crucial for maintaining comfort and preventing microbial growth, operating rooms (ORs) are the most energy-intensive areas in hospitals. We aimed to evaluate the energy consumption of three dehumidification air conditioning systems used in ORs and their corresponding air quality for ORs at rest. This study selected three ORs using a conventional heating, ventilation, and air conditioning (HVAC) system; a liquid desiccant air conditioning (LDAC) system; and a rotary desiccant air conditioning (RDAC) system, respectively. The indoor thermal&ndash;hygrometric conditions, air quality, and energy consumption of the ORs were monitored in this study. The median levels of relative humidity (RH) were 66.7% in the OR using the conventional HVAC system, 60.8% in the OR using the LDAC system, and 60.5% in the OR using the RDAC system. The median daily total energy consumption of the RDAC system (10.1 kWh/m2) and LDAC system (11.8 kWh/m2) were 28.12% and 16.54% lower, respectively, than that of the conventional HVAC system (14.1 kWh/m2). The PM&ge;0.5 levels and airborne bacterial concentrations in the ORs met the ISO 14644-1 Class 7 standard and China&rsquo;s GB50333-2013 standard, respectively. The RDAC system was clearly superior to the LDAC and conventional HVAC systems in terms of energy consumption