Miracle-dz/UniFAR-FTUs huggingface dataset:
Parallel Scientific Computing in C++ and MPI - A Seamless Approach to Parallel Algorithms and their Implementation

This book provides a seamless approach to numerical algorithms, modern programming techniques and parallel computing. These concepts and tools are usually taught serially across different courses and different textbooks, thus observing the connection between them. The necessity of integrating these subjects usually comes after such courses are concluded (e.g., during a first job or a thesis project), thus forcing the student to synthesize what is perceived to be three independent subfields into one in order to produce a solution. The book includes both basic and advanced topics and places equal emphasis on the discretization of partial differential equations and on solvers. Advanced topics include wavelets, high-order methods, non-symmetric systems and parallelization of sparse systems. A CD-ROM accompanies the text.
High temperature zone-drawing of nylon 66 microfiber prepared by CO2 laser-thinning

A high temperature zone-drawing method was applied to a nylon 66 microfiber, obtained by using CO2 laser-thinning, to develop its mechanical properties. The microfiber used for the high temperature zone-drawing was prepared by winding at 150 m min−1 the microfiber obtained by irradiating the laser at 4.0 W cm−2 to an original fiber with a diameter of 50 μm, and had a diameter of 9.6 μm and a birefringence of 0.019. The high temperature zone-drawing was carried out in two steps; the first drawing was carried out at a temperature of 230°C at supplying and winding speeds of 0.266 and 0.797 m min−1, the second at 250°C at supplying and winding speeds of 0.266 and 0.425 m min−1, respectively. The diameter of the microfiber decreased, and its birefringence increased stepwise with the processing. The high temperature zone-drawn microfiber finally obtained had a diameter of 4.2 μm, a birefringence of 0.079, total draw ratio of 4.8, tensile modulus of 12 GPa, and tensile strength of 1.0 GPa. The wide-angle X-ray diffraction photograph of the drawn microfiber showed the existence of highly oriented crystallites. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 101: 42–47, 2006
Quantum dot biosensors for ultrasensitive multiplexed diagnostics.

Time- and color-resolved detection of Foerster resonance energy transfer (FRET) from luminescent terbium complexes to different semiconductor quantum dots results in a fivefold multiplexed bioassay with sub-picomolar detection limits for all five bioanalytes (see picture). The detection of up to five biomarkers occurs with a sensitivity that is 40-240-fold higher than one of the best-established single-analyte reference assays.
Journal of Experimental & Clinical Assisted Reproduction a Comparison of Polarized and Non-polarized Human Endometrial Monolayer Culture Systems on Murine Embryo Development

Background: Co-culture of embryos with various somatic cells has been suggested as a promising approach to improve embryo development. Despite numerous reports regarding the beneficial effects of epithelial cells from the female genital tract on embryo development in a co-culture system, little is known about the effect of these cells when being cultured under a polarized condition on embryo growth. Our study evaluated the effects of in vitro polarized cells on pre-embryo development.
Optimizing Associative Information Transfer within Content-addressable Memory

This paper investigates an information-theoretic design principle, intended to support an evolution of a memory structure fitting a specific selection pressure: associative information transfer through the structure. The proposed criteria measure how much does associativity in memory add to the information transfer in terms of precision, recall and effectiveness. The study also introduces a conjectural analogy between memory retrieval and self-replication, with DNA as a partially-associative memory containing relevant information. DNA decoding by a complicated protein machinery (“cues” or ”keys”) may correspond to an associative recall: i.e., a replicated offspring is an associatively-recalled prototype. The proposed information-theoretic criteria intend to formalize the notion of information transfer involved in self-replication, and enable bio-inspired design of more effective memory structures.
k-MLE for mixtures of generalized Gaussians

We introduce an extension of the k-MLE algorithm, a fast algorithm for learning statistical mixture models relying on maximum likelihood estimators, which allows to build mixture of generalized Gaussian distributions without a fixed shape parameter. This allows us to model finely probability density functions which are made of highly non Gaussian components. We theoretically prove the local convergence of our method and show experimentally that it performs comparably to Expectation-Maximization methods while being more computationally efficient.
Secure IPsec based offload architectures for mobile data

Radio Access Network (RAN) are likely to be overloaded, and some places will not be able to provide the necessary requested bandwidth. In order to respond to the demand of bandwidth, overloaded RAN are currently offloading their traffic on WLAN. WLAN Access Points like (ISP provided xDSL boxes) are untrusted, unreliable and do not handle mobility. As a result, mobility, multihoming, and security cannot be handled by the network anymore, and must be handled by the terminal. This paper positions offload architectures based on IPsec and shows that IPsec can provide end-to-end security, as well as seamless connectivity across IP networks. Then, the remaining of the paper evaluates how mobility on these IPsec based architectures impacts the Quality of Service (QoS) for real time applications such as an audio streaming service. QoS is measured using network interruption time and POLQA. Measurements compare TCP/HLS and UDP/RTSP over various IPsec configurations.
Uptake of Glycerol-2-Phosphate via the ugp-Encoded Transporter in Escherichia coli K-12

ABSTRACT During phenotypic characterization of various Escherichia coli mutants, we observed that ΔphoA strains are capable of using glycerol-2-phosphate (G2P) as a sole source of phosphorus. Mutations in the ugpBAECQ operon eliminated this phenotype, suggesting that G2P is a previously unrecognized substrate for the binding protein-dependent Ugp transporter.
A Morphologically Informed Formulation of Poroelasticity Under Compression

Physical properties of porous media are inherently determined by their morphological features. Distinctive behaviors of soils, rocks, and cementitious media have traditionally divided researchers into separate communities. To unify these studies in each individual porous media application, a universal poromechanics theory should account for morphological distinctions among these porous media. In this study, the morphological parameters used in composite theory are introduced to formulate a morphologically informed poroelasticity. Corresponding to the underling morphologies for the two bounds of the bulk modulus, the formulas for the drainage and effective stress of the porous media are derived. For those porous media commonly met in engineering application, e.g. soils, the poroelasticity formulation will be developed in next stage based on the two bound formulation, i.e. by matching the coefficient in the effective stress formula with those of Terzaghi and Biot.
Computing Conformal Structure of Surfaces

According to Klein’s Erlangen program, different geometry branches study invariants of a space under different transformation groups. Topology and Euclidean geometry have been widely applied in computer graphics and vision. Between topological transformation group and Euclidean transformation group, there exists a conformal transformation group, which has not been well studied by computer scientists. We present a systematic way to compute the conformal invariants under this group, and to verify if two surfaces can be transformed to each other by conformal maps. The proposed conformal geometry method has many applications including global conformal surface parameterization, remeshing, geometric morphing in graphics, surface identification and classification in vision. ∗PhD in computer science. Division of Engineering and Applied Science, Harvard University, Cambridge, MA. E-mail: gu@eecs.harvard. edu, †Fields medalist. Mathematics Department, Harvard University, Cambridge, MA. E-mail: yau@math.harvard. edu 1
Language for learning complex human-object interactions

In this paper we use a Hierarchical Hidden Markov Model (HHMM) to represent and learn complex activities/task performed by humans/robots in everyday life. Action primitives are used as a grammar to represent complex human behaviour and learn the interactions and behaviour of human/robots with different objects. The main contribution is the use of a probabilistic model capable of representing behaviours at multiple levels of abstraction to support the proposed hypothesis. The hierarchical nature of the model allows decomposition of the complex task into simple action primitives. The framework is evaluated with data collected for tasks of everyday importance performed by a human user.
Markov Chain Monte Carlo Methods for State-Space Models with Point Process Observations

This letter considers how a number of modern Markov chain Monte Carlo (MCMC) methods can be applied for parameter estimation and inference in state-space models with point process observations. We quantified the efficiencies of these MCMC methods on synthetic data, and our results suggest that the Reimannian manifold Hamiltonian Monte Carlo method offers the best performance. We further compared such a method with a previously tested variational Bayes method on two experimental data sets. Results indicate similar performance on the large data sets and superior performance on small ones. The work offers an extensive suite of MCMC algorithms evaluated on an important class of models for physiological signal analysis.
Experimental study of particulate fouling in enhanced water chiller condenser tubes

This paper describes the result of accelerated particulate fouling tests performed on two enhanced tubes used in water chiller condensers. The fouling tests were performed using ferric oxide powder as the foulant material with foulant concentrations between 1000 and 2000 ppm. Data are also presented for on-line brush cleaning and high-velocity flush cleaning. The water used in these tests is much dirtier than would be expected in an actual operating system. The key purpose of the tests was to determine the fouling rate of the enhanced tubes compared to that of a plain tube.
Leveraging Advanced Data Preprocessing in the Extraction of Network Configuration Template Blocks

With the significant increase in the number of mobile devices, cellular carrier network operators face challenges in their management. For quick setup of network equipment, the network operator must be well-versed in configuring the network devices. In previous research, a configuration recommendation scheme based on semantic extraction (e.g., template blocks extraction) from the configuration data was presented for helping an network operator. In this paper, we propose an efficient configuration data preprocessing scheme compatible with the previous research. With this proposal, it is possible that the recommendation scheme can extract larger and semantically richer template blocks from configuration data.
Glycolytic enzymes in the spermatozoa and cytoplasmic droplets of bull, boar and ram, and their leakage afte shock.

Summary. A method has been developed for the simultaneous isolation of spermatozoa and cytoplasmic droplets from bull, boar and ram semen. The glycolytic enzymes, hexokinase (HK), glucose phosphate isomerase (GPI) and lactate dehydrogenase (LDH) were demonstrated in both types of particle: on a per particle basis compared with spermatozoa, droplets contained similar quantities of GPI, less HK and only one-tenth the amount of LDH. The HK was partly bound while the GPI was entirely soluble in both. The LDH was partly bound in spermatozoa but soluble in droplets. Suspensions of spermatozoa and cytoplasmic droplets were subjected to sudden cooling, freezing or hypo-osmotic shock, and leakage of GPI, HK and LDH into the extracellular medium was measured. Both spermatozoa and droplets released glycolytic enzymes during the treatments, but the droplets were more fragile than the spermatozoa. The proportion ofloss varied between enzymes, as well as between droplet and spermatozoon; considerable GPI and little HK was released from both, whereas much LDH was lost from droplets but hardly any from spermatozoa. The activities of these three glycolytic enzymes were also measured in seminal plasma from bull, boar and ram. The ratios of the activities found were compared with those in droplets or spermatozoa from the same species. It is suggested that much of the glycolytic enzyme activity in seminal plasma arises from disintegrated cytoplasmic droplets rather than from spermatozoa.
Propagating XML constraints to relations

We present a technique for refining the design of relational storage for XML data based on XML key propagation. Three algorithms are presented: one checks whether a given functional dependency is propagated from XML keys via a predefined view; the others compute a minimum cover for all functional dependencies on a universal relation given XML keys. Experimental results show that these algorithms are efficient in practice. We also investigate the complexity of propagating other XML constraints to relations, and the effect of increasing the power of the transformation language. Computing XML key propagation is a first step toward establishing a connection between XML data and its relational representation at the semantic level.
An RGD Helper Sequence in CagL of Helicobacter pylori Assists in Interactions with Integrins and Injection of CagA

Helicobacter pylori is a specific gastric pathogen that colonizes the stomach in more than 50% of the world’s human population. Infection with this bacterium can induce several types of gastric pathology, ranging from chronic gastritis to peptic ulcers and even adenocarcinoma. Virulent H. pylori isolates encode components of a type IV secretion system (T4SS), which form a pilus for the injection of virulence proteins such as CagA into host target cells. This is accomplished by a specialized adhesin on the pilus surface, the protein CagL, a putative VirB5 ortholog, which binds to host cell β1 integrin, triggering subsequent delivery of CagA across the host cell membrane. Like the human extracellular matrix protein fibronectin, CagL contains an RGD (Arg-Gly-Asp) motif and is able to trigger intracellular signaling pathways by RGD-dependent binding to integrins. While CagL binding to host cells is mediated primarily by the RGD motif, we identified an auxiliary binding motif for CagL–integrin interaction. Here, we report on a surface exposed FEANE (Phe-Glu-Ala-Asn-Glu) interaction motif in spatial proximity to the RGD sequence, which enhances the interactions of CagL with integrins. It will be referred to as RGD helper sequence (RHS). Competitive cell adhesion assays with recombinant wild type CagL and point mutants, competition experiments with synthetic cyclic and linear peptides, and peptide array experiments revealed amino acids essential for the interaction of the RHS motif with integrins. Infection experiments indicate that the RHS motif plays a role in the early interaction of H. pylori T4SS with integrin, to trigger signaling and to inject CagA into host cells. We thus postulate that CagL is a versatile T4SS surface protein equipped with at least two motifs to promote binding to integrins, thereby causing aberrant signaling within host cells and facilitating translocation of CagA into host cells, thus contributing directly to H. pylori pathogenesis.
An Arabidopsis ATPase gene involved in nematode-induced syncytium development and abiotic stress responses

The beet cyst nematode Heterodera schachtii induces syncytia in the roots of Arabidopsis thaliana, which are its only nutrient source. One gene, At1g64110, that is strongly up-regulated in syncytia as shown by RT-PCR, quantitative RT-PCR, in situ RT-PCR and promoter::GUS lines, encodes an AAA+-type ATPase. Expression of two related genes in syncytia, At4g28000 and At5g52882, was not detected or not different from control root segments. Using amiRNA lines and T-DNA mutants, we show that At1g64110 is important for syncytium and nematode development. At1g64110 was also inducible by wounding, jasmonic acid, salicylic acid, heat and cold, as well as drought, sodium chloride, abscisic acid and mannitol, indicating involvement of this gene in abiotic stress responses. We confirmed this using two T-DNA mutants that were more sensitive to abscisic acid and sodium chloride during seed germination and root growth. These mutants also developed significantly smaller roots in response to abscisic acid and sodium chloride. An in silico analysis showed that ATPase At1g64110 (and also At4g28000 and At5g52882) belong to the ‘meiotic clade’ of AAA proteins that includes proteins such as Vps4, katanin, spastin and MSP1.
Cosmological implications of two conflicting deuterium abundances

Constraints on big bang nucleosynthesis (BBN) and on cosmological parameters from conflicting deuterium observations in different high redshift QSO systems are discussed. The high deuterium observations by Carswell et al., Songaila et al., and Rugers and Hogan are consistent with ${}^{4}$He and ${}^{7}$Li observations and standard BBN ${(N}_{\ensuremath{\nu}}$ =3) and allows ${N}_{\ensuremath{\nu}}l~3.6$ at 95% C.L. , but are inconsistent with local observations of D and ${}^{3}$He in the context of conventional theories of stellar and galactic evolution. In contrast, the low deuterium observations by Tytler, Fan, and Burles and Burles and Tytler are consistent with the constraints from local galactic observations, but require ${N}_{\ensuremath{\nu}}=1.9\ifmmode\pm\else\textpm\fi{}0.3$ at 68% C.L. , excluding standard BBN at 99.9% C.L. , unless the systematic uncertainties in the ${}^{4}$He observations have been underestimated by a large amount. The high and low primordial deuterium abundances imply, respectively, ${\ensuremath{\Omega}}_{B}{h}^{2}=0.005$\char21{}$0.01$ and ${\ensuremath{\Omega}}_{B}{h}^{2}=0.02$\char21{}$0.03$ at 95% C.L. When combined with the high baryon fraction inferred from x-ray observations of rich clusters, the corresponding total mass densities (for $50l~{H}_{0}l~90)$ are ${\ensuremath{\Omega}}_{M}=0.05$\char21{}$0.20$ and ${\ensuremath{\Omega}}_{M}=0.2$\char21{}$0.7$, respectively (95% C.L.). The range of ${\ensuremath{\Omega}}_{M}$ corresponding to high D is in conflict with dynamical constraints $({\ensuremath{\Omega}}_{\mathrm{m}}g~0.2$\char21{}$0.3)$ and with the shape parameter constraint $(\ensuremath{\Gamma}={\ensuremath{\Omega}}_{M}h=0.25\ifmmode\pm\else\textpm\fi{}0.05)$ from large scale structure formation in CDM and $\ensuremath{\Lambda}$CDM models.
Stochastic Classification of Urban Terrain for Smart Wheelchair Navigation

In this paper we investigate the potential for enhancing the perception capabilities of smart wheelchair systems (SWS) in an urban environment through intensity-based terrain classification. A 3D camera system was employed that provided both range and intensity (remission) measurements to objects in the scene. Each sensor measurement was represented by a feature vector consisting of range ρ, bearing angle φ, and intensity γ values. We then constructed a stochastic model by discretizing the feature space into cells, each of which corresponded to a probability mass function (PMF) denoting the probability a point in the feature space belonged to one of four classes: grass, sidewalk, street (blacktop), or unknown. The stochastic model was generated a priori from literally millions of labeled point measurements of the different terrain classes. Bayesian filtering techniques were then used to make a terrain class assignment for ground plane cells in the local map over time. We illustrate the utility of the approach by demonstrating autonomous sidewalk following of the SWS over two hundred of meters solely through terrain class assignment. Extensions such as enhanced ground plane segmentation are also discussed.
Trade-Off between Object Selectivity and Tolerance in Monkey Inferotemporal Cortex

Object recognition requires both selectivity among different objects and tolerance to vastly different retinal images of the same object, resulting from natural variation in (e.g.) position, size, illumination, and clutter. Thus, discovering neuronal responses that have object selectivity and tolerance to identity-preserving transformations is fundamental to understanding object recognition. Although selectivity and tolerance are found at the highest level of the primate ventral visual stream [the inferotemporal cortex (IT)], both properties are highly varied and poorly understood. If an IT neuron has very sharp selectivity for a unique combination of object features (“diagnostic features”), this might automatically endow it with high tolerance. However, this relationship cannot be taken as given; although some IT neurons are highly object selective and some are highly tolerant, the empirical connection of these key properties is unknown. In this study, we systematically measured both object selectivity and tolerance to different identity-preserving image transformations in the spiking responses of a population of monkey IT neurons. We found that IT neurons with high object selectivity typically have low tolerance (and vice versa), regardless of how object selectivity was quantified and the type of tolerance examined. The discovery of this trade-off illuminates object selectivity and tolerance in IT and unifies a range of previous, seemingly disparate results. This finding also argues against the idea that diagnostic conjunctions of features guarantee tolerance. Instead, it is naturally explained by object recognition models in which object selectivity is built through AND-like tuning mechanisms.
Draft Genome Sequence of Burkholderia gladioli Strain UCD-UG_CHAPALOTE (Phylum Proteobacteria)

ABSTRACT Here, we present the draft genome of Burkholderia gladioli strain UCD-UG_CHAPALOTE. This strain is an endophyte isolated from surface sterilized seeds of an ancient Mexican landrace of corn, Chapalote. The genome contains 8,527,129 bp in 109 scaffolds.
Co-Clustering Structural Temporal Data with Applications to Semiconductor Manufacturing

Recent years have witnessed data explosion in semiconductor manufacturing due to advances in instrumentation and storage techniques. In particular, following the same recipe for a certain IC device, multiple tools and chambers can be deployed for the production of this device, during which multiple time series can be collected, such as temperature, impedance, gas flow, electric bias, etc. These time series naturally fit into a two-dimensional array (matrix), i.e., Each element in this array corresponds to a time series for one process variable from one chamber. To leverage the rich structural information in such temporal data, in this paper, we propose a novel framework named C-Struts to simultaneously cluster on the two dimensions of this array. In this framework, we interpret the structural information as a set of constraints on the cluster membership, introduce an auxiliary probability distribution accordingly, and design an iterative algorithm to assign each time series to a certain cluster on each dimension. To the best of our knowledge, we are the first to address this problem. Extensive experiments on benchmark and manufacturing data sets demonstrate the effectiveness of the proposed method.