Miracle-dz/UniFAR-FTUs huggingface dataset:
The impact of kit, environment and sampling contamination on the observed microbiome of bovine milk

Contaminants can easily outnumber bacteria that originate within the milk itself, milk microbiome research currently suffers from a critical knowledge gap; namely, does non-mastitis bovine milk contain a native microbiome? In this study, we sampled external and internal mammary epithelium, stripped and cisternal milk, used numerous negative controls to identify potential sources of microbial contamination. Two algorithms were used to mathematically remove this contamination and to track potential movement of microbes among our samples. Our results suggest that majority (i.e., >75%) of the sequence data generated from bovine milk and mammary epithelium samples represents contaminating DNA. The contaminants in milk samples were primarily sourced from the DNA extraction kits and the internal and external skin of the teat, while the teat canal and apex samples were mainly contaminated during the sampling process. After decontamination, the milk microbiome displayed a more dispersed, less diverse and compositionally distinct bacterial profile compared with the teat skin samples. Similar microbial compositions were observed between cisternal and stripped milk samples, as well as between teat apex and canal samples. Staphylococcus and Acinetobacter were the predominant genera detected in the sequences of milk samples, and bacterial culture showed growth of Staphylococcus and Corynebacterium spp. in 50% (7/14) of stripped milk samples and growth of Staphylococcus spp. in 7% (1/14) of cisternal milk samples. Our study suggests that microbiome data generated from milk samples obtained from clinically healthy bovine udders may be heavily biased by contaminants that enter the sample during the sample collection and processing workflows. Importance Obtaining a non-contaminated sample of bovine milk is challenging due to the nature of the sampling environment and the route by which milk is typically extracted from the mammary gland. Furthermore, the very low bacterial biomass of bovine milk exacerbates the impacts of contaminant sequences in downstream analyses, which can lead to severe biases. Our finding showed that bovine milk contains very low bacterial biomass, and each contamination event (including sampling procedure and DNA extraction process) introduces bacteria and/or DNA fragments that easily outnumber the native bacterial cells. This finding has important implications for our ability to draw robust conclusions from milk microbiome data, especially if the data have not been subjected to rigorous decontamination procedures. Based on these findings, we strongly urge researchers to include numerous negative controls into their sampling and sample processing workflows; and to utilize several complementary methods for identifying potential contaminants within the resulting sequence data. These measures will improve the accuracy, reliability, reproducibility, and interpretability of milk microbiome data and research.
Ancestral variation and its impact on wild house mouse genomes

Ancestral alleles are important contributors to adaptation and disease risk in populations. House mice emerged in and/or around the Indian subcontinent, but the genetic composition of this ancestral population and the extent to which ancestral variants contribute to contemporary global mouse diversity are poorly understood. To address these knowledge gaps, we assessed the origins and demographic patterning of global mouse diversity using a set of 169 wild mouse genome sequences from across the world. This dataset includes 37 mouse genomes from the broadly designated ancestral regions, providing crucial resources needed to evaluate the contributions and the impact of ancestral diversity on the genomic scale. We show that house mice emerged in the Indo-Pakistan region around 700 kya, with M. m. castaneus at the root of the M. musculus species. Migration out of the Indo-Pakistan homeland led to the subsequent emergence of the M. m. domesticus and M. m. musculus subspecies ∼360 and 260 kya, respectively. A modest fraction of ancestral alleles have persisted long-term across mouse populations through balancing selection, and we demonstrate that such regions are strongly enriched for genes with immune-related functions. Finally, we find widespread allele-sharing across Mus musculus lineages and show that this trend is largely due to incomplete lineage sorting, an interpretation contrary to some recent claims of pervasive subspecies introgression. Together, our work underscores the contributions of ancestral variants to contemporary house mouse diversity and adaptation, and refines our understanding of the natural evolutionary history of this important model species.
Transcriptomic profiling reveals host-specific evolutionary pathways promoting enhanced fitness in the plant pathogen Ralstonia pseudosolanacearum

The impact of host diversity on the genotypic and phenotypic evolution of broad-spectrum pathogens is a remaining issue. Here, we used populations of the plant pathogen Ralstonia pseudosolanacearum that were experimentally evolved on five types of host plants, either belonging to different botanical families or differing in their susceptibility or resistance to the pathogen. We investigated whether changes in transcriptomic profiles dissociated from genetic changes could occur during the process of host adaptation, and whether transcriptomic reprogramming was dependent on host type. Genomic and transcriptomic variations were established for 31 evolved clones that showed a better fitness in their experimental host than the ancestral clone. Few genomic polymorphisms were detected in these clones, but significant transcriptomic variations were observed, with a high number of differentially expressed genes (DEGs). In a very clear way, a group of genes belonging to the network of regulation of the bacterial virulence such as efpR, efpH or hrpB, among others, were deregulated in several independent evolutionary lineages and appeared to play a key role in the transcriptomic rewiring observed in evolved clones. A double hierarchical clustering based on the 400 top DEGs for each clone revealed two major patterns of gene deregulation that depend on host genotype, but not on host susceptibility or resistance to the pathogen. This work therefore highlights the existence of two major evolutionary paths that result in a significant reorganization of gene expression during adaptive evolution and underscore clusters of co-regulated genes associated to bacterial adaptation on different host lines. Data summary The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
Argumentation-Based Reinforcement Learning for RoboCup Soccer Keepaway

Reinforcement Learning (RL) suffers from several difficulties when applied to domains with no obvious goal state defined; this leads to inefficiency in RL algorithms. In this paper we consider a solution within the context of a widely-used testbed for RL, that of RoboCup Keepaway soccer. We introduce Argumentation-Based RL (ABRL), using methods from argumentation theory to integrate domain knowledge, represented by arguments, into the SMDP algorithm for RL by using potential-based reward shaping. Empirical results show that ABRL outperforms the original SMDP algorithm, for this game, by improving the optimal performance.
Formal Analysis of Workflow Systems with Security Considerations

Workflow systems play an essential role in today’s enterprises by providing automatic manipulation of business processes. As an integral part of workflow systems, workflow security has received extensive attentions, within which role-based access control (RBAC) mechanism and separation of duty (SoD) constraints are important topics. RBAC is a natural mechanism to lighten the complexity of security administration, with the basic notion that permissions are associated with roles and users are assigned to appropriate roles. However, to satisfy the complex security policies of workflow systems, SoD constraints are also necessary, which aim at reducing the risk of fraud by not allowing any individual to have sufficient authority within the system to perpetrate a fraud on his own [1]. Currently, most existing approaches to the specification of RBAC mechanism, and especially of SoD constraints are complicated and not suitable for the verification of desired security properties that workflow systems should possess; besides, the workflow process and authorization flow are separated during specification and verification in most approaches. Our goal is to propose appropriate and efficient methods to formally specify and verify workflow systems with such security considerations, and thus prove that execution of any workflow instance will be secure with respect to RBAC and SoD.
Multi-image Interpolation based on Graph-cuts and Symmetric Optical Flow Technical details

Our correspondence estimation algorithm is based on the approach presented by Steinbruecker et al. [Steinbruecker et al. 2009a]. This approach separates the data-term, i.e. the brightness constancy assumptionI1 − I2(x + w1,2) ≈ 0, and the smoothness-term, i.e. ∇w1,2 ≈ ~0, that are the basis for the estimation of the correspondence mapw1,2. It hence allows for the integration of arbitrary data-terms, especially data-terms that are not differentiable. Steinbruecker et al. already showed how to integrate patch-based dataterms into this framework [Steinbruecker et al. 2009b]. The key idea of this approach is based on the work of Zach et al. [Zach et al. 2007] where instead of direct minimization of the total-variation L1 formulation
as a Factor

Transposable elements (TEs) account for a large proportion of genomic content and are major determinants of genome structure and function in eukaryotes. The annotation of TEs is a critical part of our understanding of genomes, however, the accuracy of gene/TE annotation pipelines remains an issue as TEs are frequently underestimated or misannotated. In this paper, we report that the mammalian General Transcription Factor II-I Repeat Domain-Containing Protein 2 (GTF2IRD2) was used to erroneously annotate DNA transposons in a variety of non-mammalian species because the transcription factor contains a 3’ fused hAT transposase domain. The consequences of the misannotation of TEs as trans- regulatory elements such as transcription factors can lead to errors in phylogenetic trees based on orthologs and to signiﬁcant wasted time for investigators interested in gene regulation. This study reiterates the importance of structural analysis and effective annotation methods that minimise transitive error propagation when characterising non-mammalian genomes.
Seraph: Continuous Queries on Property Graph Streams

The high expressiveness and elasticity of graphs has led to the design of a wealth of graph models and query languages, used by practitioners to model real-world processes. The property graph model and corresponding query languages, such as the widely used Cypher, have become popular in both industry and research. However, real-time data analysis and management is becoming increasingly important for today’s businesses, but graph query languages lack the features to handle streaming graph data and their continuous query evaluation. In this work, we propose Seraph, a Cypher-based language supporting native streaming features within industry-ready property graph query languages. We formally define the Seraph semantics by combining stream processing with property graphs and time-varying relations while treating time as a first-class citizen of the underlying semantics, thus laying a formal foundation necessary for future implementations. We further propose its syntax and showcase the usage of Seraph for emerging graph-based continuous queries of real-world industrial use cases.
Implementing Shared Memory on Multi-dimensional Meshes and on the Fat-tree

We present deterministic upper and lower bounds on the slowdown required to simulate an (n; m)-PRAM on a variety of networks. The upper bounds are based on a novel scheme that exploits the splitting and combining of messages. Such a scheme can be implemented on an n-node d-dimensional mesh (d = O(1)) with O(n 1=d (log(m=n)) 1? 1=d) slowdown, and on an n-leaf pruned butterry, a variant of Leiserson's fat-tree, with O(p n log(m=n)) slowdown. These simulations attain the best worst-case slowdowns to date for such interconnections. Moreover, the one for the pruned butterry is the rst PRAM simulation scheme on an area-universal network, and employs novel sorting and routing primitives. Furthermore, the simulations are space-eecient and require a total amount of storage that is within a polylogarithmic factor of the size of the PRAM memory. Finally, under the standard point-to-point assumption, we prove a bandwidth-based lower bound on the slowdown of any deterministic PRAM simulation on an arbitrary network , formulated in terms of its decomposition tree. The general result yields lower bounds of (n 1=d (log(m=2n 2)= log log(m=2n 2)) 1? 1=d) and (p n log(m=2n 2)= loglog(m=2n 2)) when specialized to the d-dimensional mesh and the pruned butterry, respectively.
Few-Shot Adversarial Learning of Realistic Neural Talking Head Models

In Table 2, we provide a comparison of timings for the three methods. Additionally, we included the feed-forward variant of our method in the comparison, which was trained only for the VoxCeleb2 dataset. The comparison was carried out on a single NVIDIA P40 GPU. For Pix2pixHD and our method, few-shot learning was done via fine-tuning for 40 epochs on the training set of size T . For T larger than 1, we trained the models on batches of 8 images. Each measurement was averaged over 100 iterations. We see that, given enough training data, our method in feed-forward variant can outpace all other methods by a large margin in terms of few-shot training time, while keeping personalization fidelity and realism of the outputs on quite a high level (as can be seen in Figure 4). But in order to achieve the best results in terms of quality, fine-tuning has to be performed, which takes approximately four and a half minutes on the P40 GPU for 32 training images. The number of epochs and, hence, the fine-tuning speed can be optimized further on a case by case basis or via the introduction of a training scheduler, which we did not perform. On the other hand, inference speed for our method is comparable or slower than other methods, which is caused by a large number of parameters we need to encode the prior knowledge about talking heads. Though, this figure can be drastically improved via the usage of more modern GPUs (on an NVIDIA 2080 Ti, the inference time can be decreased down to 13ms per frame, which is enough for most real-time applications).
A comparative study on term weighting schemes for text categorization

The term weighting scheme, which is used to convert documents into vectors in the term spaces, is a vital step in automatic text categorization. The previous studies showed that term weighting schemes dominate the performance rather than the kernel functions of SVMs for the text categorization task. In this paper, we conducted experiments to compare various term weighting schemes with SVM on two widely-used benchmark data sets. We also presented a new term weighting scheme tf.rf for text categorization. The cross-scheme comparison was performed by using McNemar's tests. The controlled experimental results showed that the newly proposed tf.rf scheme is significantly better than other term weighting schemes. Compared with schemes related with tf factor alone, the idf factor does not improve or even decrease the term's discriminating power for text categorization. The binary and tf.chi representations significantly underperform the other term weighting schemes.
Dynamic Spatial Positioning : Physical Collaboration around an Interactive Table by Children in India

We present a study of how children demonstrate physicality during collaboration around interactive tables at school. Our results show that children tend to dynamically position themselves around the tabletop area to effect particular social meanings. These movements around the tabletop allow them to enact coordination strategies in their social interactions with each other to manage their learning and task-based activities. Our analysis indicates the importance of understanding physical strategies and behaviours when designing and deploying interactive tables in classrooms. We discuss how the design of tabletops in school can embrace the extensibility of this technology, providing access for children to define and shape their own collaboration strategies for small group learning. Author
ROBUST REAL-TIME SEGMENTATION OF IMAGES AND VIDEOS USING A SMOOTHING-SPLINE SNAKE-BASED ALGORITHM

This paper deals with fast image and video segmentation using active contours. Region based active contours using level-sets are powerful techniques for video segmentation but they suffer from large computational cost. A parametric active contour method based on B-Spline interpolation has been proposed in [26] to highly reduce the computational cost but this method is sensitive to noise. Here, we choose to re-lax the rigid interpolation constraint in order to robustify our method in the presence of noise: by using smoothing splines, we trade a tunable amount of interpolation error for a smoother spline curve. We show by experiments on natural sequences that this new flexibility yields segmentation results of higher quality at no additional computational cost. Hence real time processing for moving objects segmentation is preserved.
On Eddy Characteristics, Eddy Transports, and Mean Flow Properties

Abstract Estimates of eddy energy and eddy scales obtained previously from TOPEX/POSEIDON (T/P) altimeter data are interpreted in the context of a baroclinically unstable flow field. From the observations an integral timescale Talt can be defined that—combined with estimates of the eddy kinetic energy—sets a mixing length scale. Results are compared with theories of a baroclinically unstable flow field. For such conditions, the Eady theory predicts a timescale Tbc = Ri/f from the mean-flow Richardson number Ri, which shows some qualitative agreement with T/P results in terms of a geographical distribution. A factor of 2 difference between the timescales can be explained in terms of a systematic difference between the specific definitions of scale estimates. Although transfer length and velocity scales emerging out of scaling arguments lack resemblance with observations, a transfer length scale based on Tbc and the observed eddy kinetic energy is strikingly consistent with observed eddy scales. Primarily i.
Task-priority motion planning of underactuated systems: an endogenous configuration space approach

SUMMARY This paper presents a task-priority motion planning algorithm for underactuated robotic systems. The motion planning algorithm combines two features: the idea of the task-priority control of redundant manipulators and the endogenous configuration space approach. This combination results in the algorithm which solves the primary motion planning task simultaneously with one or more secondary tasks ordered in accordance with decreasing priorities. The performance of the task-priority motion planning algorithm has been illustrated with computer simulations of the motion planning problem for a container ship.
EVALUATION OF INNOVATION IN SOUTH WEST ASIA COUNTRIES AND DETERMINE OF IRAN’S POSITION: APPLICATION OF PROMETHEE

This paper has two purposes. The first is evaluation of innovation criteria in West-South Asia Countries as well as benchmarking of Irans' position in the region. The second purpose is description of integrated application of PROMETHEE and Entropy techniques for outranking. Initially, for these purposes, criteria of innovation assessment were determined. Then Entropy used for weighting of criteria and PROMETHEE for outranking of alternatives/countries. Results show, according complex innovation indicator, Lebanon, Georgia, Emirate, Armenia, Azerbaijan, Turkey, Kazakhstan are the first to the seventh rank. Iran, Saudi Arabia, Kyrgyz and Jordan are the seventh to tenth rank in the same group. And Pakistan, Oman, Syria situate have weak situation.
Simple Synthesis, Structural and Magnetic Properties of Zn 0.2 Co 0.4 Mn 0.4 Fe 2 O 4 System

Zn 0.2 Co 0.4 Mn 0.4 Fe 2 O 4 system was prepared by using glycine assisted combustion method. Characterizations of different composites are systematically investigated with various analytical techniques. X-Ray Diffraction (XRD) pattern and Fourier-Transform Infrared Spectroscopy (FTIR) indicate the growth of well crystalline Zn 0.2 Co 0.4 Mn 0.4 Fe 2 O 4 nanoparticles with a cubic spinel structure. The magnetic properties namely, Saturation Magnetization (M s ), Coerciv - ity (H c ), and Remanent Magnetization (M r ) of the investigated system were determined. Finally, we can be concluded that Zn 0.2 Co 0.4 Mn 0.4 Fe 2 O 4 system showed attractive multi-functional features for magnetic applications.
The ESRI Guide to GIS analysis, Volume 2: Spartial measurements and statistics

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interhemispheric subarachnoid and subdural Recognition and differentiation of Falx and interhemispheric fissure on axial CT: II.

Interhemispheric hyperdensity or unenhanced computed tomography was originally considered a sign (If subarachnoid hemorrhage, the " falx sign. " It has since been identified as a normal feature and has also been seen with interhemispheric subdural hemorrhage. To determine the differential features of interhemispheric hemorrhage, 50 patients with subarachnoid hemorrhage and 32 patients with interhemispheric subdural hematomas were reviewed. Subarachnoid hemorrhage produced anterior interhemispheric hyperdensity only, with a zigzag contour and extension from the calvarium to the rostrum of the corpus callosum. Interhemispheric subdural hematomas produce unilateral crescentic hyperdensities that are largest in the posterior superior part of the fissure, behind and above the splenium of the corpus callosum. Interhemi spheric hyperdensity in children is more complex. Because the anterior part of the fissure is narrow in younger patients, subarachnoid hemorrhage may go