Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems

Ancient DNA (aDNA) analysis of lake sediments is a promising tool for detecting shifts in past microbial assemblages in response to changing environmental conditions. We examined sediment core samples from subtropical, freshwater Laguna Blanca (Uruguay), which has been severely affected by cultural eutrophication since 1960 and where cyanobacterial blooms, particularly those of the saxitoxin‐producer Cylindrospermopsis raciborskii, have been reported since the 1990s. Samples corresponding to ~1846, 1852, 2000 and 2007 AD were selected to perform denaturing gradient gel electrophoresis (DGGE) analysis of the 16S–23S rRNA intergenic transcribed spacer (ribosomal ITS) to compare their prokaryotic assemblage composition. Each stratum showed different ITS patterns, but the composition of 21st century samples was clearly different than those of mid‐19th century. This compositional change was correlated with shifts in sediment organic matter and chlorophyll a content, which were significantly higher in recent samples. The presence of saxitoxin‐producing cyanobacteria was addressed by quantitative real‐time PCR of the sxtU gene involved in toxin biosynthesis. This gene was present only in recent samples, for which clone libraries and ITS sequencing indicated the presence of Cyanobacteria. Phylogenetic analyses identified C. raciborskii only in the 2000 sample, shortly after several years when blooms were recorded in the lake. These data suggest the utility of aDNA for the reconstruction of microbial assemblage shifts in subtropical lakes, at least on centennial scales. The application of aDNA analysis to genes involved in cyanotoxin synthesis extends the applicability of molecular techniques in palaeolimnological studies to include key microbial community characteristics of great scientific and social interest.
Improving efficiency of recommender systems

By learning from the past behaviors of user transaction records, recommender systems can help people to nd interesting products from many other products. In a collaborative ltering based recommender system, products are regarded as features. However, there are usually quite a lot of products to be considered. A recommender system would be very inefficient if such a large number of products are processed before making any recommendations. We propose a method which applies a self-constructing clustering technique to reduce the dimensionality related to the number of products. As a result, the processing time for making recommendations is much reduced without degrading the accuracy of recommendations.
The experimental investigation of thermal conductivity and the Wiedemann–Franz law for single metallic nanowires

A new method for the measurement of thermal conductivity of electrically conducting single nanowires is presented. First experimental investigations are focused on the thermal conductivity of metallic Pt nanowires with a diameter of (typically) 100 nm and a length of 10 µm. Thermal conductivity data are compared with measurements of electrical conductivity in order to test the Wiedemann–Franz law for metallic nanowires. Compared to the bulk values at room temperature, electrical and thermal conductivities of the nanowire are decreased by a factor of 2.5 and 3.4, respectively. Consequently, the Lorenz number L = λ/σT = 1.82 × 10−8 V2 K−2 of the nanowire is smaller than the bulk Lorenz number Lbulk = (π2/3)(k/e)2 = 2.44 × 10−8 V2 K−2 of metals. Furthermore, the temperature coefficient β of electrical resistivity is also reduced compared to the bulk value. These decreases of λ, σ and β can be attributed to size effects, mainly caused by grain boundary scattering of electrons.
Harvesting Management in Multiuser MIMO Systems with Simultaneous Wireless Information and Power Transfer

In this paper, we focus on a broadcast multiuser multiple-input multiple-output (MIMO) system where we consider that some terminals harvest power and, thus, recharge their batteries through wireless power transfer from the transmitter, while others are simultaneously being served with data transmission. The weighted sum-rate of the terminals that are receiving information data is considered as the optimization policy where minimum energy harvesting constraints are taken into account. We propose a procedure for managing the minimum energy to be harvested by the terminals considering the effect in the target system performance.
Constructing an associative concept space for literature-based discovery

Scientific literature is often fragmented, which implies that certain scientific questions can only be answered by combining information from various articles. In this paper, a new algorithm is proposed for finding associations between related concepts present in literature. To this end, concepts are mapped to a multidimensional space by a Hebbian type of learning algorithm using co-occurrence data as input. The resulting concept space allows exploration of the neighborhood of a concept and finding potentially novel relationships between concepts. The obtained information retrieval system is useful for finding literature supporting hypotheses and for discovering previously unknown relationships between concepts. Tests on artificial data show the potential of the proposed methodology. In addition, preliminary tests on a set of Medline abstracts yield promising results.
Sucrose Diffusion in Decellularized Heart Valves for Freeze-Drying

Decellularized heart valves can be used as starter matrix implants for heart valve replacement therapies in terms of guided tissue regeneration. Decellularized matrices ideally need to be long-term storable to assure off-theshelf availability. Freeze-drying is an attractive preservation method, allowing storage at room temperature in a dried state. However, the two inherent processing steps, freezing and drying, can cause severe damage to extracellular matrix (ECM) proteins and the overall tissue histoarchitecture and thus impair biomechanical characteristics of resulting matrices. Freeze-drying therefore requires a lyoprotective agent that stabilizes endogenous structural proteins during both substeps and that forms a protective glassy state at room temperature. To estimate incubation times needed to infiltrate decellularized heart valves with the lyoprotectant sucrose, temperature-dependent diffusion studies were done using Fourier transform infrared spectroscopy. Glycerol, a cryoprotective agent, was studied for comparison. Diffusion of both protectants was found to exhibit Arrhenius behavior. The activation energies of sucrose and glycerol diffusion were found to be 15.9 and 37.7 kJ$mol , respectively. It was estimated that 4 h of incubation at 37 C is sufficient to infiltrate heart valves with sucrose before freeze-drying. Application of a 5% sucrose solution was shown to stabilize acellular valve scaffolds during freeze-drying. Such freeze-dried tissues, however, displayed pores, which were attributed to ice crystal damage, whereas vacuum-dried scaffolds in comparison revealed no pores after drying and rehydration. Exposure to a hygroscopic sucrose solution (80%) before freeze-drying was shown to be an effective method to diminish pore formation in freeze-dried ECMs: matrix structures closely resembled those of control samples that were not freeze-dried. Heart valve matrices were shown to be in a glassy state after drying, suggesting that they can be stored at room temperature.
Improved Multi-stage Clustering Based Blind Equalisation in Distributed Environments

The recently proposed improved multi-stage clustering (IMSC) based blind equalisation algorithm in [1] gave significant performance improvement as compared to its state of the art counterparts. In that work, the performance was considered over a frequency-selective single input single output (SISO) additive white Gaussian noise (AWGN) channel. The practice of relaying is used in cooperative communications so as to give a variety of the independent signals to the receiver to choose from, the choice being dependent on the quality of the link. In other words, this results in a diversity gain at the receiver. In this paper, we propose a novel blind equalisation scheme which accepts inputs from relays, and finds a smart way of blindly fusing the incoming data, so as to reach a lower mean square deviation (MSD) from the Weiner solution. The simulations presented in this paper validate our algorithm. We also derive an expression for MSD from the Weiner solution of this algorithm as a function of step-size as in [2]. We find that it closely matches the experimentally obtained curves.
The Paradigm Compiler for Distributed-Memory Multicomputers

To harness the computational power of massively parallel distributed-memory multicomputers, users must write efficient software. This process is laborious because of the absence of global address space. The programmer must manually distribute computations and data across processors and explicitly manage communication. The Paradigm (PARAllelizing compiler for DIstributed-memory, General-purpose Multicomputers) project at the University of Illinois addresses this problem by developing automatic methods for the efficient parallelization of sequential programs. A unified approach efficiently supports regular and irregular computations using data and functional parallelism. >
Causes and consequences of the relation between area and age of the ocean floor

The distribution of area of the ocean floor with age, t, is approximately described by dA/dt = C0(1−(t/tm)) where C0 is the rate of crustal generation and tm the maximum age. A linear differential area versus age relation can be explained by a balance between crustal generation and consumption where consumption is uniformly distributed with age. The present distribution of consumption with age was estimated from the isochron map used to derive the area-age relation and a recently published set of angular velocity vectors describing present plate motions. The rate of consumption per unit age shows considerable scatter about a mean value equal to C0/tm(∼1.7×10−8 km2/yr2), but consumption is sufficiently close to being uniformly distributed with age to explain the observed degree of approximation to a linear differential area-age relation. The trenches appear to be distributed randomly with respect to age provinces in the oceans. It was not possible to discern any trend of mean subduction velocities with age apart from the smaller velocities observed for the two youngest age provinces (0–9 Ma). Changes in the rate of plate generation and the distribution of consumption with age result in shifts in the area-age distribution. In turn, these shifts produce changes in the plate driving forces which act to restore the rate of plate generation and distribution of consumption to their initial states. The ridge pushing force, for example, decreases as the rate of crustal generation increases. This coupling between driving forces and the area-age distribution provides a feedback mechanism limiting the extent of any changes. A measure of the magnitude of shifts in the area-age distribution is given by global changes in sea level. If long-term changes in sea level are less than 150 m, as suggested by recent estimates, then only small changes (∼12%) in the rate of plate generation and distribution of consumption with age are required. Sea level changes as large as 300 m require about a 50% change in the rate of crustal generation. The above area-age relation can be combined with simple expressions for depth and heat flow versus age to obtain an empirical hypsometric distribution, parameterized in terms of age, and exact expressions for the heat loss from the ocean floor. The latter is estimated to be 2.9×1013 W, with 25% of this heat being lost by seafloor younger than 5 Ma. Of the total heat loss from the mantle 26% is estimated to be transported by small-scale convection.
Design and Prototypical Implementation of an Integrated Graph-Based Conceptual Data Model

The paper introduces a new, comprehensive integrated conceptual data model in a precise way. Central language features cover core modeling concepts as classification, membership, inheritance, interfaces, structured types, aliasing, aggregation, composition, constraints, clustering and relationships. Schema states are thought of as being realized as graphs with appropriate navigation options. A prototypical graph database implementation and accompanying examples are discussed.
A study of all common subsequences in kernel machine

Counting all common subsequences (ACS) was proposed as a similarity measurement, which is conceptually different from the sequence kernel (SK) in that ACS only considers the occurrence of subsequences while SK uses the frequency of occurrences of subsequences. This difference evidently results in significant performance variety. ACS has been very competitive in the kNN classifier, however, its performance with kernel machine has been rarely investigated. This is due to the fact that whether ACS is suitable for a kernel classifier is not clear. To this end, this paper firstly proves that ACS is a valid kernel, with a delicate analysis. Then, ACS is further proved to be a good kernel with a comparison with SK in the support vector machine.
OBTENTION AND CHARACTERIZATION OF ROSEMARY AND ASH TREE SEED EXTRACTS AND STUDY OF THEIR PREVENTIVE EFFECTS ON METABOLIC DISORDERS

La prevalencia de los trastornos metabolicos esta creciendo a nivel mundial. Botanicos, como el romero (Rosmarinus officinalis L.) y las semillas de fresno (Fraxinus excelsior L.), pueden ser una alternativa para mejorar estos trastornos. El objetivo de esta tesis doctoral fue generar extractos industriales de las partes comestibles de estas plantas, identificar sus compuestos por HPLC, HPLC-MS y RMN, y determinar su eficacia y seguridad. Se desarrollaron tres extractos de romero - estandarizados al 20% de acido carnosico, 20% de acido rosmarinico, y 40% de acido ursolico. El extracto rico en acido ursolico mostro la menor capacidad antioxidante en modelos ORAC y FRAP in vitro, mientras que los otros dos extractos tuvieron capacidades mas elevadas. Sin embargo, el extracto rico en acido carnosico (RE) fue superior en la inhibicion de la oxidacion de LDL ex vivo, y fue el unico seleccionado para estudios posteriores. Se desarrollo un extracto de semilla de fresno (FE) de acuerdo a su uso tradicional en Marruecos, siendo identificados salidrosido y 9 glucosidos secoiridoides, dos de ellos fueron descubiertos por primera vez: Excelside A y Excelside B. En estudios in vitro, RE y FE activaron receptores nucleares que regulan la homeostasis de la glucosa y la energia, y actuaron sobre mecanismos contra la obesidad y la dislipidemia - RE activa PPAR? e inhibe la lipasa pancreatica, y FE estimula PPAR? y evita la diferenciacion de preadipocitos. La eficacia de ambos extractos para el control de trastornos metabolicos fue confirmada en ratones C57BL/6J administrados con una dieta baja en grasa, una dieta alta en grasa, o una dieta alta en grasa mas 0.5% RE (HFD.RE) o 0.5% FE (FED) durante 16 semanas. HFD.RE limito el aumento del peso corporal y grasa en el epididimo en un 69% (P<0.01) y 79% (P<0.001), respectivamente. HFD.RE tambien redujo la glucemia (72%, P<0.01) y los niveles de colesterol (68%, P<0.001). FED redujo la glucemia (76.52%, P<0.001), insulinemia (53.43%, P<
Modeling Somatic Evolution in Tumorigenesis

Tumorigenesis in humans is thought to be a multistep process where certain mutations confer a selective advantage, allowing lineages derived from the mutated cell to outcompete other cells. Although molecular cell biology has substantially advanced cancer research, our understanding of the evolutionary dynamics that govern tumorigenesis is limited. This paper analyzes the computational implications of cancer progression presented by Hanahan and Weinberg in The Hallmarks of Cancer. We model the complexities of tumor progression as a small set of underlying rules that govern the transformation of normal cells to tumor cells. The rules are implemented in a stochastic multistep model. The model predicts that (i) early-onset cancers proceed through a different sequence of mutation acquisition than late-onset cancers; (ii) tumor heterogeneity varies with acquisition of genetic instability, mutation pathway, and selective pressures during tumorigenesis; (iii) there exists an optimal initial telomere length which lowers cancer incidence and raises time of cancer onset; and (iv) the ability to initiate angiogenesis is an important stage-setting mutation, which is often exploited by other cells. The model offers insight into how the sequence of acquired mutations affects the timing and cellular makeup of the resulting tumor and how the cellular-level population dynamics drive neoplastic evolution.
Reactive oxygen species and redox-regulation of skeletal muscle adaptations to exercise

Skeletal muscle has been shown to generate a complex set of reactive oxygen and nitrogen species (ROS) both at rest and during contractile activity. The primary ROS generated are superoxide and nitric oxide and the pattern and magnitude of their generation is influenced by the nature of the contractile activity. It is increasingly clear that the ROS generated by skeletal muscle play an important role in influencing redox-regulated processes that control, at least some of, the adaptive responses to contractile activity. These processes are also recognized to be modified during ageing and in some disease states, providing the potential that interventions affecting ROS activity may influence muscle function or viability in these situations.
Use of multiplex PCR for simultaneous detection of four bacterial species in middle ear effusions

A multiplex PCR procedure was developed for the simultaneous detection of Alloiococcus otitidis, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae in middle ear effusions (MEEs) from patients with chronic otitis media with effusion. The bacterial 16S rRNA gene was chosen as the target, and the procedure used one common lower primer and four species-specific upper primers. The reaction was optimized by changing the primer concentrations to yield equal amounts of amplification products. The specificity of the reaction was verified with various bacterial species found in the nasopharynx. The performance of the procedure was examined with 25 MEE specimens, and the results were compared to those obtained by conventional culture methods. A detection level of 10 bacterial cells/reaction for each of the study organisms was achieved. By conventional culture methods, 8 (32%) of the specimens showed growth of one of the study organisms. In contrast, 21 (84%) of the specimens tested positive by the multiplex PCR. None of the culture-positive specimens were PCR negative, whereas three (12%) of the PCR-positive specimens tested positive for two of the four study organisms. Thus, the multiplex PCR method improves the detection rate significantly compared to that of the conventional culture method.
Stock Market Fluctuations and the Term Structure

This paper uses the term structure of interest rates to explain the variations of stock prices and stock returns. It shows that interest rates have an important impact on stock returns, especially at long horizons. The hypothesis that expected stock returns move one-for-one with ex ante interest rates, which has been rejected strongly in other studies using short horizon data, is supported by long horizon data. The paper proposes, for the first time, a single measure---the present value of forward interest rates---to summarize the information of the term structure that is useful in characterizing the comovements of the equity market and the bond market, and finds that such a single measure explains a significant part of variation in dividend-price ratios. The paper also suggests that the high volatility of the stock market is related to the high volatility of long-term bond yields and may be accounted for by changing forecasts of discount rates. The findings of this paper are quite different from the typical findings of the previous work and may provide a reasonable economic explanation for the predictability of long-horizon stock returns.
A decoupled maneuvering target tracking algorithm for practical applications

A parallel algorithm is proposed to decouple the Kalman filter into three Cartesian coordinates for maneuvering target tracking in this paper. Converted measurement noise covariance matrix is decoupled so that IMM estimator can work separately. Compared with classical coupled tracking algorithm, our algorithm can save computing resources, and the tracking performance is improved due to the algorithm's design to separate influence among three Cartesian coordinates. Monte Carlo simulation results show that the proposed three Cartesian coordinate decoupled algorithm outperforms three Cartesian coordinate coupled algorithm in tracking maneuvering target.
Type and extent of hemispheric brain infarctions and clinical outcome in early and delayed middle cerebral artery recanalization

We evaluated the influence of time of recanalization or degree of initial leptomeningeal collateral blood flow in cardioembolic or arterio-arterial middle cerebral artery (MCA) occlusion on infarct size and clinical outcome in a series of 34 consecutive acute stroke patients with main stem (N = 31) or major branch (N = 3) occlusions using CT, initial cerebral arteriography (N = 21), repetitive close-meshed transcranial Doppler ultrasonography, and a neurologic stroke scale. We treated 15 patients with tissue plasminogen activator intravenously within the first 6 hours. The type and size of infarction depended on the location of the occluding lesions within the MCA trunk. Proximal MCA occlusion always led to infarction involving the striatum and internal capsule. Sixty-five percent of patients showed recanalization of the occluded MCA within 1 week. Following MCA recanalization, hyperperfusion was present in 38 to 44% of cases. There was a marginally significant relation between size of infarction on CT and recanalization time within the first 24 hours. The more rapidly recanalization occurred, the smaller the size of the infarct. When recanalization time was greater than 8 hours, the lesions always extended to the cortex. An additional good leptomeningeal collateral blood flow significantly reduced the size of the infarct and improved clinical outcome after 17 days and after 10 months. Early recanalization of embolic MCA occlusions within up to 8 hours, in conjunction with good transcortical collateralization, has a favorable impact on infarct size and outcome and may constitute the therapeutic window of opportunity.
Knowledge-Free Induction of Morphology Using Latent Semantic Analysis

Morphology induction is a subproblem of important tasks like automatic learning of machine-readable dictionaries and grammar induction. Previous morphology induction approaches have relied solely on statistics of hypothesized stems and affixes to choose which affixes to consider legitimate. Relying on stem-and-affix statistics rather than semantic knowledge leads to a number of problems, such as the inappropriate use of valid affixes ("ally" stemming to "all"). We introduce a semantic-based algorithm for learning morphology which only proposes affixes when the stem and stem-plus-affix are sufficiently similar semantically. We implement our approach using Latent Semantic Analysis and show that our semantics-only approach provides morphology induction results that rival a current state-of-the-art system.