Modeling, simulations, and experiments to balance performance and fairness in P2P file-sharing systems

Doctor of PhilosophyDepartment of Electrical and Computer EngineeringDon GruenbacherCaterina ScoglioIn this dissertation, we investigate research gaps still existing in P2P file-sharing systems: the necessity of fairness maintenance during the content information publishing/retrieving process, and the stranger policies on P2P fairness. First, through a wide range of measurements in the KAD network, we present the impact of a poorly designed incentive fairness policy on the performance of looking up content information. The KAD network, designed to help peers publish and retrieve sharing information, adopts a distributed hash table (DHT) technology and combines itself into the aMule/eMule P2P file-sharing network. We develop a distributed measurement framework that employs multiple test nodes running on the PlanetLab testbed. During the measurements, the routing tables of around 20,000 peers are crawled and analyzed. More than 3,000,000 pieces of source location information from the publishing tables of multiple peers are retrieved and contacted. Based on these measurements, we show that the routing table is well maintained, while the maintenance policy for the source-location-information publishing table is not well designed. Both the current maintenance schedule for the publishing table and the poor incentive policy on publishing peers eventually result in the low availability of the publishing table, which accordingly cause low lookup performance of the KAD network. Moreover, we propose three possible solutions to address these issues: the self-maintenance scheme with short period renewal interval, the chunk-based publishing/retrieving scheme, and the fairness scheme. Second, using both numerical analyses and agent-based simulations, we evaluate the impact of different stranger policies on system performance and fairness. We explore that the extremely restricting stranger policy brings the best fairness at a cost of performance degradation. The varying tendency of performance and fairness under different stranger policies are not consistent. A trade-off exists between controlling free-riding and maintaining system performance. Thus, P2P designers are required to tackle strangers carefully according to their individual design goals. We also show that BitTorrent prefers to maintain fairness with an extremely restricting stranger policy, while aMule/eMule’s fully rewarding stranger policy promotes free-riders’ benefit

Enrollment Forecast for Clinical Trials at the Planning Phase with Study-Level Historical Data

Given progressive developments and demands on clinical trials, accurate enrollment timeline forecasting is increasingly crucial for both strategic decision-making and trial execution excellence. Naive approach assumes flat rates on enrollment using average of historical data, while traditional statistical approach applies simple Poisson-Gamma model using timeinvariant rates for site activation and subject recruitment. Both of them are lack of nontrivial factors such as time and location. We propose a novel two-segment statistical approach based on Quasi-Poisson regression for subject accrual rate and Poisson process for subject enrollment and site activation. The input study-level data is publicly accessible and it can be integrated with historical study data from user's organization to prospectively predict enrollment timeline. The new framework is neat and accurate compared to preceding works. We validate the performance of our proposed enrollment model and compare the results with other frameworks on 7 curated studies

The Ecological Restoration of Heavily Degraded Saline Wetland in the Yellow River Delta

As a result of discontinuous water flow, agriculture, and increasing urban use of fresh water affecting the natural wetlands of the Yellow River Delta, these areas have experienced significant degradation in the past two decades, ultimately diminishing the overall natural wetland land area in the region. This study aimed to address the issue of decreasing fresh water in the Yellow River Delta by studying the effects of three different approaches to restoration on long-term wetland recovery. The results of the study demonstrated that soil salt and available Na contents significantly decreased in response to all three restoration treatments. Impacts of the restoration treatments were more significant in 2009 than in 2010, as shown by the high rate of activity in the reed debris group. The highest phosphatase activity of the experimental period was also observed in the reed debris group. Meanwhile, a marked variation in soil nutrient elements (total carbon (TC), total nitrogen (TN), available phosphorus, and available potassium) was observed in the restoration treatment plots throughout the experimental period. TC and TN contents were generally higher in the restoration treatment groups than in the control group. Moreover, urease and phosphatase activity levels were highly correlated with one another, as well as with soil nutrient elements. In 2009, the yield of the Suaeda salsa plant was highest in the reed debris treatment group and lowest in the ploughing treatment group. The S. salsa plant did show a positive response to all of the different restoration treatments. Taken together, these results suggest that restoration approaches that implement ploughing techniques aided in the restoration of degraded saline wetlands.As a result of discontinuous water flow, agriculture, and increasing urban use of fresh water affecting the natural wetlands of the Yellow River Delta, these areas have experienced significant degradation in the past two decades, ultimately diminishing the overall natural wetland land area in the region. This study aimed to address the issue of decreasing fresh water in the Yellow River Delta by studying the effects of three different approaches to restoration on long-term wetland recovery. The results of the study demonstrated that soil salt and available Na contents significantly decreased in response to all three restoration treatments. Impacts of the restoration treatments were more significant in 2009 than in 2010, as shown by the high rate of activity in the reed debris group. The highest phosphatase activity of the experimental period was also observed in the reed debris group. Meanwhile, a marked variation in soil nutrient elements (total carbon (TC), total nitrogen (TN), available phosphorus, and available potassium) was observed in the restoration treatment plots throughout the experimental period. TC and TN contents were generally higher in the restoration treatment groups than in the control group. Moreover, urease and phosphatase activity levels were highly correlated with one another, as well as with soil nutrient elements. In 2009, the yield of the Suaeda salsa plant was highest in the reed debris treatment group and lowest in the ploughing treatment group. The S. salsa plant did show a positive response to all of the different restoration treatments. Taken together, these results suggest that restoration approaches that implement ploughing techniques aided in the restoration of degraded saline wetlands

FP-ABC: Fast and Parallel ABC Based Energy-Efficiency Live VM Allocation Policy in Data Centers

Virtual machine (VM) technology is one of the energy-efficiency approaches to save energy with acceptable quality of service (QoS). In our previous studies, Artificial Bee Colony (ABC) based VM allocation policy can make a good tradeoff between performance and energy consumption. However, there are two problems in state-of-the-art ABC based approaches: (1) how to find global optimized solutions efficiently; (2) how to minimize the decision time of VM allocation. To solve these two problems, the idea of simulated annealing is adopted to get a better global optimum, and the idea of gradient descent is applied to accelerate the speed of finding solution space in Δ . Compared with state-of-the-art ABC based policies, the experimental results show that the proposed algorithm efficiently reduces energy consumption and SLA violation

Primary lipoblastic nerve sheath tumor in an inguinal lymph node mimicking metastatic tumor: a case report and literature review

Lipoblastic nerve sheath tumors of soft tissue are characterized as schwannoma tumors that exhibit adipose tissue and lipoblast-like cells with signet-ring morphology. They have been documented to arise in various anatomic locations, including the thigh, groin, shoulder, and retroperitoneum. However, to our knowledge, this tumor has not been previously reported as a lymph node primary. We present herein the first case of a benign primary lipoblastic nerve sheath tumor arising in an inguinal lymph node in a 69-year-old man. Microscopic examination revealed a multinodular tumor comprising fascicles of spindle cells, as well as adipocytic and lipoblast-like signet-ring cell component in the context of schwannoma. Despite the presence of some bizarre cells with nuclear atypia, no obvious mitotic activity or necrosis was observed. Immunohistochemical analysis showed strong and diffuse expression of S-100, SOX10, CD56, and NSE in the spindle cells as well as in the signet-ring lipoblast-like cells and the mature adipocytes. Sequencing analysis of the neoplasm identified six non-synonymous single nucleotide variant genes, specifically NF1, BRAF, ECE1, AMPD3, CRYAB, and NPHS1, as well as four nonsense mutation genes including MRE11A, CEP290, OTOA, and ALOXE3. The patient remained alive and well with no evidence of recurrence over a period of ten-year follow-up

Wet and Dry Atmospheric Depositions of Inorganic Nitrogen during Plant Growing Season in the Coastal Zone of Yellow River Delta

The ecological problems caused by dry and wet deposition of atmospheric nitrogen have been widespread concern in the world. In this study, wet and dry atmospheric depositions were monitored in plant growing season in the coastal zone of the Yellow River Delta (YRD) using automatic sampling equipment. The results showed that SO42- and Na+ were the predominant anion and cation, respectively, in both wet and dry atmospheric depositions. The total atmospheric nitrogen deposition was ~2264.24 mg m−2, in which dry atmospheric nitrogen deposition was about 32.02%. The highest values of dry and wet atmospheric nitrogen deposition appeared in May and August, respectively. In the studied area, NO3-–N was the main nitrogen form in dry deposition, while the predominant nitrogen in wet atmospheric deposition was NH4+–N with ~56.51% of total wet atmospheric nitrogen deposition. The average monthly attribution rate of atmospheric deposition of NO3-–N and NH4+–N was ~31.38% and ~20.50% for the contents of NO3-–N and NH4+–N in 0–10 cm soil layer, respectively, suggested that the atmospheric nitrogen was one of main sources for soil nitrogen in coastal zone of the YRD

Characterization of DNA Methylation Associated Gene Regulatory Networks During Stomach Cancer Progression

DNA methylation plays a critical role in tumorigenesis through regulating oncogene activation and tumor suppressor gene silencing. Although extensively analyzed, the implication of DNA methylation in gene regulatory network is less characterized. To address this issue, in this study we performed an integrative analysis on the alteration of DNA methylation patterns and the dynamics of gene regulatory network topology across distinct stages of stomach cancer. We found the global DNA methylation patterns in different stages are generally conserved, whereas some significantly differentially methylated genes were exclusively observed in the early stage of stomach cancer. Integrative analysis of DNA methylation and network topology alteration yielded several genes which have been reported to be involved in the progression of stomach cancer, such as IGF2, ERBB2, GSTP1, MYH11, TMEM59, and SST. Finally, we demonstrated that inhibition of SST promotes cell proliferation, suggesting that DNA methylation-associated SST suppression possibly contributes to the gastric cancer progression. Taken together, our study suggests the DNA methylation-associated regulatory network analysis could be used for identifying cancer-related genes. This strategy can facilitate the understanding of gene regulatory network in cancer biology and provide a new insight into the study of DNA methylation at system level

Controls on anomalously high porosity/permeability of Middle Jurassic deeply buried tight sandstones in the Taibei Sag, Turpan-Hami Basin, northwestern China: Implications for reservoir quality prediction

The lower member of the Middle Jurassic Xishanyao Formation (J2x1+2) sandstones are significant exploratory targets for hydrocarbon resources in the Taibei Sag of the Turpan-Hami Basin, northwestern China. Formation of anomalously high porosity/permeability in deeply buried J2x1+2 sandstones and reservoir quality prediction were investigated using a variety of petrographic analyses. These results show that the J2x1+2 sandstones are mostly feldspathic litharenites and litharenites, which are characterized by moderate-to good sorting, silty to medium granularity, and point- to long grain contacts. The J2x1+2 sandstone has low porosity (avg 6.0%) and permeability (avg 1.12 mD), but shows anomalously high porosity/permeability at depth interval of 3850–4050 m. There is a noticeable variation in pore types and sizes from intergranular-intragranular dissolution pores with a size mode of 2.0 μm in anomalously high porosity (AHP) sandstones, to major intragranular dissolution pores with a size mode of 0.5 μm in normally high porosity (NHP) sandstones, to most micropores with a size mode of 0.25 μm occurred in the normally low porosity (NLP) sandstones. The compaction is the main cause of porosity destruction, resulting in an average porosity loss of 89.6%. However, the authigenic minerals have relatively little influence on reservoir quality. The combination of nappe tectonics and well-sorted particles alleviated the compaction and thus preserved more intergranular pores in the AHP sandstones. Dissolution further increases the porosity and eventually forms the AHP sandstones. The strong carbonate-cemented facies (SCC), tightly compacted facies (TC), moderately compacted with moderate dissolution facies (MCMD), and weakly compacted with strong dissolution facies (WCSD) are determined in the J2x1+2 sandstones. The sandstones with SCC and TC are recognized as the NLP reservoirs. The MCMD and WCSD correspond to the NHP and AHP reservoirs, respectively. The reservoir quality predicted using the constructed diagenetic facies charts is in good agreement with the photomicrograph observations and physical property tests. Additionally, the AHP reservoirs are still developed in the deeply buried sandstones with depths larger than 4000 m