Miracle-dz/UniFAR-FTUs huggingface dataset:
A robust speaker recognition system combining factor analysis techniques

In this paper we implement state of the art factor analysis based methods and fused their scores to gain a channel robust speaker recognition system. These two methods are joint factor analysis (JFA) and i-Vector which define low-dimensional speaker and channel dependent spaces. For score fusion we propose a simple weight computation without training step. We experiment our method on two conditions; 1) in channel matched training and test channel (telephone in training phase/telephone in test phase) task and 2) the channel mismatched condition (telephone training phase/microphone, GSM and VOIP in test phase) task. Our strategies outperform a state-of-the-art GMM-UBM based system. We obtained more than 4% absolute EER improvement for both channel dependent and channel independent condition compared to the standard GMM-UBM based method. Simulation also results that the combined system based on i-Vector and JFA gives better performance than all implemented method.
Fast automatic skinning transformations

Skinning transformations are a popular way to articulate shapes and characters. However, traditional animation interfaces require all of the skinning transformations to be specified explicitly, typically using a control structure (a rig). We propose a system where the user specifies only a subset of the degrees of freedom and the rest are automatically inferred using nonlinear, rigidity energies. By utilizing a low-order model and reformulating our energy functions accordingly, our algorithm runs orders of magnitude faster than previous methods without compromising quality. In addition to the immediate boosts in performance for existing modeling and real time animation tools, our approach also opens the door to new modes of control: disconnected skeletons combined with shape-aware inverse kinematics. With automatically generated skinning weights, our method can also be used for fast variational shape modeling.
Loss of the Oxygen Sensor PHD3 Enhances the Innate Immune Response to Abdominal Sepsis

Hypoxia and HIFs (HIF-1α and HIF-2α) modulate innate immune responses in the setting of systemic inflammatory responses and sepsis. The HIF prolyl hydroxylase enzymes PHD1, PHD2 and PHD3 regulate the mammalian adaptive response to hypoxia; however, their significance in the innate immune response has not been elucidated. We demonstrate in this study that deficiency of PHD3 (PHD3−/−) specifically shortens the survival of mice subjected to various models of abdominal sepsis because of an overwhelming innate immune response, leading to premature organ dysfunction. By contrast, this phenotype was absent in mice deficient for PHD1 (PHD1−/−) or PHD2 (PHD2+/−). In vivo, plasma levels of proinflammatory cytokines were enhanced, and recruitment of macrophages to internal organs was increased in septic PHD3-deficient mice. Reciprocal bone marrow transplantation in sublethally irradiated mice revealed that enhanced susceptibility of PHD3-deficient mice to sepsis-related lethality was specifically caused by loss of PHD3 in myeloid cells. Several in vitro assays revealed enhanced cytokine production, migration, phagocytic capacity, and proinflammatory activation of PHD3-deficient macrophages. Increased proinflammatory activity of PHD3-deficient macrophages occurred concomitantly with enhanced HIF-1α protein stabilization and increased NF-κB activity, and interference with the expression of HIF-1α or the canonical NF-κB pathway blunted their proinflammatory phenotype. It is concluded that impairment of PHD3 enzyme function aggravates the clinical course of abdominal sepsis via HIF-1α– and NF-κB–mediated enhancement of the innate immune response.
Learning location naming from user check-in histories

Many innovative location-based services have been established in order to facilitate users' everyday lives. Usually, these services cannot obtain location names automatically from users' GPS coordinates to claim their current locations. In this paper, we propose a novel location naming approach, which can provide concrete and meaningful location names to users based on their current location, time and check-in histories. In particular, when users input a GPS point, they will receive a ranked list of Points of Interest which shows the most possible semantic names for that location. In our approach, we draw an analogy between the location naming problem and the location-based search problem. We proposed a local search framework to integrate different kinds of popularity factors and personal preferences. After identifying important features by feature selection, we apply learning-to-rank technique to weight them and build our system based on 31811 check-in records from 545 users. By evaluating on this dataset, our approach is shown to be effective in automatically naming users' locations. 64.5% of test queries can return the intended location names within the top 5 results.
Efficient Locomotion on Non-wheeled Snake-like Robots

This article presents our current work on studying energy efficient locomotion on crawling snake-like robots. The aim of this work is to use existing biological inspired methods to demonstrate lateral undulation planar gaits for efficiently controlling high-speed motion as a function of the terrain surface. A multilink non-wheeled snake-like robot is being developed for experimentation and analysis of efficient serpentine locomotion based on simulation results.
Simulated Annealing Based Hierarchical Q-Routing: A Dynamic Routing Protocol

Network routing is the mechanism chosen to send packets from any source to a destination in the network. The goal of any routing algorithm is to find an efficient path to send a packet to any destination taking into account all the obstacles that may be taking place in the network at any time. The focus of this paper is to provide an efficient solution to the routing problem by making use of reinforcement learning and other heuristics. The paper proposes a routing algorithm called Simulated Annealing based Hierarchical Q-Routing which is based on an Q-Routing. Providing an hierarchy by defining network areas and roles to routers within these areas, allows us to have more updated global information and therefore much better decision making when routing packets across the network. The addition of simulated annealing as an exploration method also plays an important role in the improvement of the original Q-Routing approach. The temperature in simulated annealing adapts as a function of the waiting queue utilization of specific routers in the network. Experiments with different topologies and network loads show that the proposed method is able to improving convergence, loop avoidance, and scalability in comparison to Q-Routing.
Wasserstein distance for the fusion of multisensor multitarget particle filter clouds

In a multisensor multitarget tracking application, the evaluation of the cost of assigning particle filter clouds of different sensors as being estimates of the same target is an essential part in the particle cloud association. This paper treats the problem of evaluating the cost of particle filter clouds association based on the Wasserstein distance of different orders, analyzing the implications of clouds cardinality (for weighted particles), and of various resampling methods (for unweighted particles). As the Wasserstein distance at cloud level needs to have defined internally a metric at the particle level, the implications of using therein the Euclidean (for position components only) or Mahalanobis (including higher order components) distances are investigated. The crosscovariance of particle filter clouds is also estimated using the same Wasserstein distance and its introduction in the metric therein is explored. As a conclusion of various simulations, the design of the Wasserstein distance that is found to fit best the purpose of cloud-to-cloud association is presented.
Structure of WbdD: a bifunctional kinase and methyltransferase that regulates the chain length of the O antigen in Escherichia coli O9a

The Escherichia coli serotype O9a O‐antigen polysaccharide (O‐PS) is a model for glycan biosynthesis and export by the ATP‐binding cassette transporter‐dependent pathway. The polymannose O9a O‐PS is synthesized as a polyprenol‐linked glycan by mannosyltransferase enzymes located at the cytoplasmic membrane. The chain length of the O9a O‐PS is tightly regulated by the WbdD enzyme. WbdD first phosphorylates the terminal non‐reducing mannose of the O‐PS and then methylates the phosphate, stopping polymerization. The 2.2 Å resolution structure of WbdD reveals a bacterial methyltransferase domain joined to a eukaryotic kinase domain. The kinase domain is again fused to an extended C‐terminal coiled‐coil domain reminiscent of eukaryotic DMPK (Myotonic Dystrophy Protein Kinase) family kinases such as Rho‐associated protein kinase (ROCK). WbdD phosphorylates 2‐α‐d‐mannosyl‐d‐mannose (2α‐MB), a short mimic of the O9a polymer. Mutagenesis identifies those residues important in catalysis and substrate recognition and the in vivo phenotypes of these mutants are used to dissect the termination reaction. We have determined the structures of co‐complexes of WbdD with two known eukaryotic protein kinase inhibitors. Although these are potent inhibitors in vitro, they do not show any in vivo activity. The structures reveal new insight into O‐PS chain‐length regulation in this important model system.
A novel integrative risk index of papillary thyroid cancer progression combining genomic alterations and clinical factors

Although the majority of papillary thyroid cancer (PTC) is indolent, a subset of PTC behaves aggressively despite the best available treatment. A major clinical challenge is to reliably distinguish early on between those patients who need aggressive treatment from those who do not. Using a large cohort of PTC samples obtained from The Cancer Genome Atlas (TCGA), we analyzed the association between disease progression and multiple forms of genomic data, such as transcriptome, somatic mutations, and somatic copy number alterations, and found that genes related to FOXM1 signaling pathway were significantly associated with PTC progression. Integrative genomic modeling was performed, controlling for demographic and clinical characteristics, which included patient age, gender, TNM stages, histological subtypes, and history of other malignancy, using a leave-one-out elastic net model and 10-fold cross validation. For each subject, the model from the remaining subjects was used to determine the risk index, defined as a linear combination of the clinical and genomic variables from the elastic net model, and the stability of the risk index distribution was assessed through 2,000 bootstrap resampling. We developed a novel approach to combine genomic alterations and patient-related clinical factors that delineates the subset of patients who have more aggressive disease from those whose tumors are indolent and likely will require less aggressive treatment and surveillance (p = 4.62 × 10–10, log-rank test). Our results suggest that risk index modeling that combines genomic alterations with current staging systems provides an opportunity for more effective anticipation of disease prognosis and therefore enhanced precision management of PTC.
Single domain antibodies for the knockdown of cytosolic and nuclear proteins

Single domain antibodies (sdAbs) from camels or sharks comprise only the variable heavy chain domain. Human sdAbs comprise the variable domain of the heavy chain (VH) or light chain (VL) and can be selected from human antibodies. SdAbs are stable, nonaggregating molecules in vitro and in vivo compared to complete antibodies and scFv fragments. They are excellent novel inhibitors of cytosolic/nuclear proteins because they are correctly folded inside the cytosol in contrast to scFv fragments. SdAbs are unique because of their excellent specificity and possibility to target posttranslational modifications such as phosphorylation sites, conformers or interaction regions of proteins that cannot be targeted with genetic knockout techniques and are impossible to knockdown with RNAi. The number of inhibiting cytosolic/nuclear sdAbs is increasing and usage of synthetic single pot single domain antibody libraries will boost the generation of these fascinating molecules without the need of immunization. The most frequently selected antigenic epitopes belong to viral and oncogenic proteins, followed by toxins, proteins of the nervous system as well as plant‐ and drosophila proteins. It is now possible to select functional sdAbs against virtually every cytosolic/nuclear protein and desired epitope. The development of new endosomal escape protein domains and cell‐penetrating peptides for efficient transfection broaden the application of inhibiting sdAbs. Last but not least, the generation of relatively new cell‐specific nanoparticles such as polymersomes and polyplexes carrying cytosolic/nuclear sdAb‐DNA or –protein will pave the way to apply cytosolic/nuclear sdAbs for inhibition of viral infection and cancer in the clinic.
Imaging the Awake Visual Cortex with a Genetically Encoded Voltage Indicator

Genetically encoded voltage indicators (GEVIs) promise to reveal the membrane potential of genetically targeted neuronal populations through noninvasive, chronic imaging of large portions of cortical space. Here we test a promising GEVI in mouse cortex during wakefulness, a challenging condition due to large hemodynamic activity, and we introduce a straightforward projection method to separate a signal dominated by membrane voltage from a signal dominated by hemodynamic activity. We expressed VSFP-Butterfly 1.2 plasmid in layer 2/3 pyramidal cells of visual cortex through electroporation in utero. We then used wide-field imaging with two cameras to measure both fluorophores of the indicator in response to visual stimuli. By taking weighted sums and differences of the two measurements, we obtained clear separation of hemodynamic and voltage signals. The hemodynamic signal showed strong heartbeat oscillations, superimposed on slow dynamics similar to blood oxygen level-dependent (BOLD) or “intrinsic” signals. The voltage signal had fast dynamics similar to neural responses measured electrically, and showed an orderly retinotopic mapping. We compared this voltage signal with calcium signals imaged in transgenic mice that express a calcium indicator (GCaMP3) throughout cortex. The voltage signal from VSFP had similar signal-to-noise ratios as the calcium signal, it was more immune to vascular artifacts, and it integrated over larger regions of visual space, which was consistent with its reporting mostly subthreshold activity rather than the spiking activity revealed by calcium signals. These results demonstrate that GEVIs provide a powerful tool to study the dynamics of neural populations at mesoscopic spatial scales in the awake cortex.
Conflict adaptation and cognitive control adjustments following traumatic brain injury

Abstract Survivors of severe traumatic brain injury (TBI) often demonstrate impairments in the cognitive control functions of detecting response conflict and signaling for recruitment of cognitive resources to appropriately adjust performance. These cognitive control functions can be measured using conflict adaptation effects, wherein manifestations of conflict detection and processing are reduced following high- relative to low-conflict trials. Event-related potentials (ERPs) were collected while 18 survivors of severe traumatic brain injury (TBI) and 21 demographically matched control participants performed a modified Stroop task. The incongruent-minus-congruent trial Stroop effect for trials preceded by incongruent (high conflict) and congruent (low conflict) trials were compared for behavioral (response time [RT] and error rate) and ERP reflections of cognitive control. Behavioral data showed a reduction in the Stroop effect for both control and TBI participant RTs when preceded by incongruent trials. The magnitude of these effects did not differentiate control and TBI participants. ERP data revealed a centro-parietal conflict slow potential (conflict SP) that differentiated incongruent from congruent trials. Planned comparisons showed a decreased amplitude conflict SP when ERPs were preceded by incongruent trials in control, but not TBI participants. Results indicate subtle TBI-related impairments in conflict resolution mechanisms in the context of intact RT-related conflict adaptation. (JINS, 2009, 15, 927–937.)
Maximum empirical likelihood estimation and related topics

Abstract: This article develops a theory of maximum empirical likelihood estimation and empirical likelihood ratio testing with irregular and estimated constraint functions that parallels the theory for parametric models and is tailored for semiparametric models. The key is a uniform local asymptotic normality condition for the local empirical likelihood ratio. This condition is shown to hold under mild assumptions on the constraint function. Applications of our results are discussed to inference problems about quantiles under possibly additional information on the underlying distribution and to residual-based inference about quantiles.
Learning About Which Measure of In fl ation to Respond to in an Interest Rate Rule ∗

Which measure of inflation should an active interest rate rule (i.e. a rule where the nominal interest rate responds more than proportionally to changes in inflation) respond to in order to guarantee a unique equilibrium whose Minimal State Variable (MSV) representation is learnable in the E-stability sense proposed by Evans and Honkapohja (2001)? Using a closed economy model with a flexible-price good and a sticky-price good we find that the measure corresponds to the sticky-price inflation To obtain this result we analyze separately forward-looking, contemporaneous and backward-looking rules that can respond to three possible measures of inflation: the flexible-price inflation, the sticky price inflation and the full-inflation, i.e. a convex combination of the previous two. Although whether the flexible-price good and the sticky-price good are Edgeworth complements, substitutes or utility separable plays an important role in the analysis, we find in particular the following. Active forward-looking and contemporaneous rules that respond to either the flexible-price inflation or the full-inflation are more prone to induce multiple equilibria and E-instability of the MSV solution. More importantly active backward-looking rules that react to either the flexible-price inflation or the full-inflation may guarantee a unique equilibrium but in these cases the MSV solution is not learnable in the E-stability sense. Only responding actively to the sticky-price inflation seems to be a robust policy recommendation across timings and types of goods, in order to guarantee a unique and learnable equilibrium.
DUAL-LOCO: Distributing Statistical Estimation Using Random Projections

We present DUAL-LOCO, a communication-efficient algorithm for distributed statistical estimation. DUAL-LOCO assumes that the data is distributed according to the features rather than the samples. It requires only a single round of communication where low-dimensional random projections are used to approximate the dependences between features available to different workers. We show that DUAL-LOCO has bounded approximation error which only depends weakly on the number of workers. We compare DUAL-LOCO against a state-of-the-art distributed optimization method on a variety of real world datasets and show that it obtains better speedups while retaining good accuracy.
Bacterial Cellulose Shifts Transcriptome and Proteome of Cultured Endothelial Cells Towards Native Differentiation*

Preserving the native phenotype of primary cells in vitro is a complex challenge. Recently, hydrogel-based cellular matrices have evolved as alternatives to conventional cell culture techniques. We developed a bacterial cellulose-based aqueous gel-like biomaterial, dubbed Xellulin, which mimics a cellular microenvironment and seems to maintain the native phenotype of cultured and primary cells. When applied to human umbilical vein endothelial cells (HUVEC), it allowed the continuous cultivation of cell monolayers for more than one year without degradation or dedifferentiation. To investigate the impact of Xellulin on the endothelial cell phenotype in detail, we applied quantitative transcriptomics and proteomics and compared the molecular makeup of native HUVEC, HUVEC on collagen-coated Xellulin and collagen-coated cell culture plastic (polystyrene). Statistical analysis of 12,475 transcripts and 7831 proteins unveiled massive quantitative differences of the compared transcriptomes and proteomes. K-means clustering followed by network analysis showed that HUVEC on plastic upregulate transcripts and proteins controlling proliferation, cell cycle and protein biosynthesis. In contrast, HUVEC on Xellulin maintained, by and large, the expression levels of genes supporting their native biological functions and signaling networks such as integrin, receptor tyrosine kinase MAP/ERK and PI3K signaling pathways, while decreasing the expression of proliferation associated proteins. Moreover, CD34-an endothelial cell differentiation marker usually lost early during cell culture - was re-expressed within 2 weeks on Xellulin but not on plastic. And HUVEC on Xellulin showed a significantly stronger functional responsiveness to a prototypic pro-inflammatory stimulus than HUVEC on plastic. Taken together, this is one of the most comprehensive transcriptomic and proteomic studies of native and propagated HUVEC, which underscores the importance of the morphology of the cellular microenvironment to regulate cellular differentiation, and demonstrates, for the first time, the potential of Xellulin as versatile tool promoting an in vivo-like phenotype in primary and propagated cell culture.
GAME THEORY AND TRANSPORTATION SYSTEMS

Abstract-In this paper, correspondences are drawn between two game theory models (Nash noncooperative and Stackelberg games) and some problems in transportation systems modelling. An example of each is described in detail, namely the problem of carriers competing for intercity passenger travel and the signal optimization problem. The discussion serves to underline differences between two categories of transportation problems and introduces the game theory literature as a potential source of solution algorithms. Also it is shown that inner-outer iterative techniques for Stackelberg type problems cannot be expected to converge to the solution, and an approximate formulation of these problems is introduced which appears to be more readily solvable.