Miracle-dz/UniFAR-FTUs huggingface dataset:
Unraveling Regulation of the Small Heat Shock Proteins by the Heat Shock Factor HvHsfB2c in Barley: Its Implications in Drought Stress Response and Seed Development

The rapid increase in heat shock proteins upon exposure to damaging stresses and during plant development related to desiccation events reveal their dual importance in plant development and stress tolerance. Genome-wide sequence survey identified 20 non-redundant small heat shock proteins (sHsp) and 22 heat shock factor (Hsf) genes in barley. While all three major classes (A, B, C) of Hsfs are localized in nucleus, the 20 sHsp gene family members are localized in different cell organelles like cytoplasm, mitochondria, plastid and peroxisomes. Hsf and sHsp members are differentially regulated during drought and at different seed developmental stages suggesting the importance of chaperone role under drought as well as seed development. In silico cis-regulatory motif analysis of Hsf promoters showed an enrichment with abscisic acid responsive cis-elements (ABRE), implying regulatory role of ABA in mediating transcriptional response of HvsHsf genes. Gene regulatory network analysis identified HvHsfB2c as potential central regulator of the seed-specific expression of several HvsHsps including 17.5CI sHsp. These results indicate that HvHsfB2c is co-expressed in the central hub of small Hsps and therefore it may be regulating the expression of several HvsHsp subclasses HvHsp16.88-CI, HvHsp17.5-CI and HvHsp17.7-CI. The in vivo relevance of binding specificity of HvHsfB2C transcription factor to HSE-element present in the promoter of HvSHP17.5-CI under heat stress exposure is confirmed by gel shift and LUC-reporter assays. Further, we isolated 477 bp cDNA from barley encoding a 17.5 sHsp polypeptide, which was predominantly upregulated under drought stress treatments and also preferentially expressed in developing seeds. Recombinant HvsHsp17.5-CI protein was expressed in E. coli and purified to homogeneity, which displayed in vitro chaperone activity. The predicted structural model of HvsHsp-17.5-CI protein suggests that the α-crystallin domain is evolutionarily highly conserved.
Performance Analysis of Low-Density Parity-Check Codes over 2D Interference Channels via Density Evolution

The theoretical analysis of detection and decoding of low-density parity-check (LDPC) codes transmitted over channels with two-dimensional (2D) interference and additive white Gaussian noise (AWGN) is provided in this paper. The detection and decoding system adopts the joint iterative detection and decoding scheme (JIDDS) in which the log-domain sum-product algorithm is adopted to decode the LDPC codes. The graph representations of the JIDDS are explained. Using the graph representations, we prove that the message-flow neighborhood of the detection and decoding system will be tree-like for a sufficiently long code length. We further confirm that the performance of the JIDDS will concentrate around the performance in which message-flow neighborhood is tree-like. Based on the tree-like message-flow neighborhood, we employ a modified density evolution algorithm to track the message densities during the iterations. A threshold is calculated using the density evolution algorithm which can be considered as the theoretical performance limit of the system. Simulation results demonstrate that the modified density evolution is effective in analyzing the performance of 2D interference systems.
The current data therefore do not support the use of inhaled CO to modify the progression of ALI

Subhamay Ghosh, Michael R. Wilson, Sharmila Choudhury, Hirotoshi Yamamoto, Michael E. Goddard, Boglarka Falusi, Nandor Marczin, and Masao Takata Department of Anaesthetics and Intensive Care, Faculty of Medicine, Imperial College London, Chelsea and Westminster Hospital, London; and Department of Cardiothoracic Surgery and Anaesthetics, Imperial College London, and Heart Science Centre, Harefield Hospital, Harefield, United Kingdom
Ultra Scale‐Down To Define and Improve the Relationship between Flocculation and Disc‐Stack Centrifugation

The recovery of intracellular recombinant proteins produced in microbial systems typically requires physical, chemical or thermal treatment of the cells post‐harvest to release the product into the broth, followed by removal of the cell debris using centrifugation or tangential flow filtration. Often a precipitation or flocculation step is introduced to facilitate the liquid‐solid separation. Due to the complex nature of the cell materials and the unit operations, it is difficult to obtain data at laboratory scale that closely reflect the performance of these operations on larger scales (pilot or manufacturing). This study uses a predictive scale‐down model that enables rapid optimization of the operating conditions for a flocculation followed with a centrifugation step using only small volumes (20 mL) of a high solids (∼20% w/w) E. coli heat extract. Results obtained show that, with proper theoretical and experimental consideration to account for high cell density, conditions could be found that improve the beneficial interaction between flocculation and centrifugation. These experiments suggested that adding a higher level of a cationic polymer could substantially increase the strength of the flocculated particles produced, thereby enhancing overall clarification performance in a large scale centrifuge. This was subsequently validated at pilot scale.
DNA breaks are masked by multiple Rap1 binding in yeast: implications for telomere capping and telomerase regulation.

Eukaryotic cells distinguish their chromosome ends from accidental DNA double-strand breaks by packaging them in a protective structure referred to as the telomere "cap. " Here we investigate the nature of the telomere cap by examining events at DNA breaks generated adjacent to either natural telomeric sequences (TG repeats) or arrays of Rap1-binding sites that vary in length. Although DNA breaks adjacent to either short or long telomeric sequences are efficiently converted into stable telomeres, they elicit very different initial responses. Short telomeric sequences (80 base pair [bp]) are avidly bound by Mre11, as well as the telomere capping protein Cdc13 and telomerase enzyme, consistent with their rapid telomerase-dependent elongation. Surprisingly, little or no Mre11 binding is detected at long telomere tracts (250 bp), and this is correlated with reduced Cdc13 and telomerase binding. Consistent with these observations, ends with long telomere tracts undergo strongly reduced exonucleolytic resection and display limited binding by both Rpa1 and Mec1, suggesting that they fail to elicit a checkpoint response. Rap1 binding is required for end concealment at long tracts, but Rif proteins, yKu, and Cdc13 are not. These results shed light on the nature of the telomere cap and mechanisms that regulate telomerase access at chromosome ends.
Friending to Flame: How Social Features Affect Player Behaviours in an Online Collectible Card Game

Online Collectible Card Games (OCCGs) are enormously popular worldwide. Previous studies found that the social aspects of physical CCGs are crucial for player engagement. However, we know little about the different types of sociability that OCCGs afford. Nor to what extent they influence players' social experiences. This mixed method online survey study focuses on a representative OCCG, Hearthstone [24] to 1) identify and define social design features and examine the extent to which players' use of these features predict their sense of community; 2) investigate participants' attitudes towards and experiences with the game community. The results show that players rarely use social features, and these features contribute differently to predicting players' sense of community. We also found emergent toxic behaviors, afforded by the social features. Findings can inform the best practices and principles in the design of OCCGs, and contribute to our understanding of players' perceptions of OCCG communities.
Golgi clusters and vesicles mediate mitotic inheritance independently of the endoplasmic reticulum

We have examined the fate of Golgi membranes during mitotic inheritance in animal cells using four-dimensional fluorescence microscopy, serial section reconstruction of electron micrographs, and peroxidase cytochemistry to track the fate of a Golgi enzyme fused to horseradish peroxidase. All three approaches show that partitioning of Golgi membranes is mediated by Golgi clusters that persist throughout mitosis, together with shed vesicles that are often found associated with spindle microtubules. We have been unable to find evidence that Golgi membranes fuse during the later phases of mitosis with the endoplasmic reticulum (ER) as a strategy for Golgi partitioning (Zaal, K.J., C.L. Smith, R.S. Polishchuk, N. Altan, N.B. Cole, J. Ellenberg, K. Hirschberg, J.F. Presley, T.H. Roberts, E. Siggia, et al. 1999. Cell. 99:589–601) and suggest that these results, in part, are the consequence of slow or abortive folding of GFP–Golgi chimeras in the ER. Furthermore, we show that accurate partitioning is accomplished early in mitosis, by a process of cytoplasmic redistribution of Golgi fragments and vesicles yielding a balance of Golgi membranes on either side of the metaphase plate before cell division.
Origami-inspired bi-directional soft pneumatic actuator with integrated variable stiffness mechanism

The field of soft robotics has a wide array of applications, particularly in human-robotic interaction, from medical devices to assembly technology. In this paper, we introduce a novel design for a soft bi-directional pneumatic actuator inspired by the principles of origami. The actuator integrates a variable stiffness application using a layer jamming mechanism (LJM). LJM utilizes the effects of negative pressure on thin layers of material, providing rigidity. Incorporated into an origami bellows structure, the negative pressure causes both contractile action and stiffness, while extensive action is caused by an internal pneumatic chamber, allowing for contractile and extensive force application. Furthermore, the variable stiffness integration improved tensile force application threefold, resistance to outside linear force tenfold, and doubled sheer force resistance. The proposed origami-inspired bi-directional soft pneumatic soft actuator has immense potential to be implemented in complex biomedical applications in the near future.
In vitro evaluation of dentin tubule occlusion by three bioactive materials: A scanning electron microscopic study

Background: Dentin hypersensitivity (DH) is a common problem characterized by a short, sharp pain. Reduction of dentin permeability by occluding dentin tubules is considered as a method for treating DH. Many substances are available to decrease hypersensitivity. The aim of this study is to evaluate the ability of three different remineralizing agents for occluding dentinal tubules in comparison with positive and negative controls. Materials and Methods: In this in vitro scanning electron microscopic (SEM) study, 75 extracted premolars were cut into crown and root fragments with a bur and divided into five groups: group 1: Sodium fluoride 5% varnish was applied (positive control), Group 2: No treatment (negative control), Group 3: Treated with Remin Pro (contains hydroxyapatite and fluoride), Group 4: Treated with MI paste (contains casein phosphopeptide-amorphous calcium phosphate [CPP-ACP]) and Group 5: Treated with GC tooth mousse (contains CPP-ACP). SEM images were obtained and mean tubular diameter was measured in each group. One-way ANOVA and Duncan's tests were used for statistical analysis. A significant level of α = 0.05 was set for comparison between the groups. Results: Statistically significant difference was observed between Group 2 (negative control) and other four groups (P < 0.05). There was no significant difference between Groups 1, 3, 4, and 5 (P > 0.05). Conclusion: Under the limitations of the present in vitro study, it can be concluded that the application of a CPP-ACP paste as well as a paste which contains fluoride is effective on reduction of dentin permeability.
Coauthor Network Topic Models with Application to Expert Finding

This paper presents the coauthor network topic (CNT) model constructed based on Markov random fields (MRFs) with higher-order cliques. Regularized by the complex coauthor network structures, the CNT can simultaneously learn topic distributions as well as expertise of authors from large document collections. Besides modeling the pairwise relations, we model also higher-order coauthor relations and investigate their effects on topic and expertise modeling. We derive efficient inference and learning algorithms from the Gibbs sampling procedure. To confirm the effectiveness, we apply the CNT to the expert finding problem on a DBLP corpus of titles from six different computer science conferences. Experiments show that the higher-order relations among coauthors can improve the topic and expertise modeling performance over the case with pairwise relations, and thus can find more relevant experts given a query topic or document.
Efficient discovery of functional and approximate dependencies using partitions

Discovery of functional dependencies from relations has been identified as an important database analysis technique. We present a new approach for finding functional dependencies from large databases, based on partitioning the set of rows with respect to their attribute values. The use of partitions makes the discovery of approximate functional dependencies easy and efficient, and the erroneous or exceptional rows can be identified easily. Experiments show that the new algorithm is efficient in practice. For benchmark databases the running times are improved by several orders of magnitude over previously published results. The algorithm is also applicable to much larger datasets than the previous methods.
New insights into wifi-based device-free localization

WiFi-based device-free localization is a main indoor localization technique that has attracted much attention recently. Typically, due to the complex wireless propagation in indoor environments, WiFi-based device-free localization requires a construction of a fingerprint map that captures the signal strength characteristics when the human is standing at certain locations in the area of interest. This fingerprint requires significant overhead in construction, and thus has been one of the major drawbacks of WiFi-based device-free localization. In this paper, we leverage an automated tool for fingerprint constructions to study novel scenarios for WiFi-based device-free localization training and testing that are difficult to evaluate in a real environment. In particular, we examine the effect of changing the access points (AP) mounting location, AP technology upgrade, and outsider effect; on the accuracy of the localization system. Our analysis provides recommendations for better localization and provides insights for both researchers and practitioners.
Synergy from Silence in a Combinatorial Neural Code

The manner in which groups of neurons represent events in the external world is a central question in neuroscience. Estimation of the information encoded by small groups of neurons has shown that in many neural systems, cells carry mildly redundant information. These measures average over all the activity patterns of a neural population. Here, we analyze the population code of the salamander and guinea pig retinas by quantifying the information conveyed by specific multicell activity patterns. Synchronous spikes, even though they are relatively rare and highly informative, convey less information than the sum of either spike alone, making them redundant coding symbols. Instead, patterns of spiking in one cell and silence in others, which are relatively common and often overlooked as special coding symbols, were found to be mostly synergistic. Our results reflect that the mild average redundancy between ganglion cells that was previously reported is actually the result of redundant and synergistic multicell patterns, whose contributions partially cancel each other when taking the average over all patterns. We further show that similar coding properties emerge in a generic model of neural responses, suggesting that this form of combinatorial coding, in which specific compound patterns carry synergistic or redundant information, may exist in other neural circuits.
Positional orthology: putting genomic evolutionary relationships into context

Orthology is a powerful refinement of homology that allows us to describe more precisely the evolution of genomes and understand the function of the genes they contain. However, because orthology is not concerned with genomic position, it is limited in its ability to describe genes that are likely to have equivalent roles in different genomes. Because of this limitation, the concept of ‘positional orthology’ has emerged, which describes the relation between orthologous genes that retain their ancestral genomic positions. In this review, we formally define this concept, for which we introduce the shorter term ‘toporthology’, with respect to the evolutionary events experienced by a gene’s ancestors. Through a discussion of recent studies on the role of genomic context in gene evolution, we show that the distinction between orthology and toporthology is biologically significant. We then review a number of orthology prediction methods that take genomic context into account and thus that may be used to infer the important relation of toporthology.
Semantic Segmentation of Colon Gland with Conditional Generative Adversarial Network

Semantic segmentation of colon gland is notoriously challenging due to their complex texture, huge variation, and the scarcity of training data with accurate annotations. It is even hard for experts, let alone computer-aided diagnosis systems. Recently, some deep convolutional neural networks (DCNN) based methods have been introduced to tackle this problem, achieving much impressive performance. However, these methods always tend to miss segmented results for the important regions of colon gland or make a wrong segmenting decision.In this paper, we address the challenging problem by proposed a novel framework through conditional generative adversarial network. First, the generator in the framework is trained to learn a mapping from gland colon image to a confidence map indicating the probabilities of being a pixel of gland object. The discriminator is responsible to penalize the mismatch between colon gland image and the confidence map. This additional adversarial learning facilitates the generator to produce higher quality confidence map. Then we transform the confidence map into a binary image using a fixed threshold to fulfill the segmentation task. We implement extensive experiments on the public benchmark MICCAI gland 2015 dataset to verify the effectiveness of the proposed method. Results demonstrate that our method achieve a better segmentation result in terms of visual perception and two quantitative metrics, compared with other methods.
DDoS Incidents and their Impact: A Review

The phenomenal growth and success of Internet has changed the way traditional essential services such as banking, transportation, medicine, education and defence are operated. Now they are being progressively replaced by cheaper and more efficient Internet-based applications. In present era, the world is highly dependent on the Internet and it is considered as main infrastructure of the global information society . Therefore, the availability of Internet is very critical for the socio-economic growth of the society. However, the inherent vulnerabilities of the Internet architecture provide opportunities for a lot of attacks on its infrastructure and services. Distributed denial-of-service attack is one such kind of attack, which poses an immense threat to the availability of the Internet. One of the biggest challenges before researchers is to find details of these attacks because to avoid defamation most of the commercial sites do not even reveal that they were attacked. In this paper, an overview of distributed denial-of-service problem and Inherent vulnerabilities in the Internet architecture are provided. Real distributed denial-of-service incidents with their financial impact are critically analyzed and finally need for a comprehensive distributed denial-of-service solution is highlighted.
Embedded Advance Collision Warning System: Vehicle Images Ranging System Based on Machine Vision

EACWS (Embedded Advance Collision Warning System) is an important part of ITS (Intelligence Transportation System). It is mainly based on monocular vision algorithms, and high-speed DSP processor, real-time to complete front vehicle distance detection, and send out early warning signals to ensure driving safety. Keywords-component: monocular; vision; detection;
Location selection for ambulance stations: a data-driven approach

Emergency medical service provides a variety of services for those in need of emergency care. One of the major challenges encountered by emergency service providers is selecting the appropriate locations for ambulance stations. Prior works measure spatial proximity under Euclidean space or static road network. In this paper, we focus on locating the ambulance stations by using the real traffic information so as to minimize the average travel-time to reach the emergency requests. To this end, we estimate the travel-time of road segments using real GPS trajectories and propose an efficient PAM-based refinement for the location problem. We conduct extensive experimental evaluations using real emergency requests collected from Tianjin, and the result shows that the proposed solution can reduce the travel-time to reach the emergency requests by 29.9% when compared to the original locations of ambulance stations.
Evolving Cooperation Strategies

We propose an approach to developing cooperation strategies for multiagent problem solving situations which is different from existing techniques in two ways: strategies are incrementally constructed by repeatedly solving problems in the domain, i.e., on-line; and, we utilize an automated method of strategy formulation and modification, that relies little on domain details and human expertise, and more on performance on randomly generated problems in the domain. The genetic programming (GP) (Koza 1992) paradigm used to develop, through repeated problem solving, increasingly efficient strategies. Populations of structures are represented as Lisp symbolic expressions (Sexpressions). These are manipulated to evolve better structures by propagating and combining parts of structures that perform well compared to others in the population. To use this approach, we have to develop an encoding of strategies as S-expressions and choose an evaluation criterion for a strategy corresponding to an arbitrary S-expression. Strategies are evaluated by allowing the agents to execute them in the application domain and by measuring their efficiency and effectiveness by a set of criteria relevant to the domain.
Interactive information seeking via selective application of contextual knowledge

Exploratory search is a difficult activity that requires iterative interaction. This iterative process helps the searcher to understand and to refine the information need. It also generates a rich set of data that can be used effectively to reflect on what has been found (and found useful). While traditional information retrieval systems have focused on organizing the data that was retrieved, in this paper, we describe a systematic approach to organizing the metadata generated during the search process. We describe a framework for unifying transitions among various stages of exploratory search, and show how context from one stage can be applied to the next. The framework can be used both to describe existing information-seeking interactions, and as a means of generating novel ones. We illustrate the framework with examples from a session-based exploratory search system prototype.