Benchmark dataset for the Voronoi diagram of 3D spherical balls.

In this paper, we present a dataset to be used for the construction of the Voronoi diagram of 3D spherical balls (VD-B3). The dataset consists of sphere arrangements including general, anomaly, and extreme cases. The dataset also includes protein models downloaded from RCSB Protein Data Bank (PDB). The dataset can be used as a standard benchmark dataset to verify and validate the correctness, efficiency, and robustness of the construction algorithm. The dataset is simple and easy to understand. The details of the experiment and analysis based on this dataset are presented in the original research article: "Robust Construction of the Voronoi Diagram of Spherical Balls in the Three-Dimensional Space" which introduces the topology-oriented incremental algorithm for the construction that is thoroughly validated and compared with two implementations of the well known edge-tracing algorithm.

Production of high-calorific biogas from food waste by integrating two approaches: Autogenerative high-pressure and hydrogen injection.

Auto-generative high pressure digestion (AHPD) and hydrogen-injecting digestion (HID) have been introduced to directly produce high CH4-content biogas from anaerobic digester. However, each approach has its own technical difficulties (pH changes), and practical issues (high cost of H2) to obtain > 90% CH4 containing biogas, particularly, from the high-strength waste like food waste (FW). To overcome this problem, in this study, AHPD and HID were integrated, which can offset each drawback but maximize its benefit. Substrate concentration of FW tested here was 200 g COD/L, the highest ever applied in AHPD and HID studies. At first, the reactor was operated by elevating the autogenerative pressure from 1 to 3, 5, and 7 bar without H2 injection. With the pressure increase, the CH4 content in the biogas gradually increased from 52.4% at 1 bar to 77.4% at 7 bar. However, a drop of CH4 production yield (MPY) was observed at 7 bar, due to the pH drop down to 6.7 by excess CO2 dissolution. At further operation, H2 injection began at 5 bar, with increasing its amount. The injection was effective to increase the CH4 content to 82.8%, 87.2%, and 90.6% at 0.09, 0.13, and 0.18 L H2/g CODFW.fed of H2 injection amount, respectively. At 0.25 L H2/g CODFW.fed, there was a further increase of CH4 content to 92.1%, but the MPY was dropped with pH increase to 8.7 with residual H2 being detected (4% in the biogas). Microbial community analysis showed the increased abundance of piezo-tolerant microbe with pressure increase, and direct interspecies electron transfer contributors after H2 injection. In conclusion, the integration of two approaches enabled to directly produce high calorific biogas (90% > CH4, 180 MJ/m3 biogas) from high-strength FW at the lowest requirement of H2 (0.18 L H2/g CODFW.fed) ever reported.

Prognostic Factor and Survival Benefit of Adjuvant Chemotherapy in Stage IIA Colon Cancer.

PURPOSE: There is no clear evidence of the benefit of adjuvant chemotherapy (AC) in stage IIA colon cancer. Therefore, we aimed to evaluate the prognostic factors and survival benefit of AC in this disease. METHODS: A retrospective data collection for patients who underwent radical surgery for colon cancer between January 2008 and December 2015 was undertaken. The cohort was divided into the no-AC and AC groups. RESULTS: We included 227 patients with stage IIA colon cancer in our study cohort, including 67 and 160 patients in the no-AC and AC groups, respectively. The number of retrieved lymph nodes and the presence of tumor complications as obstruction or perforation were independent risk factors for survival. In the no-AC group, there was a significant difference in survival according to the number of retrieved lymph nodes. In the AC group, there were significant differences in survival according to sidedness and preoperative carcinoembryonic antigen (CEA). There was no significant difference in survival between the no-AC and the AC groups. CONCLUSION: The number of retrieved lymph nodes and the presence of tumor complications were prognostic factors for stage IIA colon cancer but lymphovascular and perineural invasion were not. Sidedness and preoperative CEA could be used as factors to predict the benefit of adjuvant chemotherapy. Currently, it is believed that there is no benefit of AC for stage IIA colon cancer. Further studies are needed to determine the survival benefit of adjuvant chemotherapy in stage IIA colon cancer.

Dynamic Voronoi Diagram for Moving Disks.

Voronoi diagrams are powerful for understanding spatial properties. However, few reports have been made for moving generators despite their important applications. We present a topology-oriented event-increment (TOI-E) algorithm for constructing a Voronoi diagram of moving circular disks in the plane over the time horizon [0, t∞). The proposed TOI-E algorithm computes the event history of the Voronoi diagram over the entire time horizon in O(kF logn + kC n logn) time with O(n logn) preprocessing time and O(n + kF + kC) memory for n disk generators, kF edge flips, and kC disk collisions during the time horizon. Given an event history, the Voronoi diagram of an arbitrary moment can be constructed in O(k∗ + n) time where k∗ represents the number of events in [0, t∗). An example of the collision avoidance problem among moving disks is given by predicting future conjunctions among the disks using the proposed algorithm. Dynamic Voronoi diagrams will be very useful as a platform for the planning and management of the traffics of unmanned vehicles such as cars on street, vessels on surface, drones and airplanes in air, and satellites in geospace.

Beta-complex versus Alpha-complex: Similarities and Dissimilarities.

The beta-complex is a construct derived from the Voronoi diagram of spherical balls of arbitrary radii and has proven a powerful capability for proximity reasoning among spherical balls in three-dimensional space. Important applications related to molecular shapes in structural/computational molecular biology have been correctly, efficiently, and conveniently solved in the unified framework of the beta-complex and the Voronoi diagram. The beta-complex is a generalization of the ordinary alpha-complex. However, there are similarities and dissimilarities between the two complexes and it is necessary to correctly understand these similarities and dissimilarities to choose the right complex to solve application problems at hand. This paper presents the similarities and dissimilarities between these constructs and illustrates the consequence of the dissimilarity in application problems from both theoretical and practical points of view using examples of atomic arrangements.

Effects of pig slurry acidification on methane emissions during storage and subsequent biogas production.

In addition to undesirable odorous gases, substantial amounts of greenhouse gases (GHG), particularly methane (CH4), are generated during the storage of livestock manure. To reduce the CH4 emissions, first, pig slurry (PS) was stored for 40 d at 30 °C after adjusting the pH at 5.0-7.0 using H2SO4 solution. In the control (non-acidified PS), 3.7 kg CO2 eq./ton PS of CH4 emissions was detected, which was reduced to 1.8, 0.9, 0.4, 0.2, and 0.1 kg CO2 eq./ton PS at pH 7.0, 6.5, 6.0, 5.5, and 5.0, respectively. Methanosarcina was found to be the dominant genus (67% of the total archaeal sequence) in the control, whose dominance was reduced as storage pH decreased. The results of ribonucleic acid analysis and specific methanogenic activity test further confirmed the inhibition of indigenous methanogens by acidification. Later, the biochemical CH4 potential of stored PS was tested. Compared to the control (10.6 L CH4/L PS), the acidified PS showed higher CH4 yields of 12.7-14.6 L CH4/L PS, presumably by keeping degradable organic matters in PS under acidic condition. Among different acidification pHs tested, the maximum amount of GHG reduction was achieved at pH 6.0 by reducing CH4 emission to +0.4 kg CO2 eq./ton PS during storage while increasing biogas production potential equivalent to 48.3 kWh/ton PS (-22.5 kg CO2 eq./ton PS), resulting in a further reduction of (-)9.6 kg CO2 eq./ton PS compared to the control.

High-calorific bio-hydrogen production under self-generated high-pressure condition.

For the use of biologically produced H2, removal of CO2 is an indispensable process. Unlike conventional CO2 removal methods, this study proposed a self-generated high-pressure dark fermentation (HPDF) process as a novel strategy for directly producing high-calorific bio-H2. The pressure was automatically increased by self-generated gas, while the maximum pressure inside fermenter was restricted to 1, 3, 5, 7, and 10 bar in a batch operation. As the pressure increased from 1 to 10 bar, the H2 content increased from 55% to 80%, whereas the H2 yield decreased from 1.5 to 0.9 mol H2/mol hexoseadded. The highest H2 content of 80% was obtained at both of 7 and 10 bars. Increased lactate production with increased abundance of lactic acid bacteria was observed at high-pressure. Despite the lower H2 yields at high-pressure conditions, HPDF was found to be economically beneficial for obtaining high-calorific bio-H2 owing to the low CO2 removal cost.

Biohydrogen production from food waste: Current status, limitations, and future perspectives.

Among the various biological routes for H2 production, dark fermentation is considered the most practically applicable owing to its capability to degrade organic wastes and high H2 production rate. Food waste (FW) has high carbohydrate content and easily hydrolysable in nature, exhibiting higher H2 production potential than that of other organic wastes. In this review article, first, the current status of H2 production from FW by dark fermentation and the strategies applied for enhanced performance are briefly summarized. Then, the technical and economic limitations of dark fermentation of FW are thoroughly discussed. Economic assessment revealed that the economic feasibility of H2 production from FW by dark fermentation is questionable. Current efforts to further increase H2 yield and waste removal efficiency are also introduced. Finally, future perspectives along with possible routes converting dark fermentation effluent to valuable fuels and chemicals are discussed.

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.

Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement.

More value from food waste: Lactic acid and biogas recovery.

Anaerobic digestion (AD) is one of the traditional technologies for treating organic solid wastes, but its economic benefit is sometimes questioned. To increase the economic feasibility of the treatment process, the aim of this study was to recover not only biogas from food waste but lactic acid (LA) as well. At first, LA fermentation of food waste (FW) was conducted using an indigenous mixed culture. During the operation, temperature was gradually increased from 35 °C to 55 °C, with the highest performance attained at 50 °C. At 50 °C and hydraulic retention time (HRT) of 1.0 d, LA concentration in the broth was 40 kg LA/m(3), corresponding to a yield of 1.6 mol LA/mol hexoseadded. Pyrosequencing results showed that Lactobacillus (97.6% of the total number of sequences) was the predominant species performing LA fermentation of FW. The fermented broth was then centrifuged and LA was extracted from the supernatant by the combined process of nanofiltration and water-splitting electrodialysis. The process could recover highly purified LA by removing 85% of mineral ions such as Na(+), K(+), Mg(2+), and Ca(2+) and 90% of residual carbohydrates. Meanwhile, the solid residue remained after centrifugation was further fermented to biogas by AD. At HRT 40 d (organic loading rate of 7 kg COD/m(3)/d), the highest volumetric biogas production rate of 3.5 m(3)/m(3)/d was achieved with a CH4 yield of 0.25 m(3) CH4/kg COD. The mass flow showed that 47 kg of LA and 54 m(3) of biogas could be recovered by the developed process from 1 ton of FW with COD removal efficiency of 70%. These products have a higher economic value 60 USD/ton FW compared to that of conventional AD (27 USD/ton FW).

Nanocrack-regulated self-humidifying membranes.

The regulation of water content in polymeric membranes is important in a number of applications, such as reverse electrodialysis and proton-exchange fuel-cell membranes. External thermal and water management systems add both mass and size to systems, and so intrinsic mechanisms of retaining water and maintaining ionic transport in such membranes are particularly important for applications where small system size is important. For example, in proton-exchange membrane fuel cells, where water retention in the membrane is crucial for efficient transport of hydrated ions, by operating the cells at higher temperatures without external humidification, the membrane is self-humidified with water generated by electrochemical reactions. Here we report an alternative solution that does not rely on external regulation of water supply or high temperatures. Water content in hydrocarbon polymer membranes is regulated through nanometre-scale cracks ('nanocracks') in a hydrophobic surface coating. These cracks work as nanoscale valves to retard water desorption and to maintain ion conductivity in the membrane on dehumidification. Hydrocarbon fuel-cell membranes with surface nanocrack coatings operated at intermediate temperatures show improved electrochemical performance, and coated reverse-electrodialysis membranes show enhanced ionic selectivity with low bulk resistance.

Microbial granulation for lactic acid production.

This work investigated the formation of microbial granules to boost the productivity of lactic acid (LA). The flocculated form of LA-producing microbial consortium, dominated by Lactobacillus sp. (91.5% of total sequence), was initially obtained in a continuous stirred-tank reactor (CSTR), which was fed with 2% glucose and operated at a hydraulic retention time (HRT) of 12 h and pH 5.0 ± 0.1 under a thermophilic condition (50°C). The mixed liquor in the CSTR was then transferred to an up-flow anaerobic sludge blanket reactor (UASB). The fermentation performance and granulation process were monitored with a gradual decrease of HRT from 8.0 to 0.17 h, corresponding to an increase in the substrate loading from 60 to 2,880 g glucose L(-1) d(-1) . As the operation continued, the accumulation of biomass in the UASB was clearly observed, which changed from flocculent to granular form with decrease in HRT. Up to the HRT decrease to 0.5 h, the LA concentration was maintained at 19-20 g L(-1) with over 90% of substrate removal efficiency. However, further decrease of HRT resulted in a decrease of LA concentration with increase in residual glucose. Nevertheless, the volumetric LA productivity continuously increased, reaching 67 g L-fermenter (-1) h(-1) at HRT 0.17 h. The size of LA-producing granules and hydrophobicity gradually increased with decrease in HRT, reaching 6.0 mm and 60%, respectively. These biogranules were also found to have high settling velocities and low porosities, ranging 2.69-4.73 cm s(-1) and 0.39-0.92, respectively.

BetaCavityWeb: a webserver for molecular voids and channels.

Molecular cavities, which include voids and channels, are critical for molecular function. We present a webserver, BetaCavityWeb, which computes these cavities for a given molecular structure and a given spherical probe, and reports their geometrical properties: volume, boundary area, buried area, etc. The server's algorithms are based on the Voronoi diagram of atoms and its derivative construct: the beta-complex. The correctness of the computed result and computational efficiency are both mathematically guaranteed. BetaCavityWeb is freely accessible at the Voronoi Diagram Research Center (VDRC) (http://voronoi.hanyang.ac.kr/betacavityweb).

Hydrogen fermentation of food waste by alkali-shock pretreatment: microbial community analysis and limitation of continuous operation.

In the study, at first, batch tests were performed to investigate the effect of alkali-shock on H2 production from food waste (FW). After alkali-pretreatment of FW at pH 9.0-13.0, the FW was cultivated under mesophilic condition at pH 6.0 for 30 h without external inoculum addition. The amount of H2 production from FW pretreated at pH 11.0 and 12.0 was higher than that achieved in other pretreatment pH. The main metabolite was butyrate, and Clostridium were dominant at pH 11.0 and 12.0. Meanwhile, lactate was the main metabolite with Enterococcus and Streptococcus being the dominant genus at other pretreatment pH. When the batch process was switched to a continuous mode, H2 production was significantly dropped due to the increased activity of H2-consumers. The reliability of alkali-pretreatment at pH 11.0 was proven by repeating the scale-up batch process, recording 1.57±0.11 mol H2/mol hexose(added) (17±2LH2/kg FW) and 4.39±0.32LH2/L/d.

Effect of the accuracy of pH control on hydrogen fermentation.

pH, known as the most important parameter in H2 fermentation, cannot be precisely controlled in a scaled-up fermenter as in a lab fermenter. In the preset work, to assess the effect of pH control accuracy on H2 fermentation, the pH was controlled at 6.0±0.1, 6.0±0.3, 6.0±0.5, 6.0±0.7, and 6.0±0.9 during batch fermentation of food waste. Up to deviation of ±0.3, a high H2 yield of 1.67-1.73 mol H2/mol hexose(added) was attained with producing butyrate as a major metabolite (>70% of total organic acids produced). A huge drop of H2 production, however, was observed at deviation >±0.5 with lowered substrate utilization and increased production of lactate. Next generation sequencing results showed that Clostridium was found to be the dominant genus (76.4% of total number of sequences) at deviation of ±0.1, whereas the dominant genus was changed to lactic acid bacteria such as Streptococcus and Lactobacillus with increase of deviation value.

Effect of hydraulic retention time on lactic acid production and granulation in an up-flow anaerobic sludge blanket reactor.

In the present work, lactic acid (LA) production performance with granulation was investigated at various hydraulic retention times (HRTs), 8-0.5h. Glucose was used as a feedstock, and anaerobic mixed cultures were inoculated in an up-flow anaerobic sludge blanket reactor. As HRT decreased, the average diameter and hydrophobicity of the granules increased from 0.31 to 3.4mm and from 17.5% to 38.3%, respectively, suggesting the successful formation of granules. With decreasing HRT, LA productivity increased up to 16.7gLA/L-fermenter/h at HRT 0.5h. The existence of rod-shaped organisms with pores and internal channels at granule surface was observed by scanning electron microscope. Next generation sequencing revealed that Lactobacillus was the dominant microorganism, accounting for 96.7% of total sequences, comprising LA-producing granules.

Increased solubilization of excess sludge does not always result in enhanced anaerobic digestion efficiency.

"Solubilization (SCOD/TCOD, chemical oxygen demand (COD), %)" is generally used as an indicator for the pretreatment effectiveness in anaerobic digestion (AD) of excess sludge. In the present work, ultrasonic (irradiation 5-60 min) and alkaline pretreatments (pH 9-13) were applied to excess sludge individually and in combination. Biological methane potential tests were carried out using the whole part of pretreated sludge and only the soluble fraction. Although solubilization increased with pretreatment intensity increase, methane production was inconsistent with increased solubilization, due to the lower methane yield of soluble fraction. While the soluble fraction obtained under mild pretreatment condition (pH 9+ultrasonication 5 min) showed 91% of methane yield, it was only 61% in case of severe pretreatment condition (pH 13+ultrasonication 60 min). 25.8% of the pretreated sludge at (pH 13+ultrasonication 60 min) consisted of soluble but non-biodegradable portion. These findings demonstrate that increased solubilization does not always result in enhanced AD efficiency.

Prediction of bio-methane potential and two-stage anaerobic digestion of starfish.

The present work reports the first ever evaluation of the biological CH4 potential (BMP) of starfish, classified as invasive species. Since starfish contain a large amount of inorganic matter, only the supernatant obtained through grinding and centrifugation was used for BMP test. By applying response surface methodology, the individual and interactive effects of three parameters, inoculum/substrate ratios, substrate concentrations, and buffer capacities on CH4 production were investigated, and the maximum CH4 yield of 334 mL CH4/g COD was estimated. In addition, continuous CH4 production was attempted using a two-stage (acidogenic sequencing batch reactor+methanogenic up-flow anaerobic sludge blanket reactor (UASBr)) fermentation process. Acidification efficiency was maximized at 2 days of hydraulic retention time with valerate, butyrate, and acetate as main acids, and these were converted to CH4 with showing 296 mL CH4/g COD added. Overall, the two-stage fermentation process could convert 44% of organic content in whole starfish to CH4.

Effect of temperature on continuous fermentative lactic acid (LA) production and bacterial community, and development of LA-producing UASB reactor.

A frequently used fermentation manner in lactic acid (LA) production, batch fermentation by pure cultures, has a limited practicability: low volumetric productivity and high energy consumption. In this study, continuous LA fermentation was performed in a completely stirred tank reactor at 12h HRT, inoculated with anaerobic digester sludge. Glucose (25 g COD/L) was used as a feedstock and temperature was increased from 35 to 60°C. LA production significantly increased from 50°C, which was negligible up to 45°C, with obvious bacterial community change. At 50 and 55°C, LA production was maximized, reaching 23 g COD/L, corresponding to 92% LA conversion efficiency. Pyrosequencing analysis showed that microbial diversity was simplified at 50-60°C, and the sequences closely related with Bacillus coagulans became predominant, followed by Lactobacillus fermentum. An LA-producing upflow ananerobic sludge blanket reactor was successfully developed, which enhanced the productivity up to 4.8 gLA/L/h by shortening HRT to 4h.