Miracle-dz/UniFAR-FTUs huggingface dataset:
A spatiotemporal analysis of climate change in the Greater Yellowstone Ecosystem and its effects on Pinus albicaulis

Projected climate change at a regional level is expected to shift vegetation habitat distributions over the next century. For the sub-alpine species whitebark pine (Pinus albicaulis), warming temperatures may indirectly result in loss of suitable bioclimatic habitat, reducing its distribution within its historic range. This research focuses on understanding the patterns of spatiotemporal variability for future projected P.albicaulis suitable habitat in the Greater Yellowstone Area (GYA) through a bioclimatic envelope approach. Since intermodel variability from General Circulation Models (GCMs) lead to differing predictions regarding the magnitude and direction of modeled suitable habitat area, nine bias-corrected statistically downscaled GCMs were utilized to understand the uncertainty associated with modeled projections. P.albicaulis was modeled using a Random Forests algorithm for the 1980-2010 climate period and showed strong presence/absence separations by summer maximum temperatures and springtime snowpack. Patterns of projected habitat change by the end of the century suggested a constant decrease in suitable climate area from the 2010 baseline for both Representative Concentration Pathways (RCPs) 8.5 and 4.5 climate forcing scenarios. Percent suitable climate area estimates ranged from 2-29% and 0.04-10% by 2099 for RCP 8.5 and 4.5 respectively. Habitat projections between GCMs displayed a decrease of variability over the 2010-2099 time period related to consistent warming above the 1910-2010 temperature normal after 2070 for all GCMs. A decreasing pattern of projected P.albicaulis suitable habitat area change was consistent across GCMs, despite strong differences in magnitude. Future ecological research in species distribution modeling should consider a full suite of GCM projections in the analysis to reduce extreme range contraction/expansion predictions. The results suggest that restoration strageties such as planting of seedlings and 28 controlling competing vegetation may be necessary to maintain P.albicaulis in the GYA under the more extreme future climate scenarios.
Hoosier Oncology Group Randomized Phase II Study of Docetaxel, Vinorelbine, and Estramustine in Combination in Hormone-Refractory Prostate Cancer with Pharmacogenetic Survival Analysis

Purpose: To determine the safety and efficacy of two docetaxel doublets in hormone-refractory prostate cancer (HRPC) patients and to examine the prognostic role of polymorphisms in host genes important to docetaxel metabolism and transport. Experimental Design: Sixty-four chemotherapy-naive patients with HRPC were randomized to docetaxel and vinorelbine (D, 20 mg/m2 i.v. days 1 and 8; V, 25 mg/m2 i.v. days 1 and 8) or docetaxel and estramustine phosphate (D, 60-70 mg/m2 i.v. day 1; E, 280 mg oral thrice daily days 1-5) administered q21d. Primary end point was clinically significant toxicity. A pharmacogenetic analysis of host genes was done in patients who received at least one cycle of docetaxel therapy. Results: Grade 3/4 toxicity occurred in 15.6% of DV patients and in 28.6% DE patients. Neither arm exceeded the threshold of clinically significant toxicity. In the DV arm, objective response rate was 33%, prostate-specific antigen response rate was 20%, and median survival was 16.2 months. In the DE arm, objective response rate was 67%, prostate-specific antigen response rate was 43%, and median survival was 19.7 months. Pharmacogenetic analyses showed a significant association between survival beyond 15 months and the ABCG2 421 C>A (Q141K) polymorphism compared with the wild-type (C/C) genotype (66% versus 27%; P = 0.05). Conclusions: DV and DE doublets are active with a tolerable toxicity profile in patients with HRPC; however, efficacy does not seem superior to standard single-agent docetaxel. The ABCG2 421 C>A (Q141K) polymorphism may be an important predictor of response and survival in HRPC patients treated with docetaxel-based chemotherapy.
EarthDB: scalable analysis of MODIS data using SciDB

Earth scientists are increasingly experiencing difficulties with analyzing rapidly growing volumes of complex data. Those who must perform analysis directly on low-level National Aeronautics and Space Administration (NASA) Moderate Resolution Imaging Spectroradiometer (MODIS) Level 1B calibrated and geolocated data, for example, encounter an arcane, high-volume data set that is burdensome to make use of. Instead, Earth scientists typically opt to use higher-level "canned" products provided by NASA. However, when these higher-level products fail to meet the requirements of a particular project, a cruel dilemma arises: cope with data products that don't exactly meet the project's needs or spend an enormous amount of resources extracting what is needed from the unadulterated low-level data. In this paper, we present EarthDB, a system that eliminates this dilemma by offering the following contributions: 1. Enabling painless importing of MODIS Level 1B data into SciDB, a highly scalable science-oriented database platform that abstracts away the complexity of distributed storage and analysis of complex multi-dimensional data, 2. Defining a schema that unifies storage and representation of MODIS Level 1B data, regardless of its source file, 3. Supporting fast filtering and analysis of MODIS data through the use of an intuitive, high-level query language rather than complex procedural programming and, 4. Providing the ability to easily define and reconfigure entire analysis pipelines within the SciDB database, allowing for rapid ad-hoc analysis. To demonstrate this ability, we provide sample benchmarks for the construction of true-color (RGB) and Normalized Difference Vegetative Index (NDVI) images from raw MODIS Level 1B data using relatively simple queries with scalable performance.
Beowulf Cluster Design for Scientific PDE Models

This paper details some of the basic issues that arise when designing a Beowulf cluster for particular types of scientific simulations. The general problems of interest are partial differential equations (PDEs). These equations describe natural phenomenon and can be numerically solved. Finite differencing is used to solve the system of equations. This method naturally delineates the problem into four distinct categories based on the span of the data stencil used to update the next point: Independent, Nearest Neighbor, Quasi-Global, and Global. This delineation also relates the communication requirements between the independent processes. Other important factors include computation and memory requirements of the algorithm and particular problem. Design tradeoffs are presented with regards to algorithm development, communication architecture, and node configuration.
Inventory Allocation for Online Graphical Display Advertising

We discuss a multi-objective/goal programming model for the allocation of inventory of graphical advertisements. The model considers two types of campaigns: guaranteed delivery (GD), which are sold months in advance, and non-guaranteed delivery (NGD), which are sold using real-time auctions. We investigate various advertiser and publisher objectives such as (a) revenue from the sale of impressions, clicks and conversions, (b) future revenue from the sale of NGD inventory, and (c) "fairness" of allocation. While the first two objectives are monetary, the third is not. This combination of demand types and objectives leads to potentially many variations of our model, which we delineate and evaluate. Our experimental results, which are based on optimization runs using real data sets, demonstrate the effectiveness and flexibility of the proposed model.
Linearly graded behavioural analogue performance models using support vector machines and VHDL-AMS

A concept of linearly graded statistical models for analogue performance evaluation is proposed and a suitable technique for automatic generation of analogue performance models using support vector machines is presented. The analogue system's behaviour is specified using VHDL-AMS descriptions. Practical application of the technique is demonstrated with a case study of automated analogue performance model generation for an analogue filter.
Early evidence on the effects of regulators' suicidality warnings on SSRI prescriptions and suicide in children and adolescents.

OBJECTIVE In 2003 and 2004, U.S. and European regulators issued public health warnings about a possible association between antidepressants and suicidal thinking and behavior. The authors assessed whether these warnings discouraged use of antidepressants in children and adolescents and whether they led to increases in suicide rates as a result of untreated depression. METHOD The authors examined U.S. and Dutch data on prescription rates for selective serotonin reuptake inhibitors (SSRIs) from 2003 to 2005 in children and adolescents (patients up to age 19), as well as suicide rates for children and adolescents, using available data (through 2004 in the United States and through 2005 in the Netherlands). They used Poisson regression analyses to determine the overall association between antidepressant prescription rates and suicide rates, adjusted for sex and age, during the periods preceding and immediately following the public health warnings. RESULTS SSRI prescriptions for youths decreased by approximately 22% in both the United States and the Netherlands after the warnings were issued. In the Netherlands, the youth suicide rate increased by 49% between 2003 and 2005 and shows a significant inverse association with SSRI prescriptions. In the United States, youth suicide rates increased by 14% between 2003 and 2004, which is the largest year-to-year change in suicide rates in this population since the Centers for Disease Control and Prevention began systematically collecting suicide data in 1979. CONCLUSIONS In both the United States and the Netherlands, SSRI prescriptions for children and adolescents decreased after U.S. and European regulatory agencies issued warnings about a possible suicide risk with antidepressant use in pediatric patients, and these decreases were associated with increases in suicide rates in children and adolescents.
A Road Map to Single Molecule Dynamics

Signals from single fluorescent dye molecules were first measured in non-biological environments. Some of the earliest studies acquired signals from singlefluorescence dyes embedded in a solid matrix at the temperature of liquid helium [1] and from excitation fluorescence signals [2]. In early studies carried out at room temperature, single fluorescence dye molecules spread over a film were observed using near-field scanning fluorescence microscopy [3]. In a biological environment where fluorescence is largely quenched by the surrounding water molecules, single molecule imaging was first accomplished in 1995 using total internal reflected fluorescence (TIRF) and epi-fluorescence microscopy [4] (see Chapter 2). Single fluorophores attached to myosin molecules were visualized in aqueous solution in the vicinity of a glass surface while single ATP turnover from the samemyosin molecule was measured using fluorescently-labeled ATP. TIRF microscopy has been widely used for single molecule imaging. Other studies have measured single fluorophores bound to biomolecules in solution while passing through a fixed small volume using confocal microscopy [5].
Reliability of percentage ideal weight for height

AIMS To assess the reliability of percentage ideal weight for height (%WFH) as a measure in children. METHODS Forty two dietitians calculated %WFH of six children. Eleven of the 42 repeated the calculations. RESULTS Interexaminer estimates varied by 16.5 to 40 percentage points (mean 27.8). Intraexaminer variability was also large. CONCLUSIONS %WFH is an unreliable measure of nutritional status.
Optimal robot motions for physical criteria

This paper presents an optimization-based framework for emulating the low-level capabilities of human motor coordination and learning. Our approach rests on the observation that in most biological motor learning scenarios some form of optimization with respect to a physical criterion is taking place. By appealing to techniques from the theory of Lie groups, we are able to formulate the equations of motion of complex multibody systems in such a way that the resulting optimization problems can be solved reliably and efficiently—the key lies in the ability to compute exact analytic gradients of the objective function without resorting to numerical approximations. The methodology is illustrated via a wide range of optimized, “natural” motions for robots performing various human-like tasks—for example, power lifting, diving, and gymnastics. © 2001 John Wiley & Sons, Inc.
Attacks on Lin's Mobile Dynamic Identity-based Authenticated Key Agreement Scheme using Chebyshev Chaotic Maps

In 2014, Lin proposed an authentication system with dynamic identity of the user for low-power mobile devices using Chebyshev chaotic map. The scheme is proposed to provide mutual authentication and session key agreement between a remote server and its legitimate user. The scheme provides user anonymity and untracibility, and resilience from many cryptographic attacks. However, the author of this paper showed that Lin’s scheme is no longer usable for practical applications as (i) it cannot verify the wrong identity and password at the user side in the login and password change phases, (ii) it cannot protect user impersonation attack, and (ii) it has the problem of session key forward secrecy.
Image restoration subject to a total variation constraint

Total variation has proven to be a valuable concept in connection with the recovery of images featuring piecewise smooth components. So far, however, it has been used exclusively as an objective to be minimized under constraints. In this paper, we propose an alternative formulation in which total variation is used as a constraint in a general convex programming framework. This approach places no limitation on the incorporation of additional constraints in the restoration process and the resulting optimization problem can be solved efficiently via block-iterative methods. Image denoising and deconvolution applications are demonstrated.
Lipid Nanoparticles as Carriers for RNAi against Viral Infections: Current Status and Future Perspectives

The efforts made to develop RNAi-based therapies have led to productive research in the field of infections in humans, such as hepatitis C virus (HCV), hepatitis B virus (HBV), human immunodeficiency virus (HIV), human cytomegalovirus (HCMV), herpetic keratitis, human papillomavirus, or influenza virus. Naked RNAi molecules are rapidly digested by nucleases in the serum, and due to their negative surface charge, entry into the cell cytoplasm is also hampered, which makes necessary the use of delivery systems to exploit the full potential of RNAi therapeutics. Lipid nanoparticles (LNP) represent one of the most widely used delivery systems for in vivo application of RNAi due to their relative safety and simplicity of production, joint with the enhanced payload and protection of encapsulated RNAs. Moreover, LNP may be functionalized to reach target cells, and they may be used to combine RNAi molecules with conventional drug substances to reduce resistance or improve efficiency. This review features the current application of LNP in RNAi mediated therapy against viral infections and aims to explore possible future lines of action in this field.
Video search by multi-modal and clustering analysis

We introduce a video search system using multi-modal and clustering analysis. In this system, users can make queries by keywords or by visual contents such as frames or rectangle regions within a frame, the retrieved results are then organized into clusters and only representative frames of these clusters are shown to users. Experiments on TRECVID datasets showed promising results.
A Novel Energy Efficient Source Routing for Mesh NoCs

Network on Chip (NoC) is the upcoming interconnection framework for multi-core processors. In chip-multicore processors, the performance of the underlying communication network is determined by the efficiency of the routing logic used in NoC routers. Distributed routing and source routing are the two main classification of routing techniques. For routers employing static routing policies, distributed routing leads to redundant computations in each router and increases complexity of routers. We analyse the existing state-of-art source routing technique and propose a novel alternative that makes routing process simpler and faster. Our proposed design reduces the number of bits needed to encode the route in the packet header, reduces the router pipeline latency and hence allows the network to be operated at a frequency approximately two times faster than the existing design.
Downlink Multiple Antenna Transmitter Optimization on Spatially and Temporally Correlated Channels with Delayed Channel State Information

In this paper we present multiple antenna transmitter optimization schemes that are based on linear transformations and transmit power optimization, while keeping the average transmit power conserved. We consider the downlink of a wireless system with multiple transmit antennas at the base station and a number of mobile terminals (i.e., users) each with a single receive antenna. We consider the maximum achievable sum data rates in the case of (1) zero-forcing spatial pre-filter and (2) modified zero-forcing spatial pre-filter. Using a multiple input single output (MISO) channel model with temporal and spatial correlations, we study the effect of delayed channel state information (CSI) on these schemes. It is seen that as the CSI delay increases, spatially uncorrelated channels perform worse than spatially correlated channels, which is in contrast to the case of zero delay CSI.
Impact of Aggregate Gradation and Filler Type on Marshall Properties of Asphalt Concrete

As asphalt concrete wearing course (ACWC) is the top layer in the pavement structure, the material should be able to sustain stresses caused by direct traffic loading. The objective of this study is to evaluate the influence of aggregate gradation and mineral filler type on Marshall Properties. A detailed laboratory study is carried out by preparing asphalt mixtures specimens using locally available materials including asphalt binder (40-50) penetration grade, two types of aggregate gradation representing SCRB and ROAD NOTE 31 specifications and two types of mineral filler including limestone dust and coal fly ash. Four types of mixtures were prepared and tested. The first type included SCRB specification and limestone dust, the second type included SCRB specification and coal fly ash, the third types included ROAD NOTE 31 specification and limestone dust and the fourth type included ROAD NOTE 31 specification and coal fly ash. The optimum asphalt content of each type of mixtures was determined using Marshall Method of mix design. 60 specimen were prepared and tested with dimension of 10.16 cm in diameter and 6.35 cm in height. Results of this study indicated that aggregate gradation and filler type have a significant effect on optimum asphalt content and Marshall Properties. From the experimental data, it was observed that the value of Marshall Stability is comparatively higher when using fly ash as filler as compared to limestone dust.
Learning class-to-class selectional preferences

Selectional preference learning methods have usually focused on word-to-class relations, e.g., a verb selects as its subject a given nominal class. This papers extends previous statistical models to class-to-class preferences, and presents a model that learns selectional preferences for classes of verbs. The motivation is twofold: different senses of a verb may have different preferences, and some classes of verbs can share preferences. The model is tested on a word sense disambiguation task which uses subject-verb and object-verb relationships extracted from a small sense-disambiguated corpus.
MemPod: A Clustered Architecture for Efficient and Scalable Migration in Flat Address Space Multi-level Memories

In the near future, die-stacked DRAM will be increasingly present in conjunction with off-chip memories in hybrid memory systems. Research on this subject revolves around using the stacked memory as a cache or as part of a flat address space. This paper proposes MemPod, a scalable and efficient memory management mechanism for flat address space hybrid memories. MemPod monitors memory activity and periodically migrates the most frequently accessed memory pages to the faster on-chip memory. MemPod's partitioned architectural organization allows for efficientscaling with memory system capabilities. Further, a big data analytics algorithm is adapted to develop an efficient, low-cost activity tracking technique. MemPod improves the average main memory access time of multi-programmed workloads, by up to 29% (9% on average) compared to the state of the art, and that will increase as the differential between memory speeds widens. MemPod's novel activity tracking approach leads to significant cost reduction (12800x lower storage space requirements) and improved future prediction accuracy over prior work which maintains a separatecounter per page.
Identification of new superwarfarin-type rodenticides by structural similarity. The docking of ligands on the vitamin K epoxide reductase enzyme’s active site

Abstract The rodenticide brodifacoum is highly toxic to mammals and birds, and extremely toxic to fish. It is a highly cumulative poison due to its high lipophilicity and extremely slow elimination. For this reason, it may be interesting to find similar compounds in order to enlarge the spectrum of vitamin K epoxide reductase enzyme inhibitors used today in pest control. We used the Similar Compounds search type of the Chemical Structure Search of the PubChem Compound Database to locate records that are similar to the chemical structure of brodifacoum, using pre-specified similarity thresholds. Using the threshold ≥ than 95% for the similar structures criteria, we found 14 compounds (from over 30 million entries) that meet this criteria. Two of these compounds have a better binding affinity to vitamin K epoxide reductase enzyme than brodifacoum, but the binding energy of the other 12 substances is also high, having identical or lower lipophilicity; consequently, they will eliminate faster, possibly lacking a part of the adverse effects.
Crystal structure of chloramphenicol acetyltransferase B2 encoded by the multiresistance transposon Tn2424

Wei Qiu, Rong Shi, Ming-Liang Lu, Ming Zhou, Paul H. Roy, Jacques Lapointe and Sheng-Xiang Lin* Oncology and Molecular Endocrinology Research Centre and Université Laval, Quebec, Canada Infectious Diseases Research Center, CHUL Research Center and Université Laval, Quebec, Canada Centre de Recherche sur la Fonction, la Structure et l’Ingénierie des Protéines (CREFSIP), Université Laval, Quebec, Canada Département de Biochimie et de Microbiologie, Université Laval, Quebec, Canada