Miracle-dz/UniFAR-FTUs huggingface dataset:
Achieving precise mechanical control in intrinsically noisy systems

How can precise control be realized in intrinsically noisy systems? Here, we develop a general theoretical framework that provides a way of achieving precise control in signal-dependent noisy environments. When the control signal has Poisson or supra-Poisson noise, precise control is not possible. If, however, the control signal has sub-Poisson noise, then precise control is possible. For this case, the precise control solution is not a function, but a rapidly varying random process that must be averaged with respect to a governing probability density functional. Our theoretical approach is applied to the control of straight-trajectory arm movement. Sub-Poisson noise in the control signal is shown to be capable of leading to precise control. Intriguingly, the control signal for this system has a natural counterpart, namely the bursting pulses of neurons—trains of Dirac-delta functions—in biological systems to achieve precise control performance.
(Acetonitrile){2-[bis(pyridin-2-ylmethyl-κ2 N)amino-κN]-N-(2,6-dimethylphenyl)acetamide-κO}(perchlorato-κO)zinc (acetonitrile){2-[bis(pyridin-2-ylmethyl-κ2 N)amino-κN]-N-(2,6-dimethylphenyl)acetamide-κO}zinc tris(perchlorate)

In the title salt, [Zn(C22H24N4O)(CH3CN)][Zn(ClO4)(C22H24N4O)(CH3CN)](ClO4)3, two differently coordinated zinc cations occur. In the first complex, the metal ion is coordinated by the N,N′,N′′,O-tetradentate acetamide ligand and an acetonitrile N atom, generating an approximate trigonal–bipyramidal coordination geometry, with the O atom in an equatorial site and the acetonitrile N atom in an axial site. In the second complex ion, a perchlorate ion is also bonded to the zinc ion, generating a distorted trans-ZnO2N4 octahedron. Of the uncoordinating perchlorate ions, one lies on a crystallographic twofold axis and one lies close to a twofold axis and has a site occupancy of 0.5. N—H⋯O and N—H⋯(O,O) hydrogen bonds are observed in the crystal. Disordered solvent molecules occupy about 11% of the unit-cell volume; their contribution to the scattering was removed with the SQUEEZE routine of the PLATON program [Spek (2009 ▶). Acta Cryst. D65, 148–155. ].
Predicting chemoresistance in human malignant glioma cells: The role of molecular genetic analyses

Less than 30% of malignant gliomas respond to adjuvant chemotherapy. Here, we asked whether alterations in the p53 and RB pathways and the expression of six BCL‐2 family proteins predicted acute cytotoxicity and clonogenic cell death induced by BCNU, vincristine, cytarabine, teniposide, doxorubicin, camptothecin or β‐lapachone in 12 human malignant glioma cell lines. Neither wild‐type p53 status, nor p53 protein accumulation, nor p21 or MDM‐2 levels, nor differential expression of BCL‐2 family proteins predicted drug sensitivity, except for an association of BAX with higher β‐lapachone sensitivity in acute cytotoxicity assays. p16 protein expression was associated with high doubling time and chemoresistance. We conclude that some important molecular changes, which are involved in the development of gliomas and attributed a role in regulating vulnerability to apoptosis, may not determine the response to chemotherapy in these tumors. Int. J. Cancer (Pred. Oncol.) 79:640–644, 1998. © 1998 Wiley‐Liss, Inc.
Using evolutionary demography to link life history theory, quantitative genetics and population ecology

1. There is a growing number of empirical reports of environmental change simultaneously influencing population dynamics, life history and quantitative characters. We do not have a well-developed understanding of links between the dynamics of these quantities. 2. Insight into the joint dynamics of populations, quantitative characters and life history can be gained by deriving a model that allows the calculation of fundamental quantities that underpin population ecology, evolutionary biology and life history. The parameterization and analysis of such a model for a specific system can be used to predict how a population will respond to environmental change. 3. Age-stage-structured models can be constructed from character-demography associations that describe age-specific relationships between the character and: (i) survival; (ii) fertility; (iii) ontogenetic development of the character among survivors; and (iv) the distribution of reproductive allocation. 4. These models can be used to calculate a wide range of useful biological quantities including population growth and structure; terms in the Price equation including selection differentials; estimates of biometric heritabilities; and life history descriptors including generation time. We showcase the method through parameterization of a model using data from a well-studied population of Soay sheep Ovis aries. 5. Perturbation analysis is used to investigate how the quantities listed in summary point 4 change as each parameter in each character-demography function is altered. 6. A wide range of joint dynamics of life history, quantitative characters and population growth can be generated in response to changes in different character-demography associations; we argue this explains the diversity of observations on the consequences of environmental change from studies of free-living populations. 7. The approach we describe has the potential to explain within and between species patterns in quantitative characters, life history and population dynamics.
Online Learning to Sample

Stochastic Gradient Descent (SGD) is one of the most widely used techniques for online optimization in machine learning. In this work, we accelerate SGD by adaptively learning how to sample the most useful training examples at each time step. First, we show that SGD can be used to learn the best possible sampling distribution of an importance sampling estimator. Second, we show that the sampling distribution of an SGD algorithm can be estimated online by incrementally minimizing the variance of the gradient. The resulting algorithm - called Adaptive Weighted SGD (AW-SGD) - maintains a set of parameters to optimize, as well as a set of parameters to sample learning examples. We show that AWSGD yields faster convergence in three different applications: (i) image classification with deep features, where the sampling of images depends on their labels, (ii) matrix factorization, where rows and columns are not sampled uniformly, and (iii) reinforcement learning, where the optimized and exploration policies are estimated at the same time, where our approach corresponds to an off-policy gradient algorithm.
Spike-timing prediction in cortical neurons with active dendrites

A complete single-neuron model must correctly reproduce the firing of spikes and bursts. We present a study of a simplified model of deep pyramidal cells of the cortex with active dendrites. We hypothesized that we can model the soma and its apical dendrite with only two compartments, without significant loss in the accuracy of spike-timing predictions. The model is based on experimentally measurable impulse-response functions, which transfer the effect of current injected in one compartment to current reaching the other. Each compartment was modeled with a pair of non-linear differential equations and a small number of parameters that approximate the Hodgkin-and-Huxley equations. The predictive power of this model was tested on electrophysiological experiments where noisy current was injected in both the soma and the apical dendrite simultaneously. We conclude that a simple two-compartment model can predict spike times of pyramidal cells stimulated in the soma and dendrites simultaneously. Our results support that regenerating activity in the apical dendritic is required to properly account for the dynamics of layer 5 pyramidal cells under in-vivo-like conditions.
Web Site Personalizers for Mobile Devices

The fastest growing community of web users is that of mobile visitors who browse with wireless PDAs, cell phones, and pagers. Unfortunately, most web sites today are optimized exclusively for desktop, broadband clients, and deliver content poorly suited for mobile devices — devices that can display only a few lines of text using slow wireless networks. To best serve the needs of this growing community, we propose building web site personalizers that observe the behavior of web visitors and automatically customize and adapt sites for each individual mobile visitor. In this paper, we give an overview of our approach to web site personalization as utilitymaximizing search through the space of personalized web sites. Following this framework we have implemented two personalizers: PROTEUS and MINPATH. PROTEUS allows changes to site navigation (adding or removing links) as well as content manipulation (rearranging or eliding content), and evaluates the result with a learned model of the current visitor. MINPATH concentrates exclusively on adding “shortcut” links, but uses a model learned by clustering visitors based on their sequences of page requests. We introduce PROTEUS and MINPATH, and outline our current and future directions for these personalizers.
A fine-grained permission control mechanism for external storage of Android

Android lacks fine-grained permission control for the external storage. Under the current coarse-grained mechanism, any application is able to access all the data on the external storage very easily. At the same time, many applications store sensitive data into the external storage, and some of these data are highly concerned with user privacy, which could bring severe security problems. In this paper, we propose a fine-grained permission control mechanism for external storage of Android. The mechanism is based on Filesystem in Userspace (FUSE) and offers the following features: protecting user private media files such as photos and videos; isolating the data of each application; providing access control settings for user. We implement this mechanism on the latest Android version, by introducing a new type of GID (ESDS-GID), extending the functionality of the emulated filesystem as well as the system services. The results of functional verification and performance benchmark show that with a reasonable performance overhead, this mechanism brings considerable enhancement for Android system security.
Training a Dialogue Act Tagger for Human-human and Human-computer Travel dialogues

While dialogue acts provide a useful schema for characterizing dialogue behaviors in human-computer and human-human dialogues, their utility is limited by the huge effort involved in hand-labelling dialogues with a dialogue act labelling scheme. In this work, we examine whether it is possible to fully automate the tagging task with the goal of enabling rapid creation of corpora for evaluating spoken dialogue systems and comparing them to human-human dialogues. We report results for training and testing an automatic classifier to label the information provider's utterances in spoken human-computer and human-human dialogues with DATE (Dialogue Act Tagging for Evaluation) dialogue act tags. We train and test the DATE tagger on various combinations of the DARPA Communicator June-2000 and October-2001 human-computer corpora, and the CMU human-human corpus in the travel planning domain. Our results show that we can achieve high accuracies on the human-computer data, and surprisingly, that the human-computer data improves accuracy on the human-human data, when only small amounts of human-human training data are available.
The methyltransferase Setdb 1 is essential for meiosis and mitosis in mouse oocytes and early embryos

Oocytes develop the competence for meiosis and early embryogenesis during their growth. Setdb1 is a histone H3 lysine 9 (H3K9) methyltransferase required for post-implantation development and has been implicated in the transcriptional silencing of genes and endogenous retroviral elements (ERVs). To address its role in oogenesis and pre-implantation development, we conditionally deleted Setdb1 in growing oocytes. Loss of Setdb1 expression greatly impaired meiosis. It delayed meiotic resumption, altered the dynamics of chromatin condensation, and impaired kinetochore-spindle interactions, bipolar spindle organization and chromosome segregation in more mature oocytes. The observed phenotypes related to changes in abundance of specific transcripts in mutant oocytes. Setdb1maternally deficient embryos arrested during pre-implantation development and showed comparable defects during cell cycle progression and in chromosome segregation. Finally, transcriptional profiling data indicate that Setdb1 downregulates rather than silences expression of ERVK and ERVLMaLR retrotransposons and associated chimearic transcripts during oogenesis. Our results identify Setdb1 as a newly discovered meiotic and embryonic competence factor safeguarding genome integrity at
DYNAMIC TERM WEIGHTING FOR PERSONAL PHOTO RETRIEVAL

Personal photo retrieval is different from many sea rch tasks in that all the targets are either known to the use r, or they are about something the owner has seen. For this reason , generating queries for searching personal photos wi ll more likely rely on an individual’s memory. In a pilot s udy of Personal file re-finding, the results suggested a change of retrieval efficiency over time for different types of queries due to recall reliability. While auto-annotating of the photos with contextual information, we are seeking to deve lop a query weighting strategy, which takes the recall re liability into account, and give feedback to the user based o n the searching queries to improve the searching efficien cy.
High Performance Parallel Algorithms for the Tucker Decomposition of Sparse Tensors

We investigate an efficient parallelization of a class of algorithms for the well-known Tucker decomposition of general N-dimensional sparse tensors. The targeted algorithms are iterative and use the alternating least squares method. At each iteration, for each dimension of an N-dimensional input tensor, the following operations are performed: (i) the tensor is multiplied with (N - 1) matrices (TTMc step), (ii) the product is then converted to a matrix, and (iii) a few leading left singular vectors of the resulting matrix are computed (TRSVD step) to update one of the matrices for the next TTMc step. We propose an efficient parallelization of these algorithms for the current parallel platforms with multicore nodes. We discuss a set of preprocessing steps which takes all computational decisions out of the main iteration of the algorithm and provides an intuitive shared-memory parallelism for the TTM and TRSVD steps. We propose a coarse and a fine-grain parallel algorithm in a distributed memory environment, investigate data dependencies, and identify efficient communication schemes. We demonstrate how the computation of singular vectors in the TRSVD step can be carried out efficiently following the TTMc step. Finally, we develop a hybrid MPI-OpenMP implementation of the overall algorithm and report scalability results on up to 4096 cores on 256 nodes of an IBM BlueGene/Q supercomputer.
A Journey of Discovery : Orthogonal Matrices and Wireless Communications

Real orthogonal designs were first introduced in the 1970’s, followed shortly by the introduction of complex orthogonal designs. These designs can be described simply as square matrices whose columns are formally orthogonal, and their existence criteria depend on number theoretic results from the turn of the century. In 1999, generalizations of these designs were applied in the development of successful wireless communication systems, renewing interest in the theory of these orthogonal designs. This area of study represents a beautiful marriage of classical mathematics and modern engineering. This paper has two main goals. First, we provide a brief and accessible introduction to orthogonal design theory and related wireless communication systems. We include neither the mathematical proofs of the relevant results nor the technical implementation details, rather hoping that this gentle introduction will whet the reader’s appetite for further study of the relevant mathematics, the relevant engineering implementations, or, in the best case scenario, both. Second, in light of the dedication of this paper to Joe Gallian, who was an extraordinary undergraduate research advisor to so many of us and who inspired so many of us to become undergraduate research advisors ourselves, we describe the involvement of undergraduates in research involving these orthogonal designs and related communications systems.
Association of a sequence variant in DAB2IP with coronary heart disease

Aims A sequence variant, rs7025486[A], in DAB2IP on chromosome 9q33 has recently been associated with coronary heart disease (CHD). We sought to replicate this finding and to investigate associations with a panel of inflammatory and haemostatic biomarkers. We also sought to examine whether this variant, in combination with a chromosome 9p21 CHD variant (rs10757278) and the Framingham risk score (FRS), could improve the prediction of events compared with the FRS alone. Methods and results rs7025486 was genotyped in 1386 CHD cases and 3532 controls and was associated with CHD [odds ratio (OR) of 1.16, 95% confidence interval (CI) 1.05–1.29, P= 0.003]. Meta-analysis, using data from the original report and from genome-wide association studies in both the Wellcome Trust Case Control Consortium and the Cardiovascular Health Study, comprising 9968 cases and 20 048 controls, confirmed the association (OR of 1.10, 95% CI 1.06–1.14, P= 3.2 × 10−6). There was no association with a panel of CHD biomarkers, including any lipid, inflammation, or coagulation trait, nor with telomere length. Addition to the FRS of this variant plus rs10757278 on chromosome 9p21 improved the area under the receiver-operating characteristic curve (AROC) from 0.61 to 0.64 (P= 0.03) as well as improving the reclassification (net reclassification index = 11.1%, P= 0.007). Conclusion This study replicates a previous association of a variant in DAB2IP with CHD. Addition of multiple variants improves the performance of predictive models based upon classical cardiovascular risk factors.
Inhibition of the Kit Ligand/c-Kit Axis Attenuates Metastasis in a Mouse Model Mimicking Local Breast Cancer Relapse after Radiotherapy

Purpose: Local breast cancer relapse after breast-saving surgery and radiotherapy is associated with increased risk of distant metastasis formation. The mechanisms involved remain largely elusive. We used the well-characterized 4T1 syngeneic, orthotopic breast cancer model to identify novel mechanisms of postradiation metastasis. Experimental Design: 4T1 cells were injected in 20 Gy preirradiated mammary tissue to mimic postradiation relapses, or in nonirradiated mammary tissue, as control, of immunocompetent BALB/c mice. Molecular, biochemical, cellular, histologic analyses, adoptive cell transfer, genetic, and pharmacologic interventions were carried out. Results: Tumors growing in preirradiated mammary tissue had reduced angiogenesis and were more hypoxic, invasive, and metastatic to lung and lymph nodes compared with control tumors. Increased metastasis involved the mobilization of CD11b+c-Kit+Ly6GhighLy6Clow(Gr1+) myeloid cells through the HIF1-dependent expression of Kit ligand (KitL) by hypoxic tumor cells. KitL-mobilized myeloid cells homed to primary tumors and premetastatic lungs, to give rise to CD11b+c-Kit− cells. Pharmacologic inhibition of HIF1, silencing of KitL expression in tumor cells, and inhibition of c-Kit with an anti-c-Kit–blocking antibody or with a tyrosine kinase inhibitor prevented the mobilization of CD11b+c-Kit+ cells and attenuated metastasis. C-Kit inhibition was also effective in reducing mobilization of CD11b+c-Kit+ cells and inhibiting lung metastasis after irradiation of established tumors. Conclusions: Our work defines KitL/c-Kit as a previously unidentified axis critically involved in promoting metastasis of 4T1 tumors growing in preirradiated mammary tissue. Pharmacologic inhibition of this axis represents a potential therapeutic strategy to prevent metastasis in breast cancer patients with local relapses after radiotherapy. Clin Cancer Res; 18(16); 4365–74. ©2012 AACR.
An any order generalization of JADE for complex source signals

In this paper, considering the complex case, we extend some results leading to the popular JADE algorithm to cumulants of any order greater than or equal to three. We first exhibit a new contrast function which constitutes a generalization for the underlying contrast of JADE which thus appears as a particular case. Then we generalize the link between this new contrast and a joint-diagonalization criterion of a set of matrices. Moreover, in the two sources case, we show that the generalized contrast can be written as a simple quadratic form whatever the cumulant order. Finally, some computer simulations illustrate the potential advantage one can take of considering statistics of different orders for the joint-diagonalization of cumulant matrices.
Multi-antenna Cayley differential codes

Multiple antenna differential modulation using unitary matrices requires no channel knowledge at the receiver, and so is ideal for use on wireless links where channel tracking is undesirable or infeasible, either because of rapid changes in the channel characteristics or because of limited system resources. Although this basic principle is well understood, it is not known how to generate good-performing constellations of unitary matrices, for any number of transmit and receive antennas and especially at high rates. We propose a class of Cayley codes that works with any number of antennas, and allows for polynomial-time near-maximum-likelihood decoding based on either successive nulling/cancelling or sphere decoding. The codes use the Cayley transform, which maps the highly nonlinear Stiefel manifold of unitary matrices to the linear space of skew-Hermitian matrices. This leads to a simple linear constellation structure in the Cayley transform domain and to an information-theoretic design criterion based on emulating a Cauchy random matrix. Simulations show that Cayley codes allow efficient and effective high-rate data transmission in multi-antenna communication systems without knowing the channel.
Voltage Stability Enhancement Via Model Predictive Control of Load

Impending voltage collapse can often be avoided by appropriate control of loads. However the traditional form of load control (shedding) is unpopular due to the resulting consumer disruption. Advances in communications and computer systems allow more selective load control though. Individual loads that are sacrificeable in the short-term can be switched with minimal consumer disruption. The paper considers the use of such non-disruptive load control for improving voltage stability. A control strategy that is based on model predictive control (MPC) is proposed. MPC utilizes an internal model to predict system dynamic behaviour over a finite horizon. Control decisions are based on optimizing that predicted response. MPC is a discrete- time form of control, so inaccuracies in predicted behaviour are corrected at the next control interval. A standard 10 bus voltage collapse example is used to illustrate this control strategy.