Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitochondrial quality control beyond PINK1/Parkin

Neurons strictly rely on proper mitochondrial function and turnover. They possess a high energy requirement which is mostly fueled by mitochondrial oxidative phosphorylation. Moreover the unique morphology of neurons implies that mitochondria need to be transported along the axons to sites of high energy demand. Finally, due to the non-dividing state of neurons, cellular mitosis cannot dilute dysfunctional mitochondria, which can produce harmful by-products such as reactive oxygen species (ROS) and thus a functioning mechanism of quality control (QC) is essential. The critical impact of mitochondria on neuronal function and viability explains their involvement in several neurodegenerative diseases such as Parkinson’s disease (PD) [1]. Mitophagy, a selective form of autophagy, is employed by cells to degrade dysfunctional mitochondria in order to maintain a healthy mitochondrial network, a process also called mitochondrial QC. In order for mitophagy to take place it essentially requires molecules that on the one hand sense the dysfunctional mitochondria and on the other hand tag the latter for autophagic degradation. Most studies on mitophagy are focused on a canonical pathway including the PD-related proteins PINK1 and Parkin. PINK1 is a kinase that recruits the E3 ubiquitin ligase Parkin to depolarized mitochondria, where it ubiquitinates several target proteins on the outer mitochondrial membrane (OMM) leading to their proteasomal degradation and serving as a signal to recruit the autophagic machinery [1] (Figure 1, upper left corner). A large number of studies on PINK1/Parkin mitophagy are based on treatment of cell lines with the uncoupler CCCP collapsing the mitochondrial membrane potential (ΔΨm), as well as overexpression of Parkin, conditions that are far from physiological [1]. Furthermore, Parkin translocation to mitochondria in neuronal cells occurs only under certain stimuli and is much slower, possibly due to their metabolic state and low endogenous Parkin expression [2]. Thus, in recent years several studies have highlighted pathways of mitophagy induction that are independent of PINK1 and/or Parkin and could act in parallel or addition to the latter. We want to discuss what is known about these QC mechanisms and hypothesize on their role in neuronal physiology and neurodegeneration. Alternative mitophagy pathways can basically branch into or parallel the PINK1/Parkin pathway at any point ranging from Parkin translocation to autophagosome formation. However, most studies are focused on two steps: ubiquitination of OMM proteins by E3 ubiquitin ligases Editorial
Black-box and Gray-box Strategies for Virtual Machine Migration

Virtualization can provide significant benefits in data centers by enabling virtual machine migration to eliminate hotspots. We present Sandpiper, a system that automates the task of monitoring and detecting hotspots, determining a new mapping of physical to virtual resources and initiating the necessary migrations. Sandpiper implements a black-box approach that is fully OS- and application-agnostic and a gray-box approach that exploits OS- and application-level statistics. We implement our techniques in Xen and conduct a detailed evaluation using a mix of CPU, network and memory-intensive applications. Our results show that Sandpiper is able to resolve single server hotspots within 20 seconds and scales well to larger, data center environments. We also show that the gray-box approach can help Sandpiper make more informed decisions, particularly in response to memory pressure.
Real-tim e Shadin g : Hardware Shadin

In this part of the course we will review some examples of shading algorithms that we might want to implement in a real-time or interactive system. This will help us to identify common approaches for real-time shading systems and to acquire information about feature sets required for this kind of system. The shading algorithms we will look at fall into three categories: realistic materials for local and global illumination , shadow mapping, and finally bump mapping algorithms. In this section we describe techniques for a variety of different reflection models to the computation of local illumination in hardware-based rendering. Rather than replacing the standard Phong model by another single, fixed model, we seek a method that allows us to utilize a wide variety of different models so that the most appropriate model can be chosen for each application. We will first consider the case of local illumination, i.e. light that arrives at objects directly from the light sources. The more complicated case of indirect illumination (i.e. light that bounces around in the environment before hitting the object) will be described in Section 1.3. The fundamental approach for rendering arbitrary materials works as follows. A reflection model in reflection model in computer graphics is typically given in the form of a bidirectional reflectance distribution function (BRDF), which describes the amount of light reflected for each pair of incoming (i.e. light) and outgoing (i.e. viewing) direction. This function can either be represented analytically, in which case it is called a reflection model), or it can be represented in a tabular or sampled form as a four-dimensional array (two dimensions each for the incoming and outgoing direction). The problem with both representations is that they cannot directly be used in hardware rendering: the interesting analytical models are mathematically too complex for hardware implementations, and the tabular form consumes too much memory (a four-dimensional table can easily consume dozens of MB). A different approach has been proposed by Heidrich and Sei-del [9]. It turns out that most lighting models in computer graphics can be factored into independent components that only depend on one or two angles. These can then be independently sampled and stored as lower-dimensional tables that consume much less memory. Kautz and McCool [12] described a method for factor-izing BRDFs given in tabular form into lower dimensional parts that can be rendered in a similar fashion. As an example for the treatment …
Habitat suitability modelling of Persian squirrel (Sciurus anomalus) in Zagros forests, western Iran

Habitat is one of the key parameters for species conservation and having adequate knowledge of the habitat requirements of a particular species is inevitable for developing conservation plans. In the current study habitat suitability of the Persian squirrel (Sciurus anomalus) was evaluated in four protected areas in southwestern Iran, using maximum entropy method (MaxEnt). We combined presence-only field data with nine environmental variables including aspect, slope, elevation, distance to river, distance to road, distance to village, climate type, landuse and vegetation types to map the species probability of presence and determine the factors limit its distribution. MaxEnt performed well at predicting the potential suitable habitats of the Persian squirrel with a mean AUC of 0.937. Results of the model indicated that landuse, climate type and distance from roads had the most contribution to the model performance. Persian squirrels have a strong preference for forests, therefore, land cover change due to human activities seems to be an important threat to the squirrel viability. Consequently minimizing anthropologic disturbances is required to maintain the number of Persian squirrels in the region.
Resistance to antibody neutralization in HIV-2 infection occurs in late stage disease and is associated with X4 tropism

Objectives:To characterize the nature and dynamics of the neutralizing antibody (NAb) response and escape in chronically HIV-2 infected patients. Methods:Twenty-eight chronically infected adults were studied over a period of 1–4 years. The neutralizing activity of plasma immunoglobulin G (IgG) antibodies against autologous and heterologous primary isolates was analyzed using a standard assay in TZM-bl cells. Coreceptor usage was determined in ghost cells. The sequence and predicted three-dimensional structure of the C2V3C3 Env region were determined for all isolates. Results:Only 50% of the patients consistently produced IgG NAbs to autologous and contemporaneous virus isolates. In contrast, 96% of the patients produced IgG antibodies that neutralized at least two isolates of a panel of six heterologous R5 isolates. Breadth and potency of the neutralizing antibodies were positively associated with the number of CD4+ T cells and with the titer and avidity of C2V3C3-specific binding IgG antibodies. X4 isolates were obtained only from late stage disease patients and were fully resistant to neutralization. The V3 loop of X4 viruses was longer, had a higher net charge, and differed markedly in secondary structure compared to R5 viruses. Conclusion:Most HIV-2 patients infected with R5 isolates produce C2V3C3-specific neutralizing antibodies whose potency and breadth decreases as the disease progresses. Resistance to antibody neutralization occurs in late stage disease and is usually associated with X4 viral tropism and major changes in V3 sequence and conformation. Our studies support a model of HIV-2 pathogenesis in which the neutralizing antibodies play a central role and have clear implications for the vaccine field.
THE IMPORTANCE OF SEMANTICS VISUAL WORLD STUDIES ON DRAWING INFERENCES AND RESOLVING ANAPHORS

The present thesis investigated the importance of semantics in generating inferences during discourse processing. Three aspects of semantics, gender stereotypes, implicit causality information and proto-role properties, were used to investigate whether semantics is activated elaboratively during discourse comprehension and what its relative importance is in backward inferencing compared to discourse/structural cues. Visual world eye-tracking studies revealed that semantics plays an important role in both backward and forward inferencing: Gender stereotypes and implicit causality information is activated elaboratively during online discourse comprehension. Moreover, gender stereotypes, implicit causality and protorole properties of verbs are all used in backward inferencing. Importantly, the studies demonstrated that semantic cues are weighed against discourse/structural cues. When the structural cues consist of a combination of cues that have been independently shown to be important in backward inferencing, semantic effects may be masked, whereas when the structural cues consist of a combination of fewer prominent cues, semantics can have an earlier effect than structural factors in pronoun resolution. In addition, the type of inference matters, too: During anaphoric inferencing semantics has a prominent role, while discourse/structural salience attains more prominence during non-anaphoric inferencing. Finally, semantics exhibits a strong role in inviting new inferences to revise earlier made inferences even in the case the additional inference is not needed to establish coherence in discourse. The findings are generally in line with the Mental Model approaches. Two extended model versions are presented that incorporate the current findings into the earlier literature. These models allow both forward and backward inferencing to occur at any given moment during the course of processing; they also allow semantic and discourse/structural cues to contribute to both of these processes. However, while Mental Model 1 does not assume interactions between semantic and discourse/structural factors in forward inferencing, Mental Model 2 does assume such a link.
Exploration of Proximity Heuristics in Length Normalization

Ranking functions used in information retrieval are primarily used in the search engines and they are often adopted for various language processing applications. However, features used in the construction of ranking functions should be analyzed before applying it on a data set. This paper gives guidelines on construction of generalized ranking functions with application-dependent features. The paper prescribes a specific case of a generalized function for recommendation system using feature engineering guidelines on the given data set. The behavior of both generalized and specific functions are studied and implemented on the unstructured textual data. The proximity feature based ranking function has outperformed by 52% from regular BM25.
Source (or Part of the following Source): Type Article Title Distinguishing between Parallel and Serial Accounts of Multiple Object Tracking Author(s) Distinguishing between Parallel and Serial Accounts of Multiple Object Tracking

Copyright It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content licence (like Creative Commons). UvA-DARE is a service provided by the library of the University of Amsterdam (http://dare.uva.nl) Humans can track multiple moving objects. Is this accomplished by attending to all the objects at the same time or do we attend to each object in turn? We addressed this question using a novel application of the classic simultaneous-sequential paradigm. We considered a display in which objects moved for only part of the time. In one condition, the objects moved sequentially, whereas in the other condition they all moved and paused simultaneously. A parallel model would predict that the targets are tracked independently, so the tracking of one target should not be influenced by the movement of another target. Thus, one would expect equal performance in the two conditions. Conversely, a simple serial account of object tracking would predict that an observer's accuracy should be greater in the sequential condition because in that condition, at any one time, fewer targets are moving and thus need to be attended. In fact, in our experiments we observed performance in the simultaneous condition to be equal to or greater than the performance in the sequential condition. This occurred regardless of the number of targets or how the targets were positioned in the visual field. These results are more directly in line with a parallel account of multiple object tracking.
Resequencing and Analysis of Variation in the TCF7L2 Gene in African Americans Suggests That SNP rs7903146 Is the Causal Diabetes Susceptibility Variant

OBJECTIVE Variation in the transcription factor 7-like 2 (TCF7L2) locus is associated with type 2 diabetes across multiple ethnicities. The aim of this study was to elucidate which variant in TCF7L2 confers diabetes susceptibility in African Americans. RESEARCH DESIGN AND METHODS Through the evaluation of tagging single nucleotide polymorphisms (SNPs), type 2 diabetes susceptibility was limited to a 4.3-kb interval, which contains the YRI (African) linkage disequilibrium (LD) block containing rs7903146. To better define the relationship between type 2 diabetes risk and genetic variation we resequenced this 4.3-kb region in 96 African American DNAs. Thirty-three novel and 13 known SNPs were identified: 20 with minor allele frequencies (MAF) >0.05 and 12 with MAF >0.10. These polymorphisms and the previously identified DG10S478 microsatellite were evaluated in African American type 2 diabetic cases (n = 1,033) and controls (n = 1,106). RESULTS Variants identified from direct sequencing and databases were genotyped or imputed. Fifteen SNPs showed association with type 2 diabetes (P < 0.05) with rs7903146 being the most significant (P = 6.32 × 10−6). Results of imputation, haplotype, and conditional analysis of SNPs were consistent with rs7903146 being the trait-defining SNP. Analysis of the DG10S478 microsatellite, which is outside the 4.3-kb LD block, revealed consistent association of risk allele 8 with type 2 diabetes (odds ratio [OR] = 1.33; P = 0.022) as reported in European populations; however, allele 16 (MAF = 0.016 cases and 0.032 controls) was strongly associated with reduced risk (OR = 0.39; P = 5.02 × 10−5) in contrast with previous studies. CONCLUSIONS In African Americans, these observations suggest that rs7903146 is the trait-defining polymorphism associated with type 2 diabetes risk. Collectively, these results support ethnic differences in type 2 diabetes associations.
Optimisation opportunities and evaluation for GPGPU applications on low-end mobile GPUs

Previous works in the literature have shown the feasibility of general purpose computations for non-visual applications on low-end mobile graphics processors using graphics APIs. These works focused only on the functional aspects of the software, ignoring the implementation details and therefore their performance implications due to their particular micro-architecture. Since various steps in such applications can be implemented in multiple ways, we identify optimisation opportunities, explore the different options and evaluate them. We show that the implementation details can significantly affect the obtained performance with discrepancies up to 3 orders of magnitude and we demonstrate the effectiveness of our proposal on two embedded platforms, obtaining more than 16× speedup over benchmarks designed following OpenGL ES 2 best practices.
Health promoting community radio in rural Bali: an impact evaluation.

INTRODUCTION This article reports and discusses the process and key recommendations of an evaluation of a community oriented radio station in a rural village in Bali, Indonesia. Community development and health promotion strategies were adopted with the purpose of positively impacting the health and social needs of the local community. The essential element of participation in communication for development was extended to the choice of an evaluation methodology that facilitated community empowerment. METHODS The Most Significant Change method was utilised to interview 74 participants (combination of individual interview and focus groups) and to provide the basis for the community itself to identify what it considered to be significant change brought about by the on-air and off-air interventions delivered by the radio station. RESULTS The 2007 study found that, in contrast to the findings of a needs assessment in 2004, the community now largely valued the input of the radio station with community members stating they were 'very proud of the radio station'. Changes in community perceptions are considered attributable to the radio station adopting a health promotion/community development approach to a combination of on-air programming to support off-air activities within the community. The radio station is in a valuable position to continue making a positive contribution to the village of Tulikup and to the wider region of Bali. CONCLUSION Heartline Bali FM made a positive impact on the quality of life of local people through a combination of strategically designed on- and off-air activities based on a community development and community participation approach to radio programming. Most Significant Change evaluation extended and strengthened the participatory dynamic of the 3 year project.
Receptor-like Genes in the Major Resistance Locus of Lettuce Are Subject to Divergent Selection

Disease resistance genes in plants are often found in complex multigene families. The largest known cluster of disease resistance specificities in lettuce contains the RGC2 family of genes. We compared the sequences of nine full-length genomic copies of RGC2 representing the diversity in the cluster to determine the structure of genes within this family and to examine the evolution of its members. The transcribed regions range from at least 7.0 to 13.1 kb, and the cDNAs contain deduced open reading frames of ~5.5 kb. The predicted RGC2 proteins contain a nucleotide binding site and irregular leucine-rich repeats (LRRs) that are characteristic of resistance genes cloned from other species. Unique features of the RGC2 gene products include a bipartite LRR region with >40 repeats. At least eight members of this family are transcribed. The level of sequence diversity between family members varied in different regions of the gene. The ratio of nonsynonymous (Ka) to synonymous (Ks) nucleotide substitutions was lowest in the region encoding the nucleotide binding site, which is the presumed effector domain of the protein. The LRR-encoding region showed an alternating pattern of conservation and hypervariability. This alternating pattern of variation was also found in all comparisons within families of resistance genes cloned from other species. The Ka/Ks ratios indicate that diversifying selection has resulted in increased variation at these codons. The patterns of variation support the predicted structure of LRR regions with solvent-exposed hypervariable residues that are potentially involved in binding pathogen-derived ligands.
Verifier-tuple for audio-forensic to determine speaker environment

In this paper a new concept for audio classification and analysis is presented to determine the authenticity of the speaker's environment. The overall concept's characteristic is determined through an introduced Verifier-Tuple, which enables a detailed analysis of every kind of media. The purpose, the practise as well as the need of this Verifier-Tuple is anchored in forensics. As we are clarifying in this paper, the Verifier-Tuple can have an essential impact on investigations in accumulating evidence to proof a crime. Within the Verifier-Tuple four different stages are classified, which include distinct syntax and semantic features of information. We demonstrate its application to the medium audio and list concrete features for each stage. Our background is the determination of a speaker's certain equipped, overall environment. This can be for example a train station or an airport with low quality audio devices, or a class room or laboratory with high quality equipment. The Verifier-Tuple provides an indirect channel for a speaker verification. The proposed concept is scalable for other media such as text, image, video or 3d-complexes. As a result we will show the Verifier-Tuple's impact on a new classification of information, especially audio feature extraction and in particular, the verification of the authenticity of information.
Swarm

Recent improvements in positioning technology make massive moving object data widely available. One important analysis is to find the moving objects that travel together. Existing methods put a strong constraint in defining moving object cluster, that they require the moving objects to stick together for consecutive timestamps. Our key observation is that the moving objects in a cluster may actually diverge temporarily and congregate at certain timestamps. Motivated by this, we propose the concept of swarm which captures the moving objects that move within arbitrary shape of clusters for certain timestamps that are possibly non-consecutive. The goal of our paper is to find all discriminative swarms, namely closed swarm. While the search space for closed swarms is prohibitively huge, we design a method, ObjectGrowth, to efficiently retrieve the answer. In ObjectGrowth, two effective pruning strategies are proposed to greatly reduce the search space and a novel closure checking rule is developed to report closed swarms on-the-fly. Empirical studies on the real data as well as large synthetic data demonstrate the effectiveness and efficiency of our methods.