Miracle-dz/UniFAR-FTUs huggingface dataset:
Scalable Transcriptome Preparation for Massive Parallel Sequencing

Background The tremendous output of massive parallel sequencing technologies requires automated robust and scalable sample preparation methods to fully exploit the new sequence capacity. Methodology In this study, a method for automated library preparation of RNA prior to massively parallel sequencing is presented. The automated protocol uses precipitation onto carboxylic acid paramagnetic beads for purification and size selection of both RNA and DNA. The automated sample preparation was compared to the standard manual sample preparation. Conclusion/Significance The automated procedure was used to generate libraries for gene expression profiling on the Illumina HiSeq 2000 platform with the capacity of 12 samples per preparation with a significantly improved throughput compared to the standard manual preparation. The data analysis shows consistent gene expression profiles in terms of sensitivity and quantification of gene expression between the two library preparation methods.
Comparative and Prospective Study of Different Immune Parameters in Healthy Subjects at Risk for Tuberculosis and in Tuberculosis Patients

ABSTRACT It has not been fully elucidated which of the components of the immune response against Mycobacterium tuberculosis is indicative of resistance or susceptibility. The aim of this study was to identify an immune parameter that could be indicative of either resistance or susceptibility to M. tuberculosis infection. We prospectively studied (three determinations, at months 0, 8, and 12) 15 patients with chronic pulmonary tuberculosis and 42 healthy individuals with a recent and frequent contact with tuberculosis patients. Peripheral blood mononuclear cells were stimulated with a whole-protein extract or the 30-kDa antigen of M. tuberculosis for 6 days, and several immune parameters were determined. No consistent differences between tuberculosis patients and healthy controls were detected in most immune parameters studied, including the expression of different activation antigens, cytokine secretion, lymphocyte proliferation, and nitric oxide production. However, the synthesis of tumor necrosis factor alpha, the intracellular detection of gamma interferon, and the apoptosis of monocytes under certain culture conditions tended to show clear-cut differences in cells from patients and controls (P < 0.05 in all cases for most determinations). Nevertheless, when results were analyzed on an individual basis, it was evident that a significant degree of overlapping of values from patients and controls occurred for all parameters studied. We conclude that although the immune parameters tested do not allow the identification of individuals susceptible to M. tuberculosis, the specificity and sensitivity of some of them could be improved through future studies.
Online Multiple Workflow Scheduling under Privacy and Deadline in Hybrid Cloud Environment

Organizations overcome resource shortages by utilizing the multiple services of cloud providers. This leads to sharing resources among various public and private clouds in order to improve the performance while executing the organization's complex workflow systems. Executing multiple workflows in such a hybrid environment needs an effective mapping between workflow's tasks and cloud resources that considers the trade-off between budget and time. There is also a challenge when organizations are forced to deploy workflow's tasks on public resources to execute the tasks before their requested deadlines without violating customers' privacy. In recent years, several online and static approaches were presented to schedule single or multiple workflows considering deadline and budget in cloud environments. However, these studies neglect the privacy constraint along with other SLAs such as deadline and budget. In this paper, we present two online algorithms to schedule multiple workflows under deadline and privacy constraints, while considering the dynamic nature of hybrid cloud environment. The proposed algorithms were evaluated with a series of simulation as well as real experiments using real-life privacy constrained healthcare workflows. Our two algorithms use different methods to rank the tasks: one utilises a novel technique for ranking, the other uses a similar approach to current existing studies. Results show that the novel approach outperforms the current existing ranking methods.
KMS, etc

A general form of the “Wick rotation”, starting from imaginarytime Green functions of quantum-mechanical systems in thermal equilibrium at positive temperature, is established. Extending work of H. Araki, the rôle of the KMS condition and of an associated anti-unitary symmetry operation, the “modular conjugation”, in constructing analytic continuations of Green functions from realto imaginary times, and back, is clarified. The relationship between the KMS condition for the vacuum with respect to Lorentz boosts, on one hand, and the spin-statistics connection and the PCT theorem, on the other hand, in local, relativistic quantum field theory is recalled. General results on the reconstruction of local quantum theories in various nontrivial gravitational backgrounds from “Euclidian amplitudes” are presented. In particular, a general form of the KMS condition is proposed and applied, e.g., to the Unruhand the Hawking effects. This paper is dedicated to Huzihiro Araki on the occasion of his seventieth birthday, with admiration, affection and best wishes.
Online learning for object identification by a mobile robot

Object identification for a situated robot is a first step towards many relevant behaviours such as human-robot communication, object tracking, object detection, etc. However, the dynamic and unpredictable nature of the world makes it very difficult to design such algorithms. Our goal is to endow a PIONEER 2DX autonomous mobile robot with the ability to learn how to identify objects from its environment, and to maintain this ability through time. In order to do so, we propose an architecture that continuously looks for relevant visual invariant properties related to target objects thanks to online learning techniques.
Risk Aversion, Performance Pay, and the Principal-Agent Problem

This paper calculates numerical solutions to the principal-agent problem and compares the results to the stylized facts of CEO compensation. The numerical predictions come from parameterizing the models of Grossman and Hart and of Holmstrom and Milgrom. While the correct incentives for a CEO can greatly enhance a firm's performance, providing such incentives need not be expensive. For many parameter values, CEO compensation need increase only by about $10 for every $1,000 of additional shareholder value; for some values, the amount is 0.003 cents.
A GA-Based Approach to Hide Sensitive High Utility Itemsets

A GA-based privacy preserving utility mining method is proposed to find appropriate transactions to be inserted into the database for hiding sensitive high utility itemsets. It maintains the low information loss while providing information to the data demanders and protects the high-risk information in the database. A flexible evaluation function with three factors is designed in the proposed approach to evaluate whether the processed transactions are required to be inserted. Three different weights are, respectively, assigned to the three factors according to users. Moreover, the downward closure property and the prelarge concept are adopted in the proposed approach to reduce the cost of rescanning database, thus speeding up the evaluation process of chromosomes.
Modelling MEH-PPV:PCBM (1:4) bulk heterojunction solar cells

Basic solar cell characteristics were examined in an organic bulk heterojunction device. The active layer is a spincoated organic blend of a pmaterial (MEH-PPV) and an n-material (the fullerene derivative PCBM), sandwiched between a transparent ITO-PEDOT/PSS electrode and an Al/LiF back-contact. We carried out light and dark I-V and spectral response measurements and measured the transparency of the active layer. Modelling of organic bulk-heterojunction solar cells is difficult because of the complicated geometry and because of the microscopic scale of the internal mechanisms. We applied an effective medium model in which the whole p-n nanostructure is represented by one single effective semiconductor layer, which then is fed into a standard solar cell device simulator, e.g. SCAPS. First, a parameter set was built up that simulates the measured characteristics of the MEH-PPV / PCBM blend cells. The dark and illuminated I-V, and the spectral response measurements are fitted fairly well. A parameter set for the effective medium model was sought and found that describes (with qualitative agreement) the measured I-V curves. This parameter was then used for a numerical parameter study. Critical issues for cell performance were identified, and their influence quantified (based on the actual parameter set for MEHPPV-PCBM cells). First, the cell performance is sensitive to the electron and hole mobilities in the materials: the efficiency increases monotonously with increasing mobility, over many decades. The sensitivity is about 25 % relative efficiency gain for an order of magnitude of increase of the mobilities. Second, the poor absorption of the solar illumination is a cause of weak performance. We investigated the influence on cell thickness, and of the absorption characteristic.
Hiring in the Global Stage: Profiles of Online Contributions

Managers are increasingly using online contributions to make hiring decisions. However, it is nontrivial to find the relevant information of candidates in large online, global communities. We present Visual Resume, a novel tool that aggregates information on contributions across two different types of peer production sites (a code hosting site and a technical Q&A forum). Visual Resume displays summaries of developers' contributions, and allows easy access to contribution details. It also facilitates pairwise comparisons of candidates through a card-based design. Our study, involving participants from global organizations or corporations that draw from the global community, indicates that Visual Resume facilitated hiring decisions, both technical and soft skills were important when making these decisions.
Visualizing Motion Data in Virtual Reality: Understanding the Roles of Animation, Interaction, and Static Presentation

We present a study of interactive virtual reality visualizations of scientific motions as found in biomechanics experiments. Our approach is threefold. First, we define a taxonomy of motion visualizations organized by the method (animation, interaction, or static presentation) used to depict both the spatial and temporal dimensions of the data. Second, we design and implement a set of eight example visualizations suggested by the taxonomy and evaluate their utility in a quantitative user study. Third, together with biomechanics collaborators, we conduct a qualitative evaluation of the eight example visualizations applied to a current study of human spinal kinematics. Results suggest that visualizations in this style that use interactive control for the time dimension of the data are preferable to others. Within this category, quantitative results support the utility of both animated and interactive depictions for space; however, qualitative feedback suggest that animated depictions for space should be avoided in biomechanics applications.
Drosophila Experimental evolution with

[PDF] [Full Text] [Abstract] , March 15, 2010; 213 (6): 870-880. J Exp Biol A. A. Hoffmann : patterns and implications Drosophila Physiological climatic limits in [PDF] [Full Text] [Abstract] , April 20, 2010; 107 (16): 7359-7364. PNAS Rebecca D. Schulte, Carsten Makus, Barbara Hasert, Nico K. Michiels and Hinrich Schulenburg of an animal host and its microbial parasite Multiple reciprocal adaptations and rapid genetic change upon experimental coevolution
Many-body T-matrix of a two-dimensional Bose–Einstein condensate within the Hartree–Fock–Bogoliubov formalism

In a two-dimensional Bose–Einstein condensate, the reduction in dimensionality fundamentally influences collisions between the atoms. In the crossover regime from three to two dimensions, several scattering parameters have been considered. However, finite temperature results are more difficult to obtain. In this work, we present the many-body T-matrix at finite temperatures within a gapless Hartree–Fock–Bogoliubov approach and compare to zero and finite temperature results obtained using different approaches. A semi-classical renormalization method is used to remove the ultraviolet divergence of the anomalous average.
“Put-that-there”: Voice and gesture at the graphics interface

Recent technological advances in connected-speech recognition and position sensing in space have encouraged the notion that voice and gesture inputs at the graphics interface can converge to provide a concerted, natural user modality. The work described herein involves the user commanding simple shapes about a large-screen graphics display surface. Because voice can be augmented with simultaneous pointing, the free usage of pronouns becomes possible, with a corresponding gain in naturalness and economy of expression. Conversely, gesture aided by voice gains precision in its power to reference.
The Price of Synchrony: Evaluating the Resistive Losses in Synchronizing Power Networks

This paper investigates the resistive power losses that are incurred in keeping a network of synchronous generators in a synchronous state. These losses arise due to the transient powerflow fluctuations that occur when the system is perturbed from a synchronous state by a small transient event or in the face of persistent stochastic disturbances. We call these losses the “price of synchrony,” as they reflect the real power-flow costs incurred in resynchronizing the system. In the case of small fluctuations at each generator node, we show how the total network's resistive losses can be quantified using an H2 norm of a linear system of coupled swing equations subject to distributed disturbances. This norm is shown to be a function of transmission-line and generator properties, to scale unboundedly with network size, and to be weakly dependent on the network topology. This conclusion differentiates the price of synchrony from typical power systems stability notions, which show highly connected networks to be more coherent and, thus, easier to synchronize. In particular, the price of synchrony is more dependent on a network's size than its topology. We discuss possible implications of these results in terms of the design of future power grids, which are expected to have highly distributed generation resources leading to larger networks with the potential for greater transient losses.
Spanish Version of Test MIS ( * ) with Delayed Memory Recall Normative Values and Results in a Population with Mild Cognitive Impairment

Background: Cognitive impairment becomes more common with ageing and may benefit from intervention. In a Spanish speaking population, detection of cognitive impairment by a general practitioner in Primary Care can be a problem, as many of the standard tests target English speaking populations. The Memory Impairment Screen (MIS-A) is a validated test using English words to detect Alzheimer’s Disease (AD) and other dementias. We have modified this test to suit a Spanish speaking population and added a new component, delayed recall. We have called our new test the Memory Impairment Screen with Delayed Recall (MIS-D). Objectives: 1) To test a Spanish version of MIS-A and MIS-D. 2) To assess the discriminative validity of MIS-D as a screening tool for the amnestic variant of Mild Cognitive Impairment (aMCI) in a group of Spanish speaking people aged 65 years old and over. Methods: A case-control study of a cohort of 739 native Spanish speaking residents of Buenos Aires aged 65 years old and over, of whom 436 were healthy controls and 303 had a diagnosis of aMCI. Measurements: Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NVP) were estimated for MIS-D and MIS-A. Results: Normative values for MIS-A and MIS-D were obtained from the control population. Both age and education significantly affected these values (p < 0.0001). Control participants showed significant differences for both modalities, MIS-A and MIS-D. The cut-off for MIS-A should be 7.5 and for MIS-D, 5.5. Comparison between control population and aMCI population using ROC curve gave a result of 5.5 in MIS-D, with 97% specificity and 76% sensitivity. Conclusion: MIS-D was positively predictive of aMCI, with 97% specificity and 76% sensitivity in a sample of Spanish speaking patients aged 65 years old and over in Buenos Aires.
Integrate statistical model and lexical knowledge for Chinese multiword chunking

Multiword chunking is designed as a shallow parsing technique to recognize external constituent and internal relation tags of a chunk in sentence. In this paper, we propose a new solution to deal with this problem. We design a new relation tagging scheme to represent different intra-chunk relations and make several experiments of feature engineering to select a best baseline statistical model. We also apply outside knowledge from a large-scale lexical relationship knowledge base to improve parsing performance. By integrating all above techniques, we develop a new Chinese MWC parser. Experimental results show its parsing performance can greatly exceed the rule-based parser trained and tested in the same data set.
The Influence of Light Hypothenar Contact during a Reaching Movement on the Centre of Pressure (COP) Forward Displacement

The purpose of this study was to evaluate the effect of additional light hand contact (F<1 N) in the region of the hypothenar eminence on forward movement of the center of pressure (COP) and dominant hand. Subjects sled their hypothenar eminence on a vertically-oriented pressure sensitive board while reaching forward beyond their arm length. In the two separate experiments forty nine healthy, college-aged volunteers participated in the study. Thirty subjects (mean age of 22.2±2.4 years, 6 male and 24 female) participated in the experiment on level ground and nineteen subjects (22±2.6 years, 5 male and 14 female) in the experiment on an elevated surface. The forward displacement of the COP was significantly larger (p = 0.002) when subjects were allowed to slide with the hand as compared to no contact when the activity occurred on level ground (84±10 mm and 79±11 mm, respectively), and on a one meter elevated surface (71±17 mm and 65±21 mm, respectively). The maximal forward reach of the dominant hand was significantly greater when subjects were allowed to slide with the hypothenar eminence as compared to the no contact condition on the level ground (336±35 mm and 344±38 mm, respectively, p<0.02), and on the one meter elevated surface (298±58 mm and 307±58 mm, respectively, p<0.01). This data indicate that subjects were able to use additional haptic information from the hypothenar region to bring their COP and dominant hand further forward while standing on level ground as well as on a one m elevated surface.
Robust adaptive beamforming algorithms using the constrained constant modulus criterion

The authors present a robust adaptive beamforming algorithm based on the worst-case (WC) criterion and the constrained constant modulus (CCM) approach, which exploits the constant modulus property of the desired signal. Similar to the existing worst-case beamformer with the minimum variance design, the problem can be reformulated as a second-order cone programme and solved with interior point methods. An analysis of the optimisation problem is carried out and conditions are obtained for enforcing its convexity and for adjusting its parameters. Furthermore, low-complexity robust adaptive beamforming algorithms based on the modified conjugate gradient and an alternating optimisation strategy are proposed. The proposed low-complexity algorithms can compute the existing WC constrained minimum variance and the proposed WC-CCM designs with a quadratic cost in the number of parameters. Simulations show that the proposed WC-CCM algorithm performs better than existing robust beamforming algorithms. Moreover, the numerical results also show that the performances of the proposed low-complexity algorithms are equivalent or better than that of existing robust algorithms, whereas the complexity is more than an order of magnitude lower.
Laboratoire D'arithmétique, Calcul Formel Et D'optimisation Limited Memory Solution of Complementarity Problems Arising in Video Games Limited Memory Solution of Complementarity Problems Arising in Video Games *

We describe the solution of a complementarity problem with limited memory resources. The problem arises from physical simulations occurring within video games. The motivating problem is outlined, along with a simple interior point approach for its solution. Various linear algebra issuesc arising in the implementation are explored, including preconditioning, ordering and a number of ways of solving an equivalent augmented system. Alternative approaches are briefly surveyed , and some recommendations for solving these types of problems are given.
Modelling and Control of the Barrett Hand for Grasping

Grasping of an object by robot hand is always challenging due to the uncertainties such as robot non-linearities, unstructured objects with unknown location and stiffness, unknown contact types. To address these challenges, the fundamental task is to achieve the mathematical model of the robot hand, collect information about the object and model the contact between the hand and the object. In this paper, mathematical model of a three fingered Barrett Hand is developed using the Lagrangian method. Joint and cartesian space motions are simulated on the basis of computed torque algorithm. A contact model is then developed for hand-object coupled system assuming that the object properties are well known. Contact model is also simulated under different environment stiffness. Simulation studies verify the joint and cartesian space motions along with the estimated contact force. Implementation of the control for optimizing the contact force will be presented soon.
New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq

Recent advances in high‐throughput sequencing present a new opportunity to deeply probe an organism's transcriptome. In this study, we used Illumina‐based massively parallel sequencing to gain new insight into the transcriptome (RNA‐Seq) of the human malaria parasite, Plasmodium falciparum. Using data collected at seven time points during the intraerythrocytic developmental cycle, we (i) detect novel gene transcripts; (ii) correct hundreds of gene models; (iii) propose alternative splicing events; and (iv) predict 5′ and 3′ untranslated regions. Approximately 70% of the unique sequencing reads map to previously annotated protein‐coding genes. The RNA‐Seq results greatly improve existing annotation of the P. falciparum genome with over 10% of gene models modified. Our data confirm 75% of predicted splice sites and identify 202 new splice sites, including 84 previously uncharacterized alternative splicing events. We also discovered 107 novel transcripts and expression of 38 pseudogenes, with many demonstrating differential expression across the developmental time series. Our RNA‐Seq results correlate well with DNA microarray analysis performed in parallel on the same samples, and provide improved resolution over the microarray‐based method. These data reveal new features of the P. falciparum transcriptional landscape and significantly advance our understanding of the parasite's red blood cell‐stage transcriptome.