Miracle-dz/UniFAR-FTUs huggingface dataset:
Block structure preserving model order reduction

We propose a block structure preserving model reduction (BSMOR), which generalizes the structure preserving model order reduction (SPRIM). The blocks can be derived based on specific applications such as block current characterization of the substrate. Increasing block numbers leads to more matched poles or moments using the same Krylov space and also increases the sparse ratio of the state matrices of the resulting macro-model. Experiment shows that BSMOR has a 20X smaller reduction time than PRIMA does under a same error bound. To efficiently analyze the resulting macro-model with a large number of ports, we further propose a bordered-block diagonal (BBD) partitioning with a bottom-up hierarchical clustering (BBDC) where the macro-model is partitioned into a number of subset-port models, each with a manageable model size. With a similar accuracy, BBDC obtains 30X speedup compared to the original macro-model.
Devonian Crustal Stretching in the Northern Tasmanides (Australia) and Implications for Oroclinal Bending

The Tasmanides in eastern Australia exhibit a number of orogenic curvatures (oroclines), and possibly, a continental‐scale bend that defines the continuation of the Delamerian Orogen with the Thomson Orogen. We provide an insight into the geodynamic processes associated with the origin of this orocline. We present interpretations of seismic reflection profiles and potential field data from the Thomson Orogen, which provide information on the crustal architecture and unravel major structures and kinematic relationships. Results show that a large area in the northern Tasmanides is underlain by thinned crust, bounded in the north and south by ~E‐W trending geophysical features with apparent sinistral and dextral sense of kinematics, respectively. Within the highly extended crust of the Thomson Orogen, there is evidence for widespread Devonian basins bounded by normal faults. In stark contrast to the southern Tasmanides, where rocks show evidence for an earlier (Silurian) episode of extension and Devonian contractional deformation, no evidence for Silurian synrift sedimentation is observed in the Thomson Orogen. Evidence for ~E‐W trending sinistral and dextral crustal‐scale shear zones in the northern and southern boundaries of the Thomson Orogen, respectively, may represent tear faults, which were active during the Early Devonian and were possibly accompanied by tear‐related magmatism. We suggest that crustal stretching in the northern Tasmanides was associated with Devonian back‐arc extension in response to trench retreat, bounded by zones of slab‐tearing and crustal segmentation that ultimately led to the development of the Delamerian‐Thomson Orocline.
A Window into Africa’s Past Hydroclimates: The SISAL_v1 Database Contribution

Africa spans the hemispheres from temperate region to temperate region and has a long history of hominin evolution. Although the number of Quaternary palaeoclimatic records from the continent is increasing, much of the history of spatial and temporal climatic variability is still debated. Speleothems, as archives of terrestrial hydroclimate variability, can help reveal this history. Here we review the progress made to date, with a focus on the first version of the Speleothem Isotopes Synthesis and AnaLysis (SISAL) database. The geology of Africa has limited development of large karst regions to four areas: along the northern coast bordering the Mediterranean, eastern Africa and the Horn of Africa, southwestern Africa and southern Africa. Exploitation of the speleothem palaeoclimate archives in these regions is uneven, with long histories of research, e.g., in South Africa, but large areas with no investigations such as West Africa. Consequently, the evidence of past climate change reviewed here is irregularly sampled in both time and space. Nevertheless, we show evidence of migration of the monsoon belt, with enhanced rainfall during interglacials observed in northeast Africa, southern Arabia and the northern part of southern Africa. Evidence from eastern Africa indicates significant decadal and centennial scale rainfall variability. In northwestern and southern Africa, precession and eccentricity influence speleothem growth, largely through changing synoptic storm activity.
Hpc Application Software Consortium Hpc Application Software Consortium Summit Concept Paper

Executive Summary This white paper proposes the foundation of a High Performance Computing (HPC) Application Software Consortium (ASC) of academic, research and industry partners for the development and maintenance of a framework for multiphysics simulation on HPC systems using commercial and open-source codes. The goal of the proposed consortium is to focus the technologies, resources, and expertise to lower the development and ownership costs of multiphysics and multidisciplinary simulation software for both the commercial independent software vendors (ISVs) and HPC applications users. Council on Competitiveness research has demonstrated that HPC is a major enabler for U.S. competitiveness, but that the cost of HPC simulation software and the lack of software robustness is a significant barrier [1]. Council research has also identified an industry need to customize products by simulating all life cycle considerations, including market and regulatory requirements, in one integrated environment across the product's supply chain [2]. The ISV community for the HPC market is relatively small and fragmented, therefore unable to invest sufficient resources into new breakthrough products. Overall, there is a need for improvement in sustained performance, scalability, functionality, and manage-ability of HPC software. Significant technical challenges remain to implement multidisciplinary and mul-tiphysics modeling, model validation and verification, large-scale data management, and visualization. Emerging system-level simulation software products will require a breadth of performance-value-price points to satisfy HPC users ranging from entry-level cluster users to large HPC system users. In addition, open interfaces and infrastructures are required to support multiphysics modeling, simulation, and data analysis in an interoperable multi-vendor environment. The challenge presented is to change the paradigm from tooling, independent software vendors, computing system vendors, and individual supply-chain companies working separately to having these firms collaborating on solutions, building common frameworks , and adding cumulative market value. 1 Background Based on recommendations of the Council's HPC Advisory Committee, the Council and the University of Southern California's Information Sciences Institute (ISI) have been leading an effort to assess the feasibility of an application software consortium to address the critical need for robust multiphysics and multidisciplinary simulation software for HPC systems. This effort includes: • In December 2007, the Council and ISI organized a planning workshop with a core group of volunteers from academic computing centers, government laboratories, independent software vendors (ISVs), systems vendors, and industrial HPC users to discuss issues facing the community. Topics of the planning workshop included: 1) the need to support full-system multiphysics simulation …
Porphyromonas gingivalis-induced cellular hypertrophy and MMP-9 activity via different signaling pathways in H9c2 cardiomyoblast cells.

BACKGROUND Little is known about the pathogenesis of cardiomyocyte hypertrophy caused by periodontitis pathogens. The purpose of this study was to determine the effect of the periodontal pathogen Porphyromonas gingivalis on cardiomyocyte hypertrophy. METHODS Matrix metalloproteinase (MMP)-2 and MMP-9 activities and cellular morphology were measured by gelatin zymography and immunofluorescence after P. gingivalis-medium treatment with or without SB203580 (p38 mitogen-activated protein kinase cascade [p38] inhibitor), U0126 (mitogen-activated protein kinase kinase [MAPKK] inhibitor), LY294002 (phosphoinositide 3-kinase [PI3K] inhibitor), cyclosporin A (CsA; calcineurin inhibitor), SP600125 (c-Jun N-terminal kinase [JNK] inhibitor), proinflammatory interleukin (IL)-1, or anti-inflammatory IL-10 in cultured cardiomyoblast H9c2 cells. RESULTS P. gingivalis medium increased MMP-9 activities and cellular sizes (+87%) of H9c2 cells, whereas Actinobacillus actinomycetemcomitans medium and Prevotella intermedia medium had no effects. The increased activity of MMP-9 treated with P. gingivalis medium was not mediated through p38, extracellular-regulated kinase (ERK), PI3K, calcineurin, and JNK signaling pathways and was not inhibited by IL-10. However, the hypertrophy of H9c2 cells induced with P. gingivalis medium was reduced by administration of SB203580 (-37%), U0126 (-35%), LY294002 (-49%), CsA (-49%), and SP600125 (-24%). CONCLUSIONS Our findings suggest that P. gingivalis medium elevated MMP-9 activity and induced cardiomyoblast hypertrophy. However, P. gingivalis-induced H9c2 cell hypertrophy was mediated through p38, ERK, PI3K, calcineurin, and JNK signaling pathways, which are in a totally different regulatory pathway from P. gingivalis-elevated MMP-9 activity. These findings provide evidence that P. gingivalis infection activated multiple factors via different pathways to induce the development of hypertrophy of H9c2 cardiomyoblast cells.
NC Coloring Algorithms for Permutation Graphs

We show that the problem of coloring a permutation graph of size n can be solved in O(log n log k) time using O(kn2/log k log2 n) processors on the CREW PRAM model of computation, where 1 < k < n. We estimate the parameter k on random permutation graphs and show that the coloring problem can be solved in O(log n log log n) time in the average-case on the CREW PRAM model of computation with O(n2) processors. Our computational strategy goes as follows: Given a permutation pi; or its corresponding permutation graph G[π], we first construct a directed acyclic graph G*[π] using certain combinatorial properties of π, and then compute longest paths in the directed acyclic graph using divide-and-conquer techniques. We show that the problem of coloring a permutation graph G[π] is equivalent to finding longest paths in its acyclic digraph G*[π]. The best-known parallel algorithms for the same problem run in O(log2 n) time using O(n3/log n) processors on the CREW PRAM model of computation.
Twitter use by politicians during social uprisings: an analysis of Gezi park protests in Turkey

Social uprisings clearly show that social media tools, especially Twitter, help news spread more than the press does recently. In some cases Twitter substitutes traditional media if censorship is enlarged to such a level that the mainstream media channels prefer not to reflect the actual volume of the protests. Twitter is also utilized by politicians during such events to reinforce "us vs. them" division, and to gain support and legitimization for their own actions. Using critical discourse analysis, this paper aims to investigate the recurring speech patterns in the tweets of top-level politicians during the Gezi Park protests that started in Istanbul Turkey in June 2013 and spread the country rapidly. We study the tweets to draw conclusions on whether the politicians' statements represent marginalization and polarization efforts during the Gezi Park protests. In this paper, we consider social uprising as a communal expression of both political and apolitical opposition to the party in power. Our analysis reveals that the politicians' tweets are mainly characterized by a discourse that guides the public into some conscious direction that may reproduce marginalization and polarization among the public at large.
CCL3L1-CCR5 Genotype Improves the Assessment of AIDS Risk in HIV-1-Infected Individuals

Background Whether vexing clinical decision-making dilemmas can be partly addressed by recent advances in genomics is unclear. For example, when to initiate highly active antiretroviral therapy (HAART) during HIV-1 infection remains a clinical dilemma. This decision relies heavily on assessing AIDS risk based on the CD4+ T cell count and plasma viral load. However, the trajectories of these two laboratory markers are influenced, in part, by polymorphisms in CCR5, the major HIV coreceptor, and the gene copy number of CCL3L1, a potent CCR5 ligand and HIV-suppressive chemokine. Therefore, we determined whether accounting for both genetic and laboratory markers provided an improved means of assessing AIDS risk. Methods and Findings In a prospective, single-site, ethnically-mixed cohort of 1,132 HIV-positive subjects, we determined the AIDS risk conveyed by the laboratory and genetic markers separately and in combination. Subjects were assigned to a low, moderate or high genetic risk group (GRG) based on variations in CCL3L1 and CCR5. The predictive value of the CCL3L1-CCR5 GRGs, as estimated by likelihood ratios, was equivalent to that of the laboratory markers. GRG status also predicted AIDS development when the laboratory markers conveyed a contrary risk. Additionally, in two separate and large groups of HIV+ subjects from a natural history cohort, the results from additive risk-scoring systems and classification and regression tree (CART) analysis revealed that the laboratory and CCL3L1-CCR5 genetic markers together provided more prognostic information than either marker alone. Furthermore, GRGs independently predicted the time interval from seroconversion to CD4+ cell count thresholds used to guide HAART initiation. Conclusions The combination of the laboratory and genetic markers captures a broader spectrum of AIDS risk than either marker alone. By tracking a unique aspect of AIDS risk distinct from that captured by the laboratory parameters, CCL3L1-CCR5 genotypes may have utility in HIV clinical management. These findings illustrate how genomic information might be applied to achieve practical benefits of personalized medicine.
A General Detection Method for Linear Constructed Distributed Space-Time Codes in Amplify-and-Forward Mode of Wireless Cooperation Networks

This paper presents a general detection method for linearly constructed distributed space-time codes (DSTC) in amplify-and-forward (AF) mode of wireless cooperation networks. A two-phase model for the network is utilized. In the first phase, multiple-antenna transmit nodes send signals simultaneously. Then the relays encode received signals with linearly constructed DSTC. Since linear dispersion (LD) codes subsume all linearly constructed STCs as special cases, when such DSTCs are used in AF mode of the network, a LD equivalent system model which is similar to V-BLAST structure is given in this paper. Thus, detection algorithms for V-BLAST can be utilized for the model effectively. Especially, linear complexity detection algorithms can be used in the network for practical implementations. Simulation results prove the LD equivalent model valid at last.
Neighborhoods and chronic disease onset in later life.

OBJECTIVES To strengthen existing evidence on the role of neighborhoods in chronic disease onset in later life, we investigated associations between multiple neighborhood features and 2-year onset of 6 common conditions using a national sample of older adults. METHODS Neighborhood features for adults aged 55 years or older in the 2002 Health and Retirement Study were measured by use of previously validated scales reflecting the built, social, and economic environment. Two-level random-intercept logistic models predicting the onset of heart problems, hypertension, stroke, diabetes, cancer, and arthritis by 2004 were estimated. RESULTS In adjusted models, living in more economically disadvantaged areas predicted the onset of heart problems for women (odds ratio [OR] = 1.20; P < .05). Living in more highly segregated, higher-crime areas was associated with greater chances of developing cancer for men (OR = 1.31; P < .05) and women (OR = 1.25; P < .05). CONCLUSIONS The neighborhood economic environment is associated with heart disease onset for women, and neighborhood-level social stressors are associated with cancer onset for men and women. The social and biological mechanisms that underlie these associations require further investigation.
Lower bounds for processing data with few random accesses to external memory

We consider a scenario where we want to query a large dataset that is stored in external memory and does not fit into main memory. The most constrained resources in such a situation are the size of the main memory and the number of random accesses to external memory. We note that sequentially streaming data from external memory through main memory is much less prohibitive. We propose an abstract model of this scenario in which we restrict the size of the main memory and the number of random accesses to external memory, but admit arbitrary sequential access. A distinguishing feature of our model is that it allows the usage of unlimited external memory for storing intermediate results, such as several hard disks that can be accessed in parallel. In this model, we prove lower bounds for the problem of sorting a sequence of strings (or numbers), the problem of deciding whether two given sets of strings are equal, and two closely related decision problems. Intuitively, our results say that there is no algorithm for the problems that uses internal memory space bounded by N1−ϵ and at most o(log N) random accesses to external memory, but unlimited “streaming access”, both for writing to and reading from external memory. (Here, N denotes the size of the input and ϵ is an arbitrary constant greater than 0.) We even permit randomized algorithms with one-sided bounded error. We also consider the problem of evaluating database queries and prove similar lower bounds for evaluating relational algebra queries against relational databases and XQuery and XPath queries against XML-databases.
Chronic leptin infusion increases arterial pressure.

Plasma leptin concentration is increased in hypertensive obese humans, but whether leptin contributes to the increased arterial pressure in obesity is not known. In this study, we tested whether chronic increases in leptin, to levels comparable to those in obesity, could cause a sustained increase in arterial pressure and also the importance of central nervous system (CNS) versus systemic mechanisms. Five male Sprague-Dawley rats were implanted with chronic nonoccluding catheters in the abdominal aorta and both carotid arteries for CNS infusion, and five other rats were implanted with an abdominal aorta catheter and femoral vein catheter for intravenous (I.V.) infusion. After 7 days of control, leptin was infused into the carotid arteries or femoral vein at 0.1 microg/kg/min for 5 days and 1.0 microg/kg/min for 7 days, followed by a 7-day recovery period. The carotid artery and i.v. infusions of leptin at 1 microg/kg/min significantly increased plasma leptin levels, from 1.2+/-0.4 ng/mL to 91+/-5 ng/mL and from 0.9+/-0.1 ng/mL to 94+/-9 ng/mL, respectively, but there was no significant increase in either group at the low dose. Food intake also did not change at the low dose but decreased by approximately 65% in the carotid group and 69% in the i.v. group after 7 days of the 1 microg/kg/min infusion. Mean arterial pressure (MAP) increased slightly at the low dose only in the carotid group, but this was not statistically significant. At the higher dose, however, MAP increased significantly from 86+/-1 mm Hg to 94+/-1 mm Hg in the carotid group and from 87+/-1 mm Hg to 93+/-1 mm Hg in the i.v. group. Heart rate also increased significantly in both groups at 1 microg/kg/min leptin infusion. Fasting blood glucose and insulin levels decreased significantly at 1 microg/kg/min in both the carotid artery group (-10.5% and -82.5%, respectively) and the i.v. group (-13.6% and -80.4%, respectively). All variables returned to control levels after leptin infusion was stopped. These results indicate that chronic increases in circulating leptin cause sustained increases in arterial pressure and heart rate and are consistent with a possible role for leptin in obesity hypertension.
A Cloud Enabled Social Media Monitoring Platform for Events Detection and Prediction

The data mined from social networks has been shown to have an inherent wealth of information. However the heterogeneous nature of this data along with difficulties in predetermining its rate and source makes collecting and aggregating it an often inefficiently run task. This paper presents a platform which leverages some of the architecture and features of Cloud computing in order to dynamically scale resources according to data rate, so as to collect and parse data from a variety of social media sources in an economical manner. The nature of the platform means that it may be applied to a variety of social network monitoring tasks, which may take advantage of the dynamic and economical nature of Cloud-based architectures. This paper addresses a gap in the current literature and proposes a novel Cloud Enabled Social Media Monitoring Platform for Events Detection and Prediction.
Optimal shortest path queries in a simple polygon

Let <italic>P</italic> be a simple polygon with <italic>n</italic> sides. This paper shows how to preprocess the polygon so that, given two query points <italic>p</italic> and <italic>q</italic> inside <italic>P</italic>, the length of the shortest path inside the polygon from <italic>p</italic> to <italic>q</italic> can be found in time <italic>&Ogr;</italic>(log <italic>n</italic>). The path itself must be polygonal and can be extracted in additional time proportional to the number of turns it makes. The preprocessing consists of triangulation plus a linear amount of additional work.
Knowledge-oriented secure multiparty computation

Protocols for secure multiparty computation (SMC) allow a set of mutually distrusting parties to compute a function f of their private inputs while revealing nothing about their inputs beyond what is implied by the result. Depending on f, however, the result itself may reveal more information than parties are comfortable with. Almost all previous work on SMC treats f as given. Left unanswered is the question of how parties should decide whether it is "safe" for them to compute f in the first place. We propose here a way to apply belief tracking to SMC in order to address exactly this question. In our approach, each participating party is able to reason about the increase in knowledge that other parties could gain as a result of computing f, and may choose not to participate (or participate only partially) so as to restrict that gain in knowledge. We develop two techniques---the belief set method and the SMC belief tracking method---prove them sound, and discuss their precision/performance tradeoffs using a series of experiments.