Miracle-dz/UniFAR-FTUs huggingface dataset:
A Genome-Wide RNAi Screen Identifies Core Components of the G2-M DNA Damage Checkpoint

The DNA damage response in Drosophila requires the replication preinitiation complex and the MUS312 nuclease complex. Coping with Damage Genomic integrity is critical for cell and organismal survival; therefore, elaborate mechanisms have evolved to cope with DNA damage. By knocking down each Drosophila gene, Kondo and Perrimon identified 64 that were specifically important for the G2-M checkpoint and allowed continued mitosis after DNA damage with a drug that causes double-stranded DNA breaks. The authors verified the role of two complexes in the G2-M checkpoint through in vivo analysis in imaginal discs (clusters of cells that differentiate into adult tissues): the MUS312 nuclease complex that participates in resolving double-stranded breaks and the DNA replication preinitiation complex (pre-IC). The results of the screen also point to additional regulators of the G2-M checkpoint, thus paving the way for greater understanding of the differences and similarities between fly and vertebrate checkpoint responses. The DNA damage checkpoint, the first pathway known to be activated in response to DNA damage, is a mechanism by which the cell cycle is temporarily arrested to allow DNA repair. The checkpoint pathway transmits signals from the sites of DNA damage to the cell cycle machinery through the evolutionarily conserved ATM (ataxia telangiectasia mutated) and ATR (ATM- and Rad3-related) kinase cascades. We conducted a genome-wide RNAi (RNA interference) screen in Drosophila cells to identify previously unknown genes and pathways required for the G2-M checkpoint induced by DNA double-strand breaks (DSBs). Our large-scale analysis provided a systems-level view of the G2-M checkpoint and revealed the coordinated actions of particular classes of proteins, which include those involved in DNA repair, DNA replication, cell cycle control, chromatin regulation, and RNA processing. Further, from the screen and in vivo analysis, we identified previously unrecognized roles of two DNA damage response genes, mus101 and mus312. Our results suggest that the DNA replication preinitiation complex, which includes MUS101, and the MUS312-containing nuclease complexes, which are important for DSB repair, also function in the G2-M checkpoint. Our results provide insight into the diverse mechanisms that link DNA damage and the checkpoint signaling pathway.
Virtual electrodes by current steering in retinal prostheses.

PURPOSE Retinal prostheses are an approved treatment for vision restoration in retinal degenerative diseases; however, present implants have limited resolution and simply increasing the number of electrodes is limited by design issues. In cochlear implants, virtual electrodes can be created by simultaneous stimulation of adjacent physical electrodes (current steering). The present study assessed whether this type of current steering can be adapted for retinal implants. METHODS Suprachoroidal electrode arrays were implanted in four normally sighted cat eyes. Electrode pairs were driven simultaneously at different current levels and current ratios. Multiunit spiking activity in the visual cortex was recorded. Spike distribution across channels enabled generation of cortical activation maps and calculation of centroid positions. For each current configuration, centroid shifts between two virtual electrodes were compared to shifts obtained from physical electrode stimulation. RESULTS Using current steering, virtual electrodes with different cortical activation maps could be created. Cortical centroids were found to shift as a function of the current ratio used for virtual electrodes and were similar to the centroid shifts seen when using physical electrodes. In addition, the cortical response to stimulation of a physical electrode could be reproduced by applying current steering to electrodes on either side of the physical electrode. CONCLUSIONS These results suggest that current steering can alter activation patterns in the visual cortex and could enhance visual perception in retinal implants by eliciting phosphene percepts intermediate between those elicited by physical electrodes. These results inform development of new electrode arrays that can take advantage of current steering.
Kullback-Leibler Proximal Variational Inference

We propose a new variational inference method based on a proximal framework that uses the Kullback-Leibler (KL) divergence as the proximal term. We make two contributions towards exploiting the geometry and structure of the variational bound. First, we propose a KL proximal-point algorithm and show its equivalence to variational inference with natural gradients (e.g., stochastic variational inference). Second, we use the proximal framework to derive efficient variational algorithms for non-conjugate models. We propose a splitting procedure to separate non-conjugate terms from conjugate ones. We linearize the non-conjugate terms to obtain subproblems that admit a closed-form solution. Overall, our approach converts inference in a non-conjugate model to subproblems that involve inference in well-known conjugate models. We show that our method is applicable to a wide variety of models and can result in computationally efficient algorithms. Applications to real-world datasets show comparable performances to existing methods.
Argobots: A Lightweight Low-Level Threading and Tasking Framework

In the past few decades, a number of user-level threading and tasking models have been proposed in the literature to address the shortcomings of OS-level threads, primarily with respect to cost and flexibility. Current state-of-the-art user-level threading and tasking models, however, either are too specific to applications or architectures or are not as powerful or flexible. In this paper, we present Argobots, a lightweight, low-level threading and tasking framework that is designed as a portable and performant substrate for high-level programming models or runtime systems. Argobots offers a carefully designed execution model that balances generality of functionality with providing a rich set of controls to allow specialization by end users or high-level programming models. We describe the design, implementation, and performance characterization of Argobots and present integrations with three high-level models: OpenMP, MPI, and colocated I/O services. Evaluations show that (1) Argobots, while providing richer capabilities, is competitive with existing simpler generic threading runtimes; (2) our OpenMP runtime offers more efficient interoperability capabilities than production OpenMP runtimes do; (3) when MPI interoperates with Argobots instead of Pthreads, it enjoys reduced synchronization costs and better latency-hiding capabilities; and (4) I/O services with Argobots reduce interference with colocated applications while achieving performance competitive with that of a Pthreads approach.
FPGA Based Partial Reconfigurable One Dimensional Median Filter Design

: The median of a set of samples in the word-level sorting network is often computed by first sorting the input samples and then selecting the middle value. The power consumption is reduced by decreasing the number of signal transitions in the circuit. This can be done by keeping the stored samples immobile in the window through the use of a token ring in our architecture. The experimental results have shown that, at the expense of some additional area cost, the power consumption can be successfully reduced. This paper proposes new architecture which is implemented as a two-stage pipeline, the median output, which is the sample with median rank, will also be generated at each cycle. The improvement in power consumption is achieved by utilizing a token ring in our architecture. Since the stored samples in the window are immobile, our architecture is suitable for low-power applications.
Compartmental Models Simulating a Dichotomy of Action Potential Backpropagation in Ca1 Pyramidal Neuron Dendrites

In hippocampal CA1 pyramidal neurons, action potentials are typically initiated in the axon and backpropagate into the dendrites, shaping the integration of synaptic activity and influencing the induction of synaptic plasticity. Despite previous reports describing action-potential propagation in the proximal apical dendrites, the extent to which action potentials invade the distal dendrites of CA1 pyramidal neurons remains controversial. Using paired somatic and dendritic whole cell recordings, we find that in the dendrites proximal to 280 microm from the soma, single backpropagating action potentials exhibit <50% attenuation from their amplitude in the soma. However, in dendritic recordings distal to 300 microm from the soma, action potentials in most cells backpropagated either strongly (26-42% attenuation; n = 9/20) or weakly (71-87% attenuation; n = 10/20) with only one cell exhibiting an intermediate value (45% attenuation). In experiments combining dual somatic and dendritic whole cell recordings with calcium imaging, the amount of calcium influx triggered by backpropagating action potentials was correlated with the extent of action-potential invasion of the distal dendrites. Quantitative morphometric analyses revealed that the dichotomy in action-potential backpropagation occurred in the presence of only subtle differences in either the diameter of the primary apical dendrite or branching pattern. In addition, action-potential backpropagation was not dependent on a number of electrophysiological parameters (input resistance, resting potential, voltage sensitivity of dendritic spike amplitude). There was, however, a striking correlation of the shape of the action potential at the soma with its amplitude in the dendrite; larger, faster-rising, and narrower somatic action potentials exhibited more attenuation in the distal dendrites (300-410 microm from the soma). Simple compartmental models of CA1 pyramidal neurons revealed that a dichotomy in action-potential backpropagation could be generated in response to subtle manipulations of the distribution of either sodium or potassium channels in the dendrites. Backpropagation efficacy could also be influenced by local alterations in dendritic side branches, but these effects were highly sensitive to model parameters. Based on these findings, we hypothesize that the observed dichotomy in dendritic action-potential amplitude is conferred primarily by differences in the distribution, density, or modulatory state of voltage-gated channels along the somatodendritic axis.
Magnetism with generalized-gradient-approximation density functionals.

We report generalized-gradient-approximation (GGA) density-functional studies of Cr, V, and Pd, using an all-electron, general-potential linearized-augmented-plane-wave technique. These calculations were undertaken in order to assess the utility of the GGA as an improvement over the local-density approximation in describing transition-metal magnetism. It is found that although the tendency towards magnetism is enhanced, both V and Pd are correctly predicted to be nonmagnetic with the recent GGA functional of Perdew (PW GGA-II) as with the Langreth-Mehl-Hu (LM) functional
Novel recurrently mutated genes and a prognostic mutation signature in colorectal cancer

Background Characterisation of colorectal cancer (CRC) genomes by next-generation sequencing has led to the discovery of novel recurrently mutated genes. Nevertheless, genomic data has not yet been used for CRC prognostication. Objective To identify recurrent somatic mutations with prognostic significance in patients with CRC. Method Exome sequencing was performed to identify somatic mutations in tumour tissues of 22 patients with CRC, followed by validation of 187 recurrent and pathway-related genes using targeted capture sequencing in additional 160 cases. Results Seven significantly mutated genes, including four reported (APC, TP53, KRAS and SMAD4) and three novel recurrently mutated genes (CDH10, FAT4 and DOCK2), exhibited high mutation prevalence (6–14% for novel cancer genes) and higher-than-expected number of non-silent mutations in our CRC cohort. For prognostication, a five-gene-signature (CDH10, COL6A3, SMAD4, TMEM132D, VCAN) was devised, in which mutation(s) in one or more of these genes was significantly associated with better overall survival independent of tumor-node-metastasis (TNM) staging. The median survival time was 80.4 months in the mutant group versus 42.4 months in the wild type group (p=0.0051). The prognostic significance of this signature was successfully verified using the data set from the Cancer Genome Atlas study. Conclusions The application of next-generation sequencing has led to the identification of three novel significantly mutated genes in CRC and a mutation signature that predicts survival outcomes for stratifying patients with CRC independent of TNM staging.
Optimal OSTBC sequence detection over unknown correlated fading channels

We prove that maximum-likelihood (ML) noncoherent sequence detection of orthogonal space-time block coded (OSTBC) signals can be performed in polynomial time with respect to the sequence length for time-varying Rayleigh or Ricean distributed, correlated (in general) channel coefficients, if the mean channel vector belongs to the range of the channel co-variance matrix. We develop a novel algorithm that, provided the above condition, performs ML noncoherent sequence detection with polynomial complexity the order of which equals twice the rank of the channel covariance matrix. Therefore, for Rayleigh fading, polynomial ML noncoherent detection complexity is always guaranteed; the lower the channel covariance rank the lower the receiver complexity. Instead, for Ricean fading, full-rank channel correlation is desired to guarantee polynomial ML noncoherent detection complexity.
OFDMA Capacity Analysis in MIMO Channels

In this paper, the performance of orthogonal frequency division multiple access orthogonal frequency division multiple access (OFDMA) is studied in the context of the general multiuser multicarrier multiple-input multiple-output (MIMO) (M3) system for both uplink (UP) and downlink (DL) channels. The relationship between OFDMA and the optimal M3 solution is investigated from an information theoretical point of view. Specifically, the necessary and sufficient conditions of OFDMA being the capacity-maximizing M3 transmission scheme is derived. In addition, OFDMA optimality is explicitly analyzed in some special cases.
An Adaptive MAC Protocol for Infrastructure Wireless Sensor Networks

This paper proposes ISS-Mac, an efficient MAC protocol for infrastructure-supported low-power wireless sensor networks. A central base station (sink node) is responsible for wide-network synchronization and multi-hop TDMA slots allocation. Providing an accurate topology information to the base station requires a lot of signaling overhead which affects energy efficiency of the protocol. We propose a progressive topology construction scheme to minimize this overhead and enhance scalability. In addition, the protocol facilitates integration of new nodes into the network while operation. Performance evaluation of the protocol shows that it achieves high energy savings compared to the popular S-MAC and the Full Active CSMA protocols.
Organizational Intrusion: Organization Mining Using Socialbots

In the recent years we have seen a significant growth in the usage of online social networks. Common networks like Facebook, Twitter, Pinterest, and Linked In have become popular all over the world. In these networks users write, share, and publish personal information about themselves, their friends, and their workplace. In this study we present a method for the mining of information of an organization through the use of social networks and social bots. Our social bots sent friend requests to Facebook users who work in a targeted organization. Upon accepting a socialbot's friend request, users unknowingly expose information about themselves and about their workplace. We tested the proposed method on two real organizations and successfully infiltrated both. Compared to our previous study, our method was able to discover up to 13.55% more employees and up to 18.29% more informal organizational links. Our results demonstrate once again that organizations which are interested in protecting themselves should instruct their employees not to disclose information in social networks and to be cautious of accepting friendship requests from unknown persons.
Gastrulation in Calcareous Sponges: In Search of Haeckel's Gastraea1

Abstract Haeckel's studies of development in calcareous sponges (1872) led him to develop the “Gastraea Theory,” which proposes that the ancestral mode of germ layer formation, or gastrulation, was by invagination to produce a functional gut. His observations that gastrulation in the Calcarea occurs by invagination of a ciliated larva upon settlement and metamorphosis were supported by remarkable photomicrographs of the stage by Hammer in 1908. Although no later work found the same stage, these concepts are repeated in texts today. We have re-examined embryogenesis and metamorphosis in Sycon sp. cf. S. raphanus in order to understand when gastrulation occurs. Almost all larvae settle on their ciliated anterior pole and metamorphose into a bilayered juvenile whose interior cells rapidly differentiate into choanocytes and other cells of the young sponge. After a four-year search we have found the transitory stage shown by Hammer in which the anterior cells invaginate into the posterior half of the larva. The hole closes and it is not until some days later that the sponge forms an osculum at its apical pole. To understand whether invagination comprises gastrulation and if the hole can be considered to be a blastopore we have carried out a review of the literature dealing with this brief moment in calcaronean sponge development. Despite the intrigue of this type of metamorphosis, we conclude that gastrulation occurs earlier, during formation of the two cellular regions of the larva, and that metamorphosis involves the reorganization of these already differentiated regions. Considering the pivotal position occupied by the Calcarea as the possible sister-group to all other Metazoa, these results call for a reassessment of germ layer formation and of the relationships of the primary germ layers among basal metazoan phyla.
Histopathological Analysis of the Respiratory Tract

The basic anatomy of the mouse respiratory system is similar to that of other mammals and can be usefully examined under the light microscope in phenotyping studies, inhalation toxicity studies, and studies involving mouse models of human disease. In many studies, however, only the lungs are examined, leaving the possibility that phenotypic information from the majority of the conducting airways is lost. This unit provides standard approaches for tissue collection at necropsy and subsequent selection of a range of respiratory tissues for histological and pathological analysis. The major anatomical features to be found in each section are highlighted, and potential artifacts and methods to avoid them are discussed. © 2014 by John Wiley & Sons, Inc.
Relationship between sublingual and intestinal microcirculatory perfusion in patients with abdominal sepsis*

Objective:To evaluate the relation between sublingual and intestinal microcirculatory alterations in patients with abdominal sepsis. Design:Prospective observational study. Setting:A 23-bed mixed intensive care unit of a tertiary teaching hospital. Patients:Twenty-three patients with abdominal sepsis and a newly constructed intestinal stoma were included in the study group. Nineteen outpatient healthy individuals with an intestinal stoma and ten nonsepsis patients with a <24-hr-old intestinal stoma were included as controls. Interventions:None. Measurements and Main Results:Orthogonal polarization spectral imaging of the sublingual and intestinal microcirculation was performed on days 1 and 3. In addition, variables of systemic hemodynamics, such as cardiac index, heart rate, blood pressure, central venous pressure, and dosages of vasopressor and inotropic agents, were obtained. On day 1 there was no correlation of the microvascular flow index between the sublingual and intestinal microcirculatory beds (Spearman's rho [rs] = .12; 95% confidence interval, −.51 to .31; p = .59). Furthermore, there was no significant correlation between microcirculatory alterations and variables of systemic circulation (rs ≤ .25). On day 3, however, a correlation between sublingual and intestinal microcirculatory flow appeared to be restored (rs = .74; 95% confidence interval, .28–.92; p = .006), mainly due to a normalization of flow in both regions. Conclusions:On day 1 of abdominal sepsis there is a complete dispersion of flow, not only between hemodynamic compartments of a different order but also between the sublingual and intestinal microcirculation. Over time, both sublingual and intestinal microvascular flow indexes trended to normal values.
Quantitative texture analysis for Glioblastoma phenotypes discrimination

A quantitative texture analysis for discriminating GBM phenotypes in brain magnetic resonance (MR) images is proposed. GBM phenotypes captured using semi-automatic segmentation based on 3D Slicer Scripts. Segmentation was applied on the registered images considered the T1-Weighted and FLAIR sequence. Texture feature has been extracted from the gray level co-occurrence matrix (GLCM) based on GBM phenotypes. Feature vectors are then used in training a minimum distance classifier based on Mahalanobis distance metric. Simulation results for 13 patients show the highest accuracy of 67% based on the feature extraction from GLCM with offset =1 and 8 phases. Preliminary texture analysis demonstrated that the texture feature based on the GLCM is promising to distinguish GBM phenotypes.
Predicting Internet Path Dynamics and Performance with Machine Learning

—In this paper, we study the problem of predicting Internet path changes and path performance using traceroute measurements and machine learning models. Path changes are frequently linked to path inﬂation and performance degradation; therefore, predicting their occurrence is highly relevant for performance monitoring and dynamic trafﬁc engineering. We introduce NETPerfTrace, an Internet Path Tracking system capable of forecasting path changes and path latency variations. By relying on decision trees and using empirical distribution based input features, we show that NETPerfTrace can predict (i) the remaining life time of a path before it actually changes and (ii) the number of path changes in a certain time-slot with high accuracy. Through extensive evaluation, we demonstrate that NETPerfTrace highly outperforms DTRACK, a previous system with the same prediction targets. NETPerfTrace also offers path performance forecasting capabilities. In particular, it can predict path latency metrics, providing a system which could not only predict path changes but also forecast their impact in terms of performance variations. As an additional contribution, we release NETPerfTrace as open software to the networking community.