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The mechanism exhausting CD8+ T cells is not completely clear against tumors. Literature has demonstrated that cigarette smoking disables the immunological activity, so we propose nicotine is able to exhaust CD8+ T cells. The CD8+ T cells from healthy volunteers with and without cigarette smoking and the capacity of CD8+ T cells against tumor cells were investigated. RNAseq was used to investigate the gene profiling expression in CD8+ T cells. Meanwhile, small RNAseq was also used to search novel microRNAs involved in the exhaustion of CD8+ T cells. The effect of nicotine exhausting CD8+ T cells was investigated in vitro and in the humanized tumor xenografts in vivo. We found that CD8+ T cells were able to reduce cell viability in lung cancer HCC827 and A549 cells, that secreted granzyme B, but CD8+ T cells from the healthy cigarette smokers lost anti-HCC827 effect. Moreover, nicotine suppressed the anti-HCC827 effect of CD8+ T cells. RNAseq revealed lower levels of IL2RB and GZMB in the exhausted CD8+ T cells. We identified that miR-629-5p was increased by nicotine, that targeted IL2RB. Transfection of miR-629-5p mimic reduced IL2RB and GZMB levels. We further validated that nicotine reduced granzyme B levels using a nuclear imaging technique, and demonstrated that nicotine exhausted peripheral blood mononuclear cells against HCC827 growth in the humanized tumor xenografts. This study demonstrated that nicotine exhausted CD8+ T cells against HCC827 cells through increasing miR-629-5p to suppress IL2RB.

Background In this study, our major aim is to using multiple-steps bioinformatic analysis to predict cardiogenic genes with targeting mRNA profiling for predicting cardiogenic HoxA11 gene. Methods We first analyzed the microarray data with bioinformatic measurement, including combining with panel module 1 (mouse embryonic stem cells), panel module 2 (mouse induced pluripotent stem cells), and panel module 3 (gene list form literature of heart development). A literature-based comparison of the two microarrays and a software-based (Targetscan program, www.targetscan.org) comparative analysis of the two datasets. Furthermore, we select the common central pathways and potential candidate genes involved in the cardiomyocyte-lineaged differentiation and development. Results Schematic presentation of a putative miR181a target site in Hox-A11 3'UTR. The bioinformatic result showed that potential interacted cardiogenic targets of Tbx5, Tbx20, Mal2c, Nkx2.5, cTNT, Cx43, MHC, and MCK in different treatment groups of pluripotent stem cells by using a literature-based comparison of the two microarrays and a software-based gene-lineage system. Conclusion Our findings support that mir181a is an up-stream regulating microRNA to target the 3'UTR of HoxA11 mRNA during the process of cardiomyocyte differentiation.

BACKGROUND Lung cancer is one of the major causes of carcinoma-related deaths in the world. Importantly, lung adenocarcinoma (LAC) is the most common type with poor outcome. However, the progressive clinical phenotype and biomolecular signature of lung cancer presenting the cancer stem-like and metastatic characteristics are still unclear. METHODS In this study, we identified CD44 marker in lung cancers. The capabilities, including tumorigenic and migration assays, were analyzed in CD44 expression and CD44 expression subgroups. Meanwhile, the potential bio-signature and properties of lung tumor stem-like cells were further studied. RESULTS The high expression of CD44 subpopulation (CD44-positive) in isolated lung cancer cells showed significantly higher abilities of tumorigenic colonies, tumor-sphere formation, and migratory properties when compared with the CD44 expression group. These subgroups of CD44-positive lung cancer cells further demonstrated the metastatic potential with epithelial-mesenchymal transition (EMT), as well as the high expression of Twist and Snail gene profile. Importantly, the overexpression of Snail with gene vector in CD44 expression cells further significantly promoted the properties of lung tumor stem-like cells. CONCLUSION The results of this study highlighted the role of CD44-posivite subpopulation in modulating tumor initiation and EMT-based metastatic ability of lung malignancy.

The mechanism exhausting CD8

Background: Induced pluripotent stem cells (iPSCs) have a great potential for application in patient-specific therapy. The reprogramming method that does not involve c-Myc reduces tumorigenic risk, but also largely reduces the efficiency of generation of iPSCs, especially for those reprogrammed from damaged cells. Poly(ADP-ribose) polymerase 1 (Parp1) catalyzes a reaction of poly(ADP-ribosylation) and has been reported to enhance cell reprogramming. Methods: Using Oct-4/Sox2/Klf4/Parp1 (OSKP) reprogramming method, reprogramming factors plus Parp1 were capable of generation of iPSCs from adult fibroblasts and further toward to differentiate from iPSCs status into hepatocyte-like cells. Results: Our results showed that Oct-4/Sox2/Klf4/Parp1 (OSKP)-derived iPSC exhibited regular pluripotent properties, long-term passages and more stable cellular-divided period. These OSKP-derived iPSCs can effectively differentiate into hepatocyte-like cells (OSKP-iPSC-Heps), and present high mRNA levels of Sox17, HNF3b, and HNF4a in OSKP-iPSC-Heps. The mature hepatic functions, including CYP3A4, LDL uptake, glycogen synthesis and urea secretion were analyzed and well detected in OSKP-iPSC-Heps on day 14 post-differentiation. Conclusion: In conclusion, we demonstrated that Parp1 promoted reprogramming process to generate the high quality of iPSCs, which could be used as a high quality source of hepatocytes. Keywords: Hepatocyte, Induced pluripotent stem cells, Poly(ADP-ribose) polymerase 1

The prevalence of nonalcoholic fatty liver disease (NAFLD) is usually increased with age. Non-alcoholic steatohepatitis (NASH), a serious form of NAFLD, may lead to cirrhosis and end-stage liver diseases. Induced pluripotent stem cells (iPSCs) hold promising potential in personalized medicine. Although obviation of c-Myc reduces tumorigenic risk, it also largely reduced the generation of iPSCs. Recently, Poly(ADP-ribose) polymerase 1 (Parp1) has been reported to enhance cell reprogramming. In this study, we demonstrated that forced expression of Oct4/Sox2/Klf4/Parp1 (OSKP) effectively promoted iPSC generation from senescent somatic cells from 18-month-old mouse. The iPSCs presented regular pluripotent properties, ability to form smaller teratoma with smaller size, and the potential for tridermal differentiation including hepatocyte-like cells (OSKP-iPSC-Heps). Resembled to fetal hepatocytes but not senescent hepatocytes, these OSKP-iPSC-Heps possessed antioxidant ability and were resistant to oxidative insult induced by H2O2 or exogenous fatty acid. Intrasplenic transplantation of OSKP-iPSC-Heps ameliorated the triglyceride over-accumulation and hepatitis, prevented the production of inflammatory cytokines and oxidative substances, and reduced apoptotic cells in methionine/choline-deficient diet (MCDD)-fed mice. In conclusion, we demonstrated that Parp-1 promoted iPSC generation from senescent cells, which can be used for the treatment of NASH after hepatic-specific differentiation. These findings indicated that patient-derived iPSC-Heps may offer an alternative option for treatment of NASH and NASH-associated end-stage liver diseases.

BACKGROUND The major curative remedy for advanced liver failure is hepatic transplantation. However, the conventional medicine still shows the limitations and obstacles for liver regeneration. Importantly, it is unclear whether we can get a rapid and high efficacy platform to facilitate to reprogram hepatic capability. The main work of this study was to develop a platform for a nanomedicine-based gene-delivery platform of novel nanoparticles (NNPs) to efficiently facilitate the liver function recovery. METHODS In this study, we studied the feasibility and efficiency of NNP and produced the multiple abilities of NNPs for a potential platform of gene transduction. We showed that NNPs played an important role in hepatic protection. The cytoprotective effects of NNPs in toxic-hepatic cells were investigated and evaluated by cell viability, reactive oxygen species production, in vitro cell abilities, and in vivo animal studies. RESULTS We demonstrated that NNPs possess the abilities to protect the cell after toxic-stress both in vitro and in vivo. Under the stress condition, our result showed that cell viabilities can be improved by NNP-carried hepatocyte nuclear factor 3 (HNF3) gene (NNP-HNF3), which is a famous hepatic transcriptional factor and regenerative marker to modulate essential molecular pathways activating various hepatic-specific markers. Importantly, compared to control and NNP-control, NNP-HNF3 exhibited the cytoprotective effects that prevented toxic-induced oxidative stress and cell damage in vitro as well as in vivo. Notably, our data showed that NNP-HNF3 treatment may improve toxic-induced hepatic encephalopathy. CONCLUSION Herein, we demonstrated that novel nanoparticle, such as NNP-HNF3, serves as a key regulator for protecting the damaged hepatic cell and the bioproduct-based source for the new therapeutics of hepatic failure.

Signal transducer and activator of transcription 3 (STAT3), a transcriptional factor involved in tumorigenesis and cancer stemness formation, contributes to drug resistance in cancer therapies. STAT3 not only mediates gene transcription but also participates in microRNA suppression. This study identified a STAT3-downstream micro RNA (miRNA) involved in drug resistance against regorafenib in colorectal cancer stem-like tumorspheres. Small RNAseq was used to investigate differential microRNAs in colorectal cancer cell-derived tumorspheres and in a STAT3-knockdown strain. The miRNA-mediated genes were identified by comparing RNAseq data with gene targets predicted using TargetScan. Assays for detecting cell viability and apoptosis were used to validate findings. The formation of colorectal cancer stem-like tumorspheres was inhibited by BBI608, a STAT3 inhibitor, but not by regorafenib. Additional investigations for microRNA expression demonstrated an increase in 10 miRNAs and a decrease in 13 miRNAs in HT29-derived tumorspheres. A comparison of small RNAseq results between tumorspheres and HT29shSTAT3 cells revealed the presence of four STAT3-mediated miRNAs in HT29-derived tumorspheres: hsa-miR-215-5p, hsa-miR-4521, and hsa-miR-215-3p were upregulated, whereas miR-30a-5p was downregulated. Furthermore, hsa-miR-4521 was associated with poor overall survival probability, and miR-30a-5p was associated with better overall survival probability in patients with rectum cancer. Comparisons of RNAseq findings between HCT116- and HT29-derived tumorspheres revealed that HSPA5 were mediated by the STAT3-miR-30a-5p axis, which is overexpressed in colorectal tumorspheres associating to anti-apoptosis. In addition, the transfection of miR-30a-5p and inhibition of HSPA5 by HA15 significantly reduced cell viability and increased apoptosis in HT29 cells. In conclusion, a STAT3-miR-30a-5p-HSPA5 axis was observed against regorafenib-mediated apoptosis in colorectal cancer tumorspheres. The expression of miR-30a-5p was repressed by STAT3, in addition, HSPA5 was identified as the target gene of miR-30a-5p and contributed to both tumorsphere formation and anti-apoptosis.

Although the theories of habitus evolution enrich the perspective of cultural reproduction, their agentic approach doesn’t explain how excellent working-class students exercise agency to create cultural capital for themselves. In order to examine this issue, this study employed nonparticipant observation and interview methods to collect data about an excellent working-class student. The findings showed that the subject actively adopted creative strategies for discovering and using academic resources available outside her family’s social space. This agency was initiated by the subject’s envisagement of education as a path of liberation from the expected fate of the working classes. Its practice was further supported by significant others, who provided the subject with crucial help, including inspiration, encouragement, instruction and educational resources.

The epidermal growth factor (EGF) receptor (EGFR) overexpressed in many cancers, including lung and head and neck cancers, and is involved in cancer cell progression and survival. PD-L1, increases in tumor cells to evade and inhibit CD8+ T cells, is a clinical immunotherapeutic target. This study investigated the molecular mechanism of EGF on regulating PD-L1 in EGFR-positive cancers and determined potential agents to reduce PD-L1 expression. RNA sequencing (RNAseq) and bioinformatics analysis were performed to determine potential driver genes that regulate PD-L1 in tumor cells-derived tumorspheres which mimicking cancer stem cells. Then, the specific inhibitors targeting EGFR were applied to reduce the expression of PD-L1 in vitro and in vivo. We validated that EGF could induce PD-L1 expression in the selected EGFR-positive cancers. RNAseq results revealed that STAT1 increased as a driver gene in KOSC-3-derived tumorspheres; these data were analyzed using PANTHER followed by NetworkAnalyst. The blockade of EGFR by afatinib resulted in decreased STAT1 and IRF-1 levels, both are transcriptional factors of PD-L1, and disabled the IFNr-STAT1-mediated PD-L1 axis in vitro and in vivo. Moreover, STAT1 knockdown significantly reduced EGF-mediated PD-L1 expression, and ruxolitinib, a JAK1/JAK2 inhibitor, significantly inhibited STAT1 phosphorylation to reduce the IFNr-mediated PD-L1 axis. These results indicate that EGF exacerbates PD-L1 by increasing the protein levels of STAT1 to enforce the IFNr-JAK1/2-mediated signaling axis in selected EGFR-positive cancers. The inhibition of EGFR by afatinib significantly reduced PD-L1 and may be a potential strategy for enhancing immunotherapeutic efficacy.

Summary Gallbladder perforation is a rare complication of cholecystitis. Similarly, septic thrombophlebitis of the portal vein, also called pylephlebitis, is another rare complication of intra-abdominal infections including cholecystitis. Both gallbladder perforation and pylephlebitis are associated with significantly higher morbidity and mortality. Herein, we report a patient with an atypical presentation of gallbladder perforation and liver abscess formation. A 68-year-old man suffered from malaise, poor appetite, and body weight loss for 1 month. Liver mass lesion and portal vein thrombosis were detected by ultrasound at a local clinic. He was referred to our institution under the tentative diagnosis of hepatocellular carcinoma. He underwent abdominal ultrasound and computed tomography examinations at our hospital. Cholecystitis with gallbladder perforation was highly suspected. Broad-spectrum antibiotics were administered immediately. Percutaneous transhepatic gallbladder drainage was performed in this case, and pigtail drainage for liver abscess was done later. The patient's condition—cholecystitis, liver abscess, and pylephlebitis (followed by ultrasound)—improved after treatment. Furthermore, the patient recovered his appetite and his body weight increased.

A biologically regenerated tooth may provide a new treatment for tooth loss. In this study, a tissue engineering approach was applied to demonstrate the tooth regeneration. The dental buds of the second molar tooth from 1.5-month-old miniature pigs were harvested by surgical operation before eruption. The dental bud tissues were cultured and expanded in vitro for three weeks to obtain dental bud cells (DBCs). The phenotypes of DBCs were identified with a flowcytometry, and the DBCs were seeded into a gelatin–chondroitin–hyaluronan tri-copolymer (GCHT) scaffold. The DBCs/GCHT scaffold constructs were implanted under dermis of nude mice's thoracic dorsum. Mice were sacrificed at predetermined intervals, and the developing tooth-like tissues were harvested for histological examinations. The present results of flowcytometry showed that the DBCs expressed specific surface markers of mesenchymal stem cells. Animal study revealed that the tooth-like structures expressed cytokeratin 14 at 4, 8, and 12 weeks postoperatively. The vascular endothelial growth factor was expressed on 12 weeks. Dentin-like mineralized tissue and dentin genetic-like cells were generated that expressed dentin martrix protein-1 on 16 and 20 weeks. Osteocytes were formed on 24 weeks and expressed osteopontin. This study reveals that the DBCs combined with an appropriate scaffold regenerated tooth-like structure with specific proteins for odontogenesis in nude mice.

The purpose of this study is to use a tissue engineering approach for tooth regeneration. The swine dental bud cells (DBCs) were isolated from the developing mandibular teeth, expanded in vitro, and cultured onto cylinder scaffold gelatin-chrondroitin-hyaluronan-tri-copolymer (GCHT). After culturing in vitro, the DBCs/GCHT scaffold was autografted back into the original alveolar socket. Hematoxylin and eosin (H&E) staining combined with immunohistochemical staining were applied for identification of regenerated tooth structure. After 36-week post-transplantation, tooth-like structures, including well-organized dentin-pulp complex, cementum, and periodontal ligament, were evident in situ in two of six experimental animals. The size of the tooth structure (1 × 0.5 × 0.5 cm3 and 0.5 × 0.5 × 0.5 cm3 size) appeared to be dictated by the size of the GCHT scaffold (1 × 1 × 1.5 cm3). The third swine was demonstrated with irregular dentin-bony like calcified tissue about 1 cm in diameter without organized tooth or periodontal ligament formation. The other three swine in the experimental group showed normal bone formation and no tooth regeneration in the transplantation sites. The successful rate of tooth regeneration from DBCs/GCHT scaffolds' was about 33.3%. In the control group, three swine's molar teeth buds were removed without DBCs/GCHT implantation, the other three swine received GCHT scaffold implants without DBCs. After evaluation, no regenerated tooth was found in the transplantation site of the control group. The current results using DBSs/GCHT scaffold autotransplantation suggest a technical breakthrough for tooth regeneration. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res 2008

A 2-dimensional finite-element model for density-dependent flow and transport through saturated-unsaturated porous media has been developed. The combined flow and transport model can handle a wide range of real-world problems, including the simulations of flow alone, contaminant transport alone, and combined flow and transport. The conventional finite-element methods and a hybrid Lagrangian-Eulerian finite-element method were incorporated in the transport module. Saltwater intrusion problems and instability caused by denser water on the top were investigated in this paper. Because the fundamental mechanism causing saltwater intrusion most likely is caused by density-induced convection and dispersion, the developed model was used to assess the interplay between density-driven flow and the subsurface media through which the saltwater intrusion occurs. The mathematical formulation of the model is comprised of fluid flow and solute transport equations, coupled by fluid density. In the specific case of saltwater intrusion and unstable brine transport problems, this set of governing equations is nonlinear and requires iterative methods to solve them simultaneously. Three case studies, which include a wide spectrum of physical conditions, show the verification and effectiveness of the model by comparing previously published solutions from other researchers with the simulation results of the present model. Two demonstrated problems examine the model capabilities to handle saltwater intrusion problems through unsaturated-saturated porous media and density-dependent flow and transport under unstable conditions.

Background Genome-wide single-nucleotide polymorphism (SNP) arrays containing hundreds of thousands of SNPs from the human genome have proven useful for studying important human genome questions. Data quality of SNP arrays plays a key role in the accuracy and precision of downstream data analyses. However, good indices for assessing data quality of SNP arrays have not yet been developed. Results We developed new quality indices to measure the quality of SNP arrays and/or DNA samples and investigated their statistical properties. The indices quantify a departure of estimated individual-level allele frequencies (AFs) from expected frequencies via standardized distances. The proposed quality indices followed lognormal distributions in several large genomic studies that we empirically evaluated. AF reference data and quality index reference data for different SNP array platforms were established based on samples from various reference populations. Furthermore, a confidence interval method based on the underlying empirical distributions of quality indices was developed to identify poor-quality SNP arrays and/or DNA samples. Analyses of authentic biological data and simulated data show that this new method is sensitive and specific for the detection of poor-quality SNP arrays and/or DNA samples. Conclusions This study introduces new quality indices, establishes references for AFs and quality indices, and develops a detection method for poor-quality SNP arrays and/or DNA samples. We have developed a new computer program that utilizes these methods called SNP Array Quality Control (SAQC). SAQC software is written in R and R-GUI and was developed as a user-friendly tool for the visualization and evaluation of data quality of genome-wide SNP arrays. The program is available online (http://www.stat.sinica.edu.tw/hsinchou/genetics/quality/SAQC.htm).

Growth factors and morphogens secreted by bone marrow mesenchymal stem cells (BMSCs) of bone marrow fluid may promote tooth regeneration. Accordingly, a tissue engineering approach was utilized to develop an economical strategy for obtaining the growth factors and morphogens from BMSCs. Unerupted second molar tooth buds harvested from miniature pigs were cultured in vitro to obtain dental bud cells (DBCs). Bone marrow fluid, which contains BMSCs, was collected from the porcine mandible before operation. DBCs suspended in bone marrow fluid were seeded into a gelatin/chondoitin-6-sulfate/hyaluronan tri-copolymer scaffold (GCHT scaffold). The DBCs/bone marrow fluid/GCHT scaffold was autografted into the original alveolar sockets of the pigs. Radiographic and histological examinations were applied to identify the structure of regenerated tooth at 40 weeks postimplantation. The present results showed that one pig developed a complete tooth with crown, root, pulp, enamel, dentin, odontoblast, cementum, blood vessel, and periodontal ligament in indiscriminate shape. Three animals had an unerupted tooth that expressed dentin matrix protein-1, vascular endothelial growth factor, and osteopontin; and two other pigs also had dental-like structure with dentin tubules. This study reveals that DBCs adding bone marrow fluid and a suitable scaffold can promote the tooth regeneration in autogenic cell transplantation.

Growth factors and morphogens secreted by bone marrow mesenchymal stem cells (BMSCs) of bone marrow fluid may promote tooth regeneration. Accordingly, a tissue engineering approach was utilized to develop an economical strategy for obtaining the growth factors and morphogens from BMSCs. Unerupted second molar tooth buds harvested from miniature pigs were cultured in vitro to obtain dental bud cells (DBCs). Bone marrow fluid, which contains BMSCs, was collected from the porcine mandible before operation. DBCs suspended in bone marrow fluid were seeded into a gelatin/chondoitin-6-sulfate/hyaluronan tri-copolymer scaffold (GCHT scaffold). The DBCs/bone marrow fluid/GCHT scaffold was autografted into the original alveolar sockets of the pigs. Radiographic and histological examinations were applied to identify the structure of regenerated tooth at 40 weeks postimplantation. The present results showed that one pig developed a complete tooth with crown, root, pulp, enamel, dentin, odontoblast, cementum, blood vessel, and periodontal ligament in indiscriminate shape. Three animals had an unerupted tooth that expressed dentin matrix protein-1, vascular endothelial growth factor, and osteopontin; and two other pigs also had dental-like structure with dentin tubules. This study reveals that DBCs adding bone marrow fluid and a suitable scaffold can promote the tooth regeneration in autogenic cell transplantation.

The emerging IEEE 802.16e Broadband Wireless Access (BWA) network is one of the most promising solutions to provide ubiquitous wireless access with high data rates, high mobility, and wide coverage. In the paper we develop a novel Connection Admission Control (CAC) algorithm for IEEE 802.16e mobile BWA networks to simultaneously improve the utilization efficiency of network resources and guarantee Quality of Services (QoS) for handoff connections. The proposed CAC scheme dynamically adjusts the amount of reserved bandwidth for handoff users according to the arrival distributions of handoff and new coming connections. Simulation results demonstrate that the proposed CAC algorithm can increase the number of admitted connections and also provide handoff QoS.

In the past 30 years, lumped-parameter watershed models have been employed for integrated surface water and groundwater modeling to calculate surface and base runoffs. Physics-based, process-level models that employ consistent sets of governing equations for integrated overland, river, vadose, and groundwater flow have been practically nonexistent until early 1990s. This paper presents the development of an integrated media, physics-based watershed model. Complete coupling simulations among system components of land surfaces, river networks, vadose zones, and groundwater or partial couplings between any two components can be conducted with the model. Various rigorous coupling strategies based on physics and numerics for interactions among these components are described. Two examples were employed to discuss the issues of coupling. One was used to demonstrate differences and implications between continuity and linkage approaches when the surface water and groundwater are in direct connection. Another one, a watershed modeling in Florida, was used to illustrate that complete and partial couplings yield quite different simulations.

Peritoneal dialysis (PD) has been applied to patients with end-stage renal disease for more than 2 decades. It should raise physicians' concern about the serious complications of prolonged PD therapy, particularly encapsulating peritoneal sclerosis (EPS), the most potentially life-threatening one. The prevalence and mortality rate of EPS increase as PD duration increases. We report a case of EPS presented with blood-tinged effluents and abdominal pain.

The parallel WASH123D is designed to simulate watershed systems using a coupled system of one-dimensional (1-D) channels, 2-D overland areas, and 3- D subsurface media on parallel scalable computers. The U.S. Department of Defense High Performance Computing Modernization Program funds the parallelization of the watershed model through the Common High Performance Computing Software Initiative in order to solve one aspect of the battlespace environment, which in- cludes space, weather, ocean, and soil, to develop a complete coupled battlespace environment. Tasks in this project include parallel algorithm development, software toolkit development, and performance studies. Currently, the parallel version, which includes coupled 2-D overland and 3-D subsurface flows, is completed and packaged for application projects, such as calibration and validation of the coupled 2-D/3-D Biscayne Bay Coastal Wetland inland flow model presented in this paper, on various computer architectures.

The parallel WASH123D, which is supported by the DoD CHSSI (Department of Defense Common High Performance Computing Software Support Initiative), is designed to solve watershed problems on scalable computing systems. WASH123D is a first-principle, physics-based model to compute water flow and/or contaminant and sediment transport within a watershed system. In the WASH123D model, a watershed is conceptualized as a coupled system of one-dimensional (1-D) channel network, two-dimensional (2-D) overland regime, and three-dimensional (3-D) subsurface media. It aims to address the environmental issues concerning both water quantity and quality. To reach numerical solutions with reasonable and tolerable computer time for simulations that embrace large meshes, numerical algorithm improvement and code parallelization are two essential tasks. Mathematically, 1-D channel flow and 2-D overland flow are described with the St. Venant equations, which are solved with either the Semi-Lagrangian or the Eulerian finite element method. The 3-D subsurface flow is governed by the modified Richards equation, which is solved with the Eulerian finite element method. The contaminant transport and sediment transport equations, which are solved with the Lagrangian-Eulerian finite element method, are derived based on the mass conservation principle. A parallel in-element particle-tracking algorithm for unsteady flow is applied to backtrack fictitious particles from global nodes to determine the so-called Lagrangian values when the Semi-Lagrangian or the Lagrangian-Eulerian method is used. This paper addresses the parallelization of such a complex numerical model. In phase I, tasks including data structure and software design, software tool development, as well as tool integration are accomplished. The 2- and 3-D flow modules are expected to be employed in the production stage.

In the past 30 years, lumped-parameter watershed models have been employed for integrated surface and groundwater modeling to calculate surface runoff and total maximum daily loads (TMDL) on various temporal and spatial scales of hydrologic regimes. Physics-based, process-level models that have the design capability to cover various scales have been practically nonexistent until recently. It has long been recognized that only such models have the potential to further the understanding of the fundamental biological, chemical and physical factors that take place in nature hydrologic regimes, and give mechanistic predictions. However, there are severe limitations with these models that inhibit their use. These are, among other things, the ad hoc approaches of coupling between various media and the excessive demand of computational time. This paper presents the development of a first principle, physicsbased watershed model to address these issues. A rigorous coupling strategy is described for interactions among overland regime, rivers/streams/canals networks, and subsurface media. Introductions of non-physics parameters such as linkage terms are avoided. The cultivation of innovative numerical algorithms to increase the computational speed are discussed.

An open channel flow is usually three-dimensional consisting of the primary and secondary flows. The primary flow is defined herein as the flow component in the longitudinal direction of the channel, while the secondary flow includes the remaining flow components in the vertical and transverse directions of the channel. In an alluvial channel the channel cross sections and, thus, the three-dimensional flow structure vary irregularly or randomly along the flow. A technique has been developed and presented herein that can be used to compute secondary currents and, thus, the irregular three-dimensional structure of open channel flow. The technique uses analytical, hydrodynamic equations along with measured data of channel geometry and primary flow velocity distribution. Illustrative examples are presented with results of practical applications of the technique, describing the variability of the direction and magnitude of secondary currents with time, space, and discharge rate.

Techniques combining the deterministic and stochastic methods have been developed to compute and simulate various hydraulic processes in open channels, such as the three-dimensional distribution of flow velocity, steady and unsteady flows, flow resistance, secondary currents, and unsteady dispersion. The deterministic approach, using a curvilinear coordinate system based on the velocity distribution of flow, is used to deal with the basic hydrodynamic part of analysis. The stochastic approach is used to treat the irregular channel geometry that tends to cause uncertainties in simulated hydraulic processes in open channels. The techniques can be used to simulate the three-dimensional velocity distribution of (primary) flow, unsteady dispersion, and sediment transport, secondary currents, steady and unsteady flows, and flow resistance (Manning’s n.) In computing an unsteady flow it was found that the use of mean cross sections, without the geometrical irregularity of channel, causes errors in the peak and recession part of computed hydrographs, although it has the advantages of being simple and insensitive to uncertain Manning’s n.

Background Allele frequency is one of the most important population indices and has been broadly applied to genetic/genomic studies. Estimation of allele frequency using genotypes is convenient but may lose data information and be sensitive to genotyping errors. Results This study utilizes a unified intensity-measuring approach to estimating individual-level allele frequencies for 1,104 and 1,270 samples genotyped with the single-nucleotide-polymorphism arrays of the Affymetrix Human Mapping 100K and 500K Sets, respectively. Allele frequencies of all samples are estimated and adjusted by coefficients of preferential amplification/hybridization (CPA), and large ethnicity-specific and cross-ethnicity databases of CPA and allele frequency are established. The results show that using the CPA significantly improves the accuracy of allele frequency estimates; moreover, this paramount factor is insensitive to the time of data acquisition, effect of laboratory site, type of gene chip, and phenotypic status. Based on accurate allele frequency estimates, analytic methods based on individual-level allele frequencies are developed and successfully applied to discover genomic patterns of allele frequencies, detect chromosomal abnormalities, classify sample groups, identify outlier samples, and estimate the purity of tumor samples. The methods are packaged into a new analysis tool, ALOHA (Allele-frequency/Loss-of-heterozygosity/Allele-imbalance). Conclusions This is the first time that these important genetic/genomic applications have been simultaneously conducted by the analyses of individual-level allele frequencies estimated by a unified intensity-measuring approach. We expect that additional practical applications for allele frequency analysis will be found. The developed databases and tools provide useful resources for human genome analysis via high-throughput single-nucleotide-polymorphism arrays. The ALOHA software was written in R and R GUI and can be downloaded at http://www.stat.sinica.edu.tw/hsinchou/genetics/aloha/ALOHA.htm.