Miracle-dz/UniFAR-FTUs huggingface dataset:
SPARQL query processing with Apache Spark

The number of linked data sources and the size of the linked open data graph keep growing every day. As a consequence, semantic RDF services are more and more confronted to various "big data" problems. Query processing is one of them and needs to be efficiently addressed with executions over scalable, highly available and fault tolerant frameworks. Data management systems requiring these properties are rarely built from scratch but are rather designed on top of an existing cluster computing engine. In this work, we consider the processing of SPARQL queries with Apache Spark. We propose and compare five different query processing approaches based on different join execution models and Spark components. A detailed experimentation, on real-world and synthetic data sets, emphasizes that two approaches tailored for the RDF data model outperform the other ones on all major query shapes, i.e., star, snowflake, chain and hybrid.
Deciphering Patterns and Drivers of Heat and Carbon Storage in the Southern Ocean

The storage of anomalous heat and carbon in the Southern Ocean in response to increasing greenhouse gases greatly mitigates atmospheric warming and exerts a large impact on the marine ecosystem. However, the mechanisms driving the ocean storage patterns are uncertain. Here using recent hydrographic observations, we compare for the first time the spatial patterns of heat and carbon storage, which show substantial differences in the Southern Ocean, in contrast with the conventional view of simple passive subduction into the thermocline. Using an eddy‐rich global climate model, we demonstrate that redistribution of the preindustrial temperature field is the dominant control on the heat storage pattern, whereas carbon storage largely results from passive transport of anthropogenic carbon uptake at the surface. Lastly, this study highlights the importance of realistic representation of wind and surface buoyancy flux in climate models to improve future projection of circulation change and thus heat and carbon storage.
Randomized Controlled Trial of Zoledronic Acid plus Chemotherapy versus Chemotherapy Alone as Neoadjuvant Treatment of HER2-Negative Primary Breast Cancer (JONIE Study)

Purpose Zoledronic acid (ZOL) is a nitrogen-containing bisphosphonate that induces osteoclast apoptosis and inhibits bone resorption by inhibiting the mevalonate pathway. Its benefit for the prevention of skeletal complications due to bone metastases has been established. However, the antitumor efficacy of ZOL, although suggested by multiple preclinical and clinical studies, has not yet been clinically proven. We performed the present randomized Phase 2 trial to investigate the antitumor effect of ZOL with chemotherapy (CT). Methods Asian patients with HER2-negative invasive breast cancer were randomly assigned to either the CT or CT+ZOL (CTZ) group. One hundred and eighty-eight patients were randomized to either the CT group (n = 95) or the CTZ group (n = 93) from March 2010 to April 2012, and 180 patients were assessed. All patients received four cycles of FEC100 (fluorouracil 500 mg/m2, epirubicin 100 mg/m2, and cyclophosphamide 500 mg/m2), followed by 12 cycles of paclitaxel at 80 mg/m2 weekly. ZOL (4 mg) was administered three to four times weekly for 7 weeks to the patients in the CTZ group. The primary endpoint was the pathological complete response (pCR) rate, which was defined as no invasive cancer in the breast tissue specimen. Safety was assessed in all patients who received at least one dose of the study drug. Results This randomized controlled trial indicated that the rates of pCR in CTZ group (14.8%) was doubled to CT group (7.7%), respectively (one-sided chi-square test, p = 0.068), though the additional efficacy of zoledronic acid was not demonstrated statistically. The pCR rate in postmenopausal patients was 18.4% and 5.1% in the CTZ and CT groups, respectively (one-sided Fisher’s exact test, p = 0.071), and that in patients with triple-negative breast cancer was 35.3% and 11.8% in the CTZ and CT groups, respectively (one-sided Fisher’s exact test, p = 0.112). Thus the addition of ZOL to neoadjuvant CT has potential anticancer benefits in postmenopausal patients and patients with triple-negative breast cancer. Further investigation is warranted. Trial Registration University Hospital Medical Information Network. UMIN000003261.
Systems Modeling for IP-Based Handoff Using Timed Petri Nets

The mechanisms and design principles needed for achieving optimized handoff for mobile Internet services are poorly understood and need better analysis. This paper contributes to the general theory of optimized handoff and addresses the need for a formal model that can characterize a mobility event and the associated mobility optimization methodologies. It provides a systematic and formal approach to analyzing a mobility event. After a thorough analysis of the abstract operations associated with several mobility protocols, it determines that these basic handoff operations form a set of discrete events that can be modeled as Discrete Event Dynamic System (DEDS). It then uses Deterministic Timed Petri nets to model the mobility event and evaluate the performance under different scheduling schemes. This model also helps to validate optimization methodologies that could lead to a set of design principles for any new mobility protocol as well as evaluate its effectiveness.
Persistent Code Caching: Exploiting Code Reuse Across Executions and Applications

Run-time compilation systems are challenged with the task of translating a program's instruction stream while maintaining low overhead. While software managed code caches are utilized to amortize translation costs, they are ineffective for programs with short run times or large amounts of cold code. Such program characteristics are prevalent in real-life computing environments, ranging from graphical user interface (GUI) programs to large-scale applications such as database management systems. Persistent code caching addresses these issues. It is described and evaluated in an industry-strength dynamic binary instrumentation system - Pin. The proposed approach improves the intra-execution model of code reuse by storing and reusing translations across executions, thereby achieving inter-execution persistence. Dynamically linked programs leverage inter-application persistence by using persistent translations of library code generated by other programs. New translations discovered across executions are automatically accumulated into the persistent code caches, thereby improving performance over time. Inter-execution persistence improves the performance of GUI applications by nearly 90%, while inter-application persistence achieves a 59% improvement. In more specialized uses, the SPEC2K INT benchmark suite experiences a 26% improvement under dynamic binary instrumentation. Finally, a 400% speedup is achieved in translating the Oracle database in a regression testing environment
Extracting ultra-scale Lattice Boltzmann performance via hierarchical and distributed auto-tuning

We are witnessing a rapid evolution of HPC node architectures and on-chip parallelism as power and cooling constraints limit increases in microprocessor clock speeds. In this work, we demonstrate a hierarchical approach towards effectively extracting performance for a variety of emerging multicore-based supercomputing platforms. Our examined application is a structured grid-based Lattice Boltzmann computation that simulates homogeneous isotropic turbulence in magnetohydrodynamics. First, we examine sophisticated sequential auto-tuning techniques including loop transformations, virtual vectorization, and use of ISA-specific intrinsics. Next, we present a variety of parallel optimization approaches including programming model exploration (flat MPI, MPI/OpenMP, and MPI/Pthreads), as well as data and thread decomposition strategies designed to mitigate communication bottlenecks. Finally, we evaluate the impact of our hierarchical tuning techniques using a variety of problem sizes via large-scale simulations on state-of-the-art Cray XT4, Cray XE6, and IBM BlueGene/P platforms. Results show that our unique tuning approach improves performance and energy requirements by up to 3.4x using 49,152 cores, while providing a portable optimization methodology for a variety of numerical methods on forthcoming HPC systems.
A Method for Estimating Walking Speed by Using Magnetic Signature to Grasp People Flow in Indoor Passages

The goal of our study is to grasp people flow velocity in indoor passages, by collecting the data of people's walking speeds and the area through which they have walked (walked section). In this paper, we propose a method that estimates the walking speed and walked section of a pedestrian by using a smartphone equipped with a magnetometer. To grasp people flow velocity, the walking speed of a pedestrian is an important scale. Besides this, to grasp low flow velocity spots such as an intersection and an area in front of a door, we need to estimate the walked section, that is, the area between two points that a pedestrian walked within a period of time. In our proposed method, first we measure magnetic field data series while a participant is walking, and we generate magnetic signatures by relating each magnetic field datum to the corresponding position. Secondly, we detect partial magnetic signature that is similar to the magnetic field data series of an unknown walked section by using DTW (Dynamic Time Warping), and we obtain the walked section from the detected partial magnetic signature. Finally, we calculate walking speed from the distance of walked section and walked time. We conducted an experiment to evaluate the accuracy of walking speed estimation and walked section estimation. The results in a crowded passage showed that the average error of walking speed estimation was 0.09 m/s and the average error of walked section estimation was 0.7 m in the proposed method.
Mycobacterium tuberculosis Infects Dendritic Cells with High Frequency and Impairs Their Function In Vivo1

Mycobacterium tuberculosis (Mtb) is thought to reside in macrophages, although infected dendritic cells (DCs) have been observed. Thus, although cellular associations have been made, global characterization of the cells harboring Mtb is lacking. We have performed temporal and quantitative characterization of the cells harboring Mtb following aerosol infection of mice by using GFP-expressing bacteria and flow cytometry. We discovered that Mtb infects phagocytic cells of diverse phenotypes, that the predominant infected cell populations change with time, and that myeloid DCs are the major cell population infected with Mtb in the lungs and lymph nodes. We also found that the bacteria in the lung-draining lymph node are transported there from the lungs by a CCL19/21-dependent mechanism and that the transport of bacteria to the lymph node is a transient phenomenon despite chronic infection. In addition, we found that the lymph node cell subsets that are most efficacious in stimulating Mtb-specific, TCR-transgenic CD4+ T lymphocytes are not infected with the bacteria and are scarce or absent from the lungs of infected mice. Finally, we found that the lung cell populations that are infected with Mtb at high frequency are relatively ineffective at stimulating Ag-specific CD4+ T lymphocytes, and we have obtained evidence that live Mtb can inhibit MHC class II Ag presentation without a decrease in the surface expression of MHC class II. These results indicate that Mtb targets DC migration and Ag presentation in vivo to promote persistent infection.
EFFECTS OF FARMING OPERATIONS ON GROUNDWATER QUALITY IN BASAWA, ZARIA-AREA, NIGERIA

Anthropogenic activities, mostly related to farming are some of the causes of increased dispersion of polluting substances into soil and to the subsurface water mass. Though, the interaction of water with geologic materials during movement also serves as major determinant of its chemical characteristics. Agriculture is viewed as a significant non-point source of groundwater contamination, which poses a serious challenge to the government and other stakeholders involved in environmental pollution abatement and control, on design methodologies or approach to be adopted, to prevent pollution by fertilizers and pesticides. Groundwater sources (e.g. hand dug wells, concrete wells and deep wells), in Basawa area were monitored by monthly sampling and analyses from February to September. Static water level of monitored sites varies between 0.03 and 9.0 m, with the exception of boreholes and a pH range of 5.7 to 8.1. The electrical conductivity, nitrate and phosphate concentration values are within the ranges of 46 to 1,517 µS/cm, 0.39 to 35.21 mg/L and 0.00 to 6.12 mg/L throughout the entire period of monitoring. The intensity of contamination of ground water sources due to the farming activities was found to be in decreasing order of dug wells, concrete wells, and deep wells.
Exploring the Potential for Artificial Reefs in Coral Reef Restoration: Responses and Interactions of Associated Biota to Varying Experimental Treatments in the Mexican Caribbean

4 Chapter 1 – Introduction: Coral Reef Restoration 1.1 Background . 6 1.2 Significance and Purpose . 15 1.3 Hypotheses . 17 Chapter 2 – Methodology 2.1 Artificial Reefs and Survey Design . 19 2.1.1 Experimental Design . 19 2.1.2 Restoration Interventions . 21 2.1.3 Artificial Reef Design and Treatment Applications . 23 2.1. 4 Recovery Assessment . 25 2.2 Study Location . 27 2.2.1 Regional Setting, Local Partners, and Site Selection . 25 2.2.2 Substrate Module Deployment Sites and Natural Reference Reefs . 33 a) Puerto Morelos . 33 b) Akumal . 36 2.3 Project Implementation: Artificial Reef Construction and Deployment . 38 2.3. 1 Laying the Groundwork . 38 2.3. 2 Artificial Reef Construction . 40 2.3. 3 Artificial Reef Deployment.41 2.4 Coral Transplanting and Settlement Plate Deployment . 45 2.4. 1 Coral Collection and Transplanting . 45 2.4. 2 Settlement Plate Deployment . 47 2.5 Monitoring and Data Collection Methods . 48 2.5. 1 Monitoring Schedule and Logistical Planning . 48 2.5. 2 Fish Counts . 49 2.5. 3 Coral Recruit Surveys . 50 2.5. 4 Quadrat and Coral Transplant Framer Photos – Substrate Modules.52 2.5. 5 Quadrat and Reference Coral Framer Photos – Natural Reef . 54 2.5. 6 In Situ Quadrat Surveys . 57 2.5. 7 Processing and Analysis of Quadrat Photos . 57 2.5. 8 Artificial Substrate Pad Collection . 58 2.5. 9 Settlement Plate Collection . 60 2.5. 10 Other Surveys and Tasks . 61
Capacity-achieving iterative LMMSE detection for MIMO-NOMA systems

This paper considers a iterative Linear Minimum Mean Square Error (LMMSE) detection for the uplink Multiuser Multiple-Input and Multiple-Output (MU-MIMO) systems with Non-Orthogonal Multiple Access (NOMA). The iterative LMMSE detection greatly reduces the system computational complexity by departing the overall processing into many low-complexity distributed calculations. However, it is generally considered to be sub-optimal and achieves relatively poor performance. In this paper, we firstly present the matching conditions and area theorems for the iterative detection of the MIMO-NOMA systems. Based on the proposed matching conditions and area theorems, the achievable rate region of the iterative LMMSE detection is analysed. We prove that by properly design the iterative LMMSE detection, it can achieve (i) the optimal sum capacity of MU-MIMO systems, (ii) all the maximal extreme points in the capacity region of MU-MIMO system, and (iii) the whole capacity region of two-user MIMO systems.
Patient-centric authorization framework for sharing electronic health records

In modern healthcare environments, a fundamental requirement for achieving continuity of care is the seamless access to distributed patient health records in an integrated and unified manner, directly at the point of care. However, Electronic Health Records (EHRs) contain a significant amount of sensitive information, and allowing data to be accessible at many different sources increases concerns related to patient privacy and data theft. Access control solutions must guarantee that only authorized users have access to such critical records for legitimate purposes, and access control policies from distributed EHR sources must be accurately reflected and enforced accordingly in the integrated EHRs. In this paper, we propose a unified access control scheme that supports patient-centric selective sharing of virtual composite EHRs using different levels of granularity, accommodating data aggregation and various privacy protection requirements. We also articulate and handle the policy anomalies that might occur in the composition of discrete access control policies from multiple data sources.
Associations between XPD Asp312Asn Polymorphism and Risk of Head and Neck Cancer: A Meta-Analysis Based on 7,122 Subjects

Background To investigate the association between XPD Asp312Asn polymorphism and head and neck cancer risk through this meta-analysis. Methods We performed a meta-analysis of 9 published case-control studies including 2,670 patients with head and neck cancer and 4,452 controls. An odds ratio (OR) with a 95% confidence interval (CI) was applied to assess the association between XPD Asp312Asn polymorphism and head and neck cancer risk. Results Overall, no significant association between XPD Asp312Asn polymorphism and head and neck cancer risk was found in this meta-analysis (Asn/Asn vs. Asp/Asp: OR = 0.95, 95%CI = 0.80–1.13, P = 0.550, P heterogeneity = 0.126; Asp/Asn vs. Asp/Asp: OR = 1.11, 95%CI = 0.99–1.24, P = 0.065, P heterogeneity = 0.663; Asn/Asn+Asp/Asn vs. Asp/Asp: OR = 1.07, 95%CI = 0.97–1.19, P = 0.189, P heterogeneity = 0.627; Asn/Asn vs. Asp/Asp+Asp/Asn: OR = 0.87, 95%CI = 0.68–1.10, P = 0.243, P heterogeneity = 0.089). In the subgroup analysis by HWE, ethnicity, and study design, there was still no significant association detected in all genetic models. Conclusions This meta-analysis demonstrates that XPD Asp312Asn polymorphism may not be a risk factor for developing head and neck cancer.
The Impact of Slab Rollback on Earth's Surface: Uplift and Extension in the Hinterland of the North American Cordillera

Slab rollback processes alter the intraplate force balance and buoyancy of the overriding plate, driving surface uplift or extension. From ca. 55–24 Ma, Farallon slab rollback produced migrating volcanism and sedimentation across the western United States as stress on the North American plate transitioned from subduction‐driven compression to widespread extension. Hypotheses regarding rollback‐driven surface deformation differ widely in timing and magnitude. Here we combine hydrogen isotope ratios with high‐resolution geochronology to show that a high‐elevation plateau extended westward from the Sevier‐Laramide fold‐thrust belt across Utah and eastern Nevada prior to slab rollback. Quantitative paleoelevation estimates show that this plateau had obtained over 80% of peak paleoelevations by middle Eocene. Slab rollback, heating, and lithospheric delamination generated 400–600 m of Oligocene surface uplift. Concurrent extension limited overall uplift and rollback‐induced mantle flow likely contributed to the propagation of upper crustal extension that formed the Basin and Range province.
UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models

UMass Morph Server (UMMS) has been developed for the broad impact on the study of molecular dynamics (MD). The elastic network model (ENM) of a given macromolecule has been proven as a useful tool for analyzing thermal behaviors locally and predicting folding pathways globally. UMMS utilizes coarse-grained ENMs at various levels. These simplifications remarkably save computation time compared with all-atom MD simulations so that one can bring down massive computational problems from a supercomputer to a PC. To improve computational efficiency and physical reality of ENMs, the symmetry-constrained, rigid-cluster, hybrid and chemical-bond ENMs have been developed and implemented at UMMS. One can request both harmonic normal mode analysis of a single macromolecule and anharmonic pathway generation between two conformations of a same molecule using elastic network interpolation at .
A Comparison of the Expression and Metabolizing Activities of Phase I and II Enzymes in Freshly Isolated Human Lung Parenchymal Cells and Cryopreserved Human Hepatocytes

The pulmonary and hepatic expression and catalytic activities of phase I and II drug-metabolizing enzymes were compared using human lung and liver tissue, and lung parenchymal cells (LPCs) and cryopreserved hepatocytes. Cytochrome P450 gene expression was generally lower in lung than in liver and CYP3A4 expression in lung was negligible. Esterase gene expression was similar in lung and liver. Expression of all sulfotransferase isoforms in lung was similar to or higher than that in liver. Lung tissue expressed low levels of UGT. However, the expression of UGT2A1 in lung was higher than that in liver. There was a range of catalytic activities in LPCs, including cytochrome P450, esterase, and sulfation pathways. Phase I activities were generally less than 10% of those determined in hepatocytes. Rates of ester hydrolysis and sulfation in LPCs were similar to those in hepatocytes. When measurable, glucuronidation in LPCs was present at very low levels, reflecting the gene expression data. The metabolism of salbutamol, formoterol, and budesonide was also investigated. Production of salbutamol-4-O-sulfate and budesonide oleate was observed in LPCs from at least two of three donor preparations studied. Formoterol sulfate and low levels of formoterol glucuronide were detected in one of three donors. In general, drug-metabolizing capability of LPCs is low compared with liver, although some evidence for substantial sulfation and deesterification capacity was observed. Therefore, these data support the use of this cell-based system for the investigation of key routes of xenobiotic metabolism in human lung parenchyma.
Inherent Barriers to the Use of Social Media for Public Policy Informatics

Social media has the potential to foster interactions between policy makers, government officials, and their constituencies. Opportunities to receive feedback from residents, inform them of government-provided opportunities, and increase engagement with the governance process have all been proposed as ways social media can play a role in Governance 2.0. However, the ability to realize these potential benefits faces inherent barriers in terms of perceptions of social media, ability of administrators to make effective use of social media tools, and the design of software used to operationalize social media. In this paper, we provide a case study of an attempt to use social media to engage with stakeholders, the AdvanceMichigan project, and discuss the various factors that hindered the success of that project.