Miracle-dz/UniFAR-FTUs huggingface dataset:
The RFTS Domain of Raf2 Is Required for Cul4 Interaction and Heterochromatin Integrity in Fission Yeast

Centromeric heterochromatin assembly in fission yeast is critical for faithful chromosome segregation at mitosis. Its assembly requires a concerted pathway of events whereby the RNA interference (RNAi) pathway guides H3K9 methylation to target sequences. H3K9 methylation, a hallmark of heterochromatin structure, is mediated by the single histone methyltransferase Clr4 (equivalent to metazoan Suv3-9), a component of the CLRC complex. Loss of or defects in CLRC components disrupts heterochromatin formation due to loss of H3K9 methylation, thus an intact, fully functional CLRC complex is required for heterochromatin integrity. Despite its importance, little is known about the contribution of the CLRC component Raf2 to H3K9 methylation and heterochromatin assembly. We demonstrate that Raf2 is concentrated at centromeres and contrary to other analyses, we find that loss of Raf2 does not affect CENP-ACnp1 localisation or recruitment to centromeres. Our sequence alignments show that Raf2 contains a Replication Foci Targeting Sequence (RFTS) domain homologous to the RFTS domain of the human DNA methyltransferase DNMT1. We show that the Raf2 RFTS domain is required for centromeric heterochromatin formation as its mutation disrupts H3K9 methylation but not the processing of centromeric transcripts into small interfering RNAs (siRNAs) by the RNAi pathway. Analysis of biochemical interactions demonstrates that the RFTS domain mediates an interaction between Raf2 and the CLRC component Cul4. We conclude that the RFTS domain of Raf2 is a protein interaction module that plays an important role in heterochromatin formation at centromeres.
Beyond the phenotypic gambit: molecular behavioural ecology and the evolution of genetic architecture

Most studies of behaviour examine traits whose proximate causes include sensory input and neural decision‐making, but conflict and collaboration in biological systems began long before brains or sensory systems evolved. Many behaviours result from non‐neural mechanisms such as direct physical contact between recognition proteins or modifications of development that coincide with altered behaviour. These simple molecular mechanisms form the basis of important biological functions and can enact organismal interactions that are as subtle, strategic and interesting as any. The genetic changes that underlie divergent molecular behaviours are often targets of selection, indicating that their functional variation has important fitness consequences. These behaviours evolve by discrete units of quantifiable phenotypic effect (amino acid and regulatory mutations, often by successive mutations of the same gene), so the role of selection in shaping evolutionary change can be evaluated on the scale at which heritable phenotypic variation originates. We describe experimental strategies for finding genes that underlie biochemical and developmental alterations of behaviour, survey the existing literature highlighting cases where the simplicity of molecular behaviours has allowed insight to the evolutionary process and discuss the utility of a genetic knowledge of the sources and spectrum of phenotypic variation for a deeper understanding of how genetic and phenotypic architectures evolve.
Baboons' Response Speed Is Biased by Their Moods

The affect-as-information hypothesis (e.g., Schwarz & Clore, 2003), predicts that the positive or negative valence of our mood differentially affects our processing of the details of the environment. However, this hypothesis has only been tested with mood induction procedures and fairly complex cognitive tasks in humans. Here, six baboons (Papio papio) living in a social group had free access to a computerized visual search task on which they were over-trained. Trials that immediately followed a spontaneously expressed emotional behavior were analyzed, ruling out possible biases due to induction procedures. RTs following negatively valenced behaviors are slower than those following neutral and positively valenced behaviors, respectively. Thus, moods affect the performance of nonhuman primates tested in highly automatized tasks, as it does in humans during tasks with much higher cognitive demands. These findings reveal a presumably universal and adaptive mechanism by which moods influence performance in various ecological contexts.
Pioglitazone Acutely Reduces Energy Metabolism and Insulin Secretion in Rats

Our objective was to determine if the insulin-sensitizing drug pioglitazone acutely reduces insulin secretion and causes metabolic deceleration in vivo independently of change in insulin sensitivity. We assessed glucose homeostasis by hyperinsulinemic-euglycemic and hyperglycemic clamp studies and energy expenditure by indirect calorimetry and biotelemetry in male Wistar and obese hyperinsulinemic Zucker diabetic fatty (ZDF) rats 45 min after a single oral dose of pioglitazone (30 mg/kg). In vivo insulin secretion during clamped hyperglycemia was reduced in both Wistar and ZDF rats after pioglitazone administration. Insulin clearance was slightly increased in Wistar but not in ZDF rats. Insulin sensitivity in Wistar rats assessed by the hyperinsulinemic-euglycemic clamp was minimally affected by pioglitazone at this early time point. Pioglitazone also reduced energy expenditure in Wistar rats without altering respiratory exchange ratio or core body temperature. Glucose-induced insulin secretion (GIIS) and oxygen consumption were reduced by pioglitazone in isolated islets and INS832/13 cells. In conclusion, pioglitazone acutely induces whole-body metabolic slowing down and reduces GIIS, the latter being largely independent of the insulin-sensitizing action of the drug. The results suggest that pioglitazone has direct metabolic deceleration effects on the β-cell that may contribute to its capacity to lower insulinemia and antidiabetic action.
A Foray into Conficker's Logic and Rendezvous Points

We present an in depth static analysis of the Conficker worm, primarily through the exploration of the client-side binary logic. In this paper, we summarize various aspects of the inner workings of binary variants A and B, which were the first in a chain of recent revisions aimed to keep this epidemic resistant to ongoing eradication attempts. These first two variants have combined to produce a multi-million node population of infected hosts, whose true main purpose has yet to be fully understood. We further validate aspects of our analysis through in-situ network analyses, and discuss some attribution links about its origins.
Observer-based Backstepping liquid level controller for a quadruple tank process

This paper deals with the design of a nonlinear sensorless controller for a quadruple tank process. So to provide an economic liquid level control, a novel output feedback control scheme is developed. In the proposed approach, a model-based Backstepping controller combined with a second order sliding mode observer is designed for the four-tank liquid levels system. In fact, only two sensors are used to measure the liquid levels in the two bottom tanks and the other process's states are assumed unavailable. The nonlinear Backstepping controller is synthesized in order to ensure globally asymptotical stabilization for this nonlinear system. The super twisting observer converges in a finite time. It leads to a good estimation of the liquid levels in the two top tanks. A good track of the liquid level in the bottom tank with the reference trajectory is achieved by the proposed controller. To highlight the applicability and the efficiency of the proposed control scheme, simulation results are provided and discussed.
A Golgi retention signal in a membrane-spanning domain of coronavirus E1 protein

The E1 glycoprotein from an avian coronavirus is a model protein for studying retention in the Golgi complex. In animal cells expressing the protein from cDNA, the E1 protein is targeted to cis Golgi cisternae (Machamer, C. E., S. A. Mentone, J. K. Rose, and M. G. Farquhar. 1990. Proc. Natl. Acad. Sci. USA. 87:6944-6948). We show that the first of the three membrane-spanning domains of the E1 protein can retain two different plasma membrane proteins in the Golgi region of transfected cells. Both the vesicular stomatitis virus G protein and the alpha- subunit of human chorionic gonadotropin (anchored to the membrane by fusion with the G protein membrane-spanning domain and cytoplasmic tail) were retained in the Golgi region of transfected cells when their single membrane-spanning domains were replaced with the first membrane- spanning domain from E1. Single amino acid substitutions in this sequence released retention of the chimeric G protein, as well as a mutant E1 protein which lacks the second and third membrane-spanning domains. The important feature of the retention sequence appears to be the uncharged polar residues which line one face of a predicted alpha helix. This is the first retention signal to be defined for a resident Golgi protein. The fact that it is present in a membrane-spanning domain suggests a novel mechanism of retention in which the membrane composition of the Golgi complex plays an instrumental role in retaining its resident proteins.
Low complexity hybrid rate control for lower complexity Wyner-ZIV video decoding

Wyner-Ziv (WZ) video coding is an emerging paradigm which promises to lower the encoding complexity at the cost of additional decoding complexity regarding predictive coding solutions. However, the current decoding complexity increase is huge, very likely unacceptable for the relevant applications, asking for solutions which allow reducing this cost without negatively impacting the RD performance and the encoding complexity. This paper proposes hybrid rate control solutions which allow reaching the objectives above for Stanford-like WZ video codecs.
Microbial adherence to and invasion through proteoglycans

A large array of glycoproteins, glycolipids, and proteoglycans decorate the surfaces of animal cells. These glycoconjugates mediate many fundamental cellular processes, including cell-cell and cell-matrix adhesion, motility, growth, and signaling (28, 110). Over time, many pathogenic microorganisms have learned to exploit cell surface glycoconjugates as receptors for attachment, a process which ultimately facilitates tissue colonization and invasion. The interaction of specific proteins on the surface of microorganisms (adhesins) with carbohydrate chains on the glycoconjugate (receptors) enables the microbes to take their first step towards establishing an infection. This review concentrates on proteoglycans as adhesion receptors for bacteria, viruses, and parasites. Microbial binding to glycolipids and glycoproteins also occurs and has been discussed elsewhere (27, 40, 61–63, 85, 94). Proteoglycans are ubiquitous among animal cells, and as discussed below, their carbohydrate chains (glycosaminoglycans) bind many different protein ligands. Different experimental criteria have been used to establish a role for proteoglycans in attachment and invasion of host cells, including direct binding measurements, identification of microbial carbohydrate-binding proteins, competition studies with defined polysaccharides, loss of adhesion upon enzymatic removal of host glycans, and altered adherence to animal cell mutants with defective glycosaminoglycan biosynthesis. Overall, the experimental evidence for microbial adhesion to host cell proteoglycans is compelling, and future molecular studies may provide a basis for designing therapeutic strategies based on these interactions.
Apolipoprotein AIV regulates chylomicron metabolism-mechanism and 1 function 2 3

42 43 Dietary fat is an important mediator of atherosclerosis and obesity. Despite its 44 importance in mediating metabolic disease, there is still much unknown about 45 dietary fat absorption in the intestine, and especially the detailed biological roles 46 of intestinal apolipoproteins involved in that process. We were specifically 47 interested in determining the physiological role of the intestinal apolipoprotein A48 IV (A-IV) using A-IV knockout (KO) mice. A-IV is stimulated by fat absorption in 49 the intestine, and is secreted on nascent chylomicrons into intestinal lymph. We 50 found that A-IV KO mice had reduced plasma triglyceride (TG) and cholesterol 51 levels, and that this hypolipidemia persisted on a high fat diet. A-IV KO did not 52 cause abnormal intestinal lipid absorption, food intake, or adiposity. Additionally, 53 A-IV KO did not cause abnormal liver TG and cholesterol metabolism, as 54 assessed by measuring hepatic lipid content, lipogenic and cholesterol synthetic 55 gene expression, and in vivo VLDL secretion. Instead, A-IV KO resulted in the 56 secretion of larger chylomicrons from the intestine into the lymph, and those 57 chylomicrons were cleared from the plasma more slowly than WT chylomicrons. 58 This data suggests that A-IV has a previously unknown role in mediating the 59 metabolism of chylomicrons, and therefore may be important in regulating 60 plasma lipid metabolism. 61
Emotion recognition in natural scene images based on brain activity and gist

Artificial emotion study will be of utmost importance in future artificial intelligence research. In this paper, an emotion understanding system based on brain activity and ldquoGISTrdquo is newly proposed to categorize emotions reflected by natural scenes. According to the strong relationship of human emotion and the brain activity, functional magnetic resonance imaging (fMRI) and electroencephalography (EEG) are used to analyze and classify emotional states stimulated by a natural scene. The ldquoGISTrdquo is used to represent the emotional gist of the natural scene. In other words, by taking the way human brain responding to the same stimulus into consideration, a machine will be able to visually extract the emotional features of natural scenes and achieve interaction with a human in terms of emotional sharing. The experimental results show that positive and negative emotions can be distinguished, and a monkey robot head that can share emotion with human subject during watching an image is implemented.
Small-target selection with gaze alone

Accessing the smallest targets in mainstream interfaces using gaze alone is difficult, but interface tools that effectively increase the size of selectable objects can help. In this paper, we propose a conceptual framework to organize existing tools and guide the development of new tools. We designed a discrete zoom tool and conducted a proof-of-concept experiment to test the potential of the framework and the tool. Our tool was as fast as and more accurate than the currently available two-step magnification tool. Our framework shows potential to guide the design, development, and testing of zoom tools to facilitate the accessibility of mainstream interfaces for gaze users.
The Concept of Development Conventions: Some Suggestions for a Research Agenda

Abstract: Development conventions are broadly defined as socially shared systems of rules of thought or behavior (institutions) regarding development, with the properties of conformity with conformity and arbitrariness. Conformity with conformity means that the fact that others have adopted a convention, or are expected to adopt it, plays a role in leading someone else to adopt it. Arbitrariness means that a non-inferior alternative exists or is conceivable. This article identifies several social mechanisms through which the conformity of others leads one to conform. It also relates arbitrariness to the possibility of assessing development from various viewpoints, to the inconclusiveness of evidence, and to uncertainty about future consequences.
Greedy local algorithm for overlapping community detection in online social networks

Due to rapid growth of Social Networking Sites, a significant number of people interact with each other without any barriers of geographical distances or language. This communication among people is selective in the sense that they communicate only with likeminded people, and people of similar interests. This selective communication creates a typical structure in the networks which is known as community. Community structure is a significant property of social networks and hence its detection of prime importance in social network analysis and research. This paper presents Greedy Local Algorithm (GLA) for detecting overlaps between communities in social networks, which can detect dense overlaps between communities and results in lesser number of outliers.
Adaptive Mode-Control : A Low-Leakage , Power-Efficient Cache Design

With the advent of deep sub-micron circuit technology, the ratio of static-to-dynamic power in on-chip memories has become an increasingly important issue. At the circuit level, designers propose low-leakage SRAM operation modes (i.e., sleep mode or standby mode) and at architecture level, there are increasing interests in how to efficiently integrate such features into the design. In this paper, we propose an approach to low leakage on-chip cache design called Adaptive Mode-Control (AMC) that adaptively controls the operation mode of individual cache lines in the data store. By maintaining the tag store information, our method has the ability to track the miss rate with respect to the ideal miss rate (the miss rate with conventional cache) so as to control the overall performance. Our simulations show an average of 74% I-cache lines and 50% D-cache lines can be put into sleep-mode with an average impact on IPC of 1.6%.
Flocking of mobile robots by bounded feedback

This paper addresses the problem of flocking of mobile robots by bounded feedback. A control problem is formulated with the multiple goals: velocity consensus, collision avoidance, and cohesion maintenance. The flocking protocol is then obtained by means of control design. Particularly, a Lyapunov-like function is presented, the velocity control is designed to achieve coordination and linear speed consensus, and the steering control is designed for consensus on orientation. The convergence is verified via Barbalat's lemma. Simulation results with a group of mobile robots are presented to show the effectiveness of the proposed flocking control.
Rethinking Motor Lateralization: Specialized but Complementary Mechanisms for Motor Control of Each Arm

Motor lateralization in humans has primarily been characterized as “handedness”, resulting in the view that one arm-hemisphere system is specialized for all aspects of movement while the other is simply a weaker analogue. We have proposed an alternative view that motor lateralization reflects proficiency of each arm for complementary functions that arises from a specialization of each hemisphere for distinct movement control mechanisms. However, before this idea of hemispheric specialization can be accepted, it is necessary to precisely identify these distinct, lateralized mechanisms. Here we show in right-handers that dominant arm movements rely on predictive mechanisms that anticipate and account for the dynamic properties of the arm, while the non-dominant arm optimizes positional stability by specifying impedance around equilibrium positions. In a targeted-reaching paradigm, we covertly and occasionally shifted the hand starting location either orthogonal to or collinear with a particular direction of movement. On trials on which the start positions were shifted orthogonally, we did not notice any strong interlimb differences. However, on trials on which start positions were shifted orthogonally, the dominant arm largely maintained the direction and straightness of its trajectory, while the non-dominant arm deviated towards the previously learned goal position, consistent with the hypothesized control specialization of each arm-hemisphere system. These results bring together two competing theories about mechanisms of movement control, and suggest that they coexist in the brain in different hemispheres. These findings also question the traditional view of handedness, because specialized mechanisms for each arm-hemisphere system were identified within a group of right-handers. It is likely that such hemispheric specialization emerged to accommodate increasing motor complexity during evolution.
A comparison of organization-centered and agent-centered multi-agent systems

Whereas most classical multi-agent systems have the agent in center, there has recently been a development towards focusing more on the organization of the system, thereby allowing the designer to focus on what the system goals are, without considering how the goals should be fulfilled. We have developed and evaluated two teams of agents for a variant of the well-known Bomberman computer game. One team is based on the basic Jason system, which is an implementation in Java of an extension of the logic-based agent-oriented programming language AgentSpeak. The other team is based on the organizational model Moise+, which is combined with Jason in the middleware called J-Moise+. We have investigated whether taking the organization-oriented approach had any clear advantages to the classical way of implementing multi-agent systems. Although not decisive the investigation did indicate that the agent-oriented approach has a number of advantages when it comes to game-like scenarios with just a few different character types.
Food insecurity and maternal depression in rural, low-income families: a longitudinal investigation

Abstract Objective The purpose of the present study was to examine the relationship between household food insecurity and maternal depression in a rural sample to determine whether food insecurity predicted mothers’ depression over time or vice versa. Design The study employed a prospective design using three waves of data from ‘Rural Families Speak’, a multi-state study of low-income rural families in the USA. Food insecurity was measured using the Core Food Security Module and depression was measured using the Center for Epidemiologic Studies–Depression Scale. A structural equation model was fit to the data using the AMOS software package. Setting Sixteen states in the USA (California, Indiana, Kentucky, Louisiana, Massachusetts, Maryland, Michigan, Minnesota, Nebraska, New Hampshire, New York, Ohio, Oregon, South Dakota, West Virginia, Wyoming) between 2000 and 2002. Subjects Subjects included 413 women with at least one child under the age of 13 years living in the home. Results Findings based on the 184 subjects with complete data indicated that the causal relationship between household food insecurity and depression is bidirectional (P = 0·034 for causation from depression to food insecurity, P = 0·003 for causation from food insecurity to depression, χ2/df = 1·835, root-mean-square error of approximation = 0·068, comparative fit index = 0·989). Findings based on all 413 subjects after imputation of missing values also indicated bidirectionality. Conclusions The recursive relationship between food insecurity and depression has implications for US nutrition, mental health and poverty policies. The study highlights the need to integrate programmes addressing food insecurity and poor mental health for the population of rural, low-income women.