Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Beneficial Mutations in pykF Gene Vary over Time and across Replicate Populations in a Long-Term Experiment with Bacteria

Abstract The fitness effects of mutations can depend on the genetic backgrounds in which they occur and thereby influence future opportunities for evolving populations. In particular, mutations that fix in a population might change the selective benefit of subsequent mutations, giving rise to historical contingency. We examine these effects by focusing on mutations in a key metabolic gene, pykF, that arose independently early in the history of 12 Escherichia coli populations during a long-term evolution experiment. Eight different evolved nonsynonymous mutations conferred similar fitness benefits of ∼10% when transferred into the ancestor, and these benefits were greater than the one conferred by a deletion mutation. In contrast, the same mutations had highly variable fitness effects, ranging from ∼0% to 25%, in evolved clones isolated from the populations at 20,000 generations. Two mutations that were moved into these evolved clones conferred similar fitness effects in a given clone, but different effects between the clones, indicating epistatic interactions between the evolved pykF alleles and the other mutations that had accumulated in each evolved clone. We also measured the fitness effects of six evolved pykF alleles in the same populations in which they had fixed, but at seven time points between 0 and 50,000 generations. Variation in fitness effects was high at intermediate time points, and declined to a low level at 50,000 generations, when the mean fitness effect was lowest. Our results demonstrate the importance of genetic context in determining the fitness effects of different beneficial mutations even within the same gene.
Performance analyses and improvement of multilayer neural networks

Recently, deep neural networks have been widely used in many applications with successful results. Each layer of multilayer neural networks can be viewed as non-linear dimension expansion and the final layer can be viewed as linear classification. It is observed that adding more layers doesn't always improve the classification performance in some cases. In this paper, we analyze the discriminant powers of multilayer neural networks. Examination of outputs of hidden layers indicates that class separability doesn't always improve as more hidden neuron layers are added. Analyses of discriminating powers of hidden layers are presented along with a possible way to improve class separability using non-linear classifiers.
Evidence for cue-independent spatial representation in the human auditory cortex during active listening

Significance Individuals determine horizontal sound location based on precise calculations of sound level and sound timing differences at the two ears. Although these cues are processed independently at lower levels of the auditory system, their cortical processing remains poorly understood. This study seeks to address two key questions. (i) Are these cues integrated to form a cue-independent representation of space? (ii) How does active listening to sound location alter cortical response to these cues? We use functional brain imaging to address these questions, demonstrating that cue responses overlap in the cortex, that voxel patterns from one cue can predict the other cue and vice versa, and that active spatial listening enhances cortical responses independently of specific features of the sound. Few auditory functions are as important or as universal as the capacity for auditory spatial awareness (e.g., sound localization). That ability relies on sensitivity to acoustical cues—particularly interaural time and level differences (ITD and ILD)—that correlate with sound-source locations. Under nonspatial listening conditions, cortical sensitivity to ITD and ILD takes the form of broad contralaterally dominated response functions. It is unknown, however, whether that sensitivity reflects representations of the specific physical cues or a higher-order representation of auditory space (i.e., integrated cue processing), nor is it known whether responses to spatial cues are modulated by active spatial listening. To investigate, sensitivity to parametrically varied ITD or ILD cues was measured using fMRI during spatial and nonspatial listening tasks. Task type varied across blocks where targets were presented in one of three dimensions: auditory location, pitch, or visual brightness. Task effects were localized primarily to lateral posterior superior temporal gyrus (pSTG) and modulated binaural-cue response functions differently in the two hemispheres. Active spatial listening (location tasks) enhanced both contralateral and ipsilateral responses in the right hemisphere but maintained or enhanced contralateral dominance in the left hemisphere. Two observations suggest integrated processing of ITD and ILD. First, overlapping regions in medial pSTG exhibited significant sensitivity to both cues. Second, successful classification of multivoxel patterns was observed for both cue types and—critically—for cross-cue classification. Together, these results suggest a higher-order representation of auditory space in the human auditory cortex that at least partly integrates the specific underlying cues.
An Adaptive Intrusion-Tolerant Server Architecture

We describe a general architecture for intrusion-tolerant enterprise systems and the implementation of an intrusion-tolerant Web server as a specific instance. The architecture comprises functionally redundant COTS servers running on diverse operating systems and platforms, hardened intrusion-tolerance proxies that mediate client requests and verify the behavior of servers and other proxies, and monitoring and alert management components based on the EMERALD intrusion-detection framework. Integrity and availability are maintained by dynamically adapting the system configuration in response to intrusions or other faults. The dynamic configuration specifies the servers assigned to each client request, the agreement protocol used to validate server replies, and the resources spent on monitoring and detection. Alerts trigger increasingly strict regimes to ensure continued service, with graceful degradation of performance, even if some servers or proxies are compromised or faulty. The system returns to less stringent regimes as threats diminish. Servers and proxies can be isolated, repaired, and reinserted without interrupting service.
Wearable Social Sensing and Its Application in Anxiety Assesment

It is meaningful to assess people's physical and mental health as well as the determination the sense of social behavior of using wearable equipment and analyze their voice and behavioral characteristics. Microphones, accelerometers and gyroscopes are embedded in wearable devices, which provides opportunities for non-invasive monitoring of anxiety and stress in real situation. In this paper, we devise a wearable platform that can be used to calculate and analyze social behavior signals. Experiment results shows that behavioral and linguistic features can show a variety of personal anxiety. This study has potential to objectively determine social behavior consciousness.
Direct Pro-Inflammatory Effects of Prorenin on Microglia

Neuroinflammation has been implicated in hypertension, and microglia have been proposed to play an important role in the progression of this disease. Here, we have studied whether microglia are activated within cardiovascular regulatory area(s) of the brain during hypertension, especially in high blood pressure that is associated with chronic activation of the renin-angiotensin-system. In addition, we determined whether prorenin, an essential component of the renin-angiotensin-system, exerts direct pro-inflammatory effects on these microglia. Our data indicate that two rodent models which display neurogenic hypertension and over activation of the renin-angiotensin-system in the brain (sRA mice and spontaneously hypertensive rats) exhibit microglial activation, and increased levels of pro-inflammatory cytokines, in the paraventricular nucleus of the hypothalamus, an area crucial for regulation of sympathetic outflow. Further, the renin-angiotensin-system component prorenin elicits direct activation of hypothalamic microglia in culture and induction of pro-inflammatory mechanisms in these cells, effects that involve prorenin receptor-induced NFκB activation. In addition, the prorenin-elicited increases in cytokine expression were fully abolished by microglial inhibitor minocycline, and were potentiated by pre-treatment of cells with angiotensin II. Taken together with our previous data which indicate that pro-inflammatory processes in the paraventricular nucleus are involved in the hypertensive action of renin-angiotensin-system, the novel discovery that prorenin exerts direct stimulatory effects on microglial activation and pro-inflammatory cytokine production provides support for the idea that renin-angiotensin-system -induced neurogenic hypertension is not restricted to actions of angiotensin II alone.
The Motivational Salience of Infant Faces Is Similar for Men and Women

Infant facial features are thought to be powerful elicitors of caregiving behaviour. It has been widely assumed that men and women respond in different ways to those features, such as a large forehead and eyes and round protruding cheeks, colloquially described as ‘cute’. We investigated experimentally potential differences using measures of both conscious appraisal (‘liking’) and behavioural responsivity (‘wanting’) to real world infant and adult faces in 71 non-parents. Overall, women gave significantly higher ‘liking’ ratings for infant faces (but not adult faces) compared to men. However, this difference was not seen in the ‘wanting’ task, where we measured the willingness of men and women to key-press to increase or decrease viewing duration of an infant face. Further analysis of sensitivity to cuteness, categorising infants by degree of infantile features, revealed that both men and women showed a graded significant increase in both positive attractiveness ratings and viewing times to the ‘cutest’ infants. We suggest that infant faces may have similar motivational salience to men and women, despite gender idiosyncrasies in their conscious appraisal.
Information, Estimation, and Lookahead in the Gaussian Channel

We consider mean squared estimation with lookahead of a continuous-time signal corrupted by additive white Gaussian noise. We show that the mutual information rate function, i.e., the mutual information rate as function of the signal-to-noise ratio (SNR), does not, in general, determine the minimum mean squared error (MMSE) with fixed finite lookahead, in contrast to the special cases with 0 and infinite lookahead (filtering and smoothing errors), respectively, which were previously established in the literature. Further, we investigate the simple class of continuous-time stationary Gauss-Markov processes (Ornstein-Uhlenbeck processes) as channel inputs, and explicitly characterize the behavior of the minimum mean squared error (MMSE) with finite lookahead and signal-to-noise ratio (SNR). We extend our results to mixtures of Ornstein-Uhlenbeck processes, and use the insight gained to present lower and upper bounds on the MMSE with lookahead for a class of stationary Gaussian input processes, whose spectrum can be expressed as a mixture of Ornstein-Uhlenbeck spectra.
How Can Nanotechnology Help to Repair the Body? Advances in Cardiac, Skin, Bone, Cartilage and Nerve Tissue Regeneration

Nanotechnologists have become involved in regenerative medicine via creation of biomaterials and nanostructures with potential clinical implications. Their aim is to develop systems that can mimic, reinforce or even create in vivo tissue repair strategies. In fact, in the last decade, important advances in the field of tissue engineering, cell therapy and cell delivery have already been achieved. In this review, we will delve into the latest research advances and discuss whether cell and/or tissue repair devices are a possibility. Focusing on the application of nanotechnology in tissue engineering research, this review highlights recent advances in the application of nano-engineered scaffolds designed to replace or restore the followed tissues: (i) skin; (ii) cartilage; (iii) bone; (iv) nerve; and (v) cardiac.
Flow ambiguity: A path towards classically driven blind quantum computation

Blind quantum computation protocols allow a user to delegate a computation to a remote quantum computer in such a way that the privacy of their computation is preserved, even from the device implementing the computation. To date, such protocols are only known for settings involving at least two quantum devices: either a user with some quantum capabilities and a remote quantum server or two or more entangled but noncommunicating servers. In this work, we take the first step towards the construction of a blind quantum computing protocol with a completely classical client and single quantum server. Specifically, we show how a classical client can exploit the ambiguity in the flow of information in measurement-based quantum computing to construct a protocol for hiding critical aspects of a computation delegated to a remote quantum computer. This ambiguity arises due to the fact that, for a fixed graph, there exist multiple choices of the input and output vertex sets that result in deterministic measurement patterns consistent with the same fixed total ordering of vertices. This allows a classical user, computing only measurement angles, to drive a measurement-based computation performed on a remote device while hiding critical aspects of the computation.
Immune Responce in Mice Immunized with Live Cold-Adapted Influenza Vaccine in Combination with Chitosan-Based Adjuvants

An influence of intranasal combined injection of live cold-adapted influenza vaccine with chitosan derivatives as adjuvants on the subpopulation structure of mononuclear leukocytes of mouse spleen which reflects the orientation of the immune response was studied. It is found that the inclusion of chitosan preparations promotes activation of cellular-level of immune response. Keywords—Immunophenotype, chitosan, cold-adapted vaccine, intranasal injection.
A study on turning motion control of a 3-joint fish robot using sliding mode based controllers

The fish robot is a new type of biomimetic underwater robot. Because it moves silently, saves energy, and is flexible in its operation in comparison to other kinds of underwater robot such as ROVs (Remotely Operated Vehicles) or AUVs (Autonomous Underwater Vechicles) or UUV (Unmanned Underwater Vehicle) and etc, the fish robot can be applied to many underwater research projects in recent years. In this paper, a model of 3-joint (4 links) Carangiform fish robot type is presented at initial. Then, the dynamic model of fish robot is developed which is based on Lagrange's method. This dynamic model also includes the heading motion of fish robot which is not covered much in other researches. Then, the Sliding Mode Controller (SMC) and the Fuzzy Sliding Mode Controller (FSMC) are proposed to control the straight motion and turning motion of fish robot. Finally, some numerical simulations are conducted to show the feasibility and the merit of the proposed controllers.
A note on efficient aggregate queries in sensor networks

We consider a scenario where nodes in a sensor network hold numeric items, and the task is to evaluate simple functions of the distributed data. In this note we present distributed protocols for computing the median with sublinear space and communication complexity per node. Specifically, we give a deterministic protocol for computing median with polylog complexity and a randomized protocol that computes an approximate median with polyloglog communication complexity per node. On the negative side, we observe that any deterministic protocol that counts the number of distinct data items must have linear complexity in the worst case.
Adsorption of Fluorinated Ethers and Alcohols on Graphite

As part of a research program to determine the nature of the interactions of perfluoropolyalkyl ether lubricants with the surfaces of magnetic data storage media, we have studied the desorption of several model compounds from the surface of graphite. In this instance we have been modeling the chemical functionality of the lubricant Fomblin Zdol by using perfluorodiethyl ether ((CF3CF2)2O) to represent the ether linkages of its backbone and 2,2,2-trifluoroethanol (CF3CH2OH) to represent its hydroxyl end groups. The desorption kinetics of these compounds from the basal plane of graphite have been compared with those of their hydrocarbon analogues (CH3CH2)2O and CH3CH2OH. More importantly, the desorption of these compounds from graphite has been compared with prior measurements of their desorption from numerous types of amorphous carbon films. The desorption from graphite occurs with zero-order kinetics and well-defined desorption energies. The results of these measurements indicate that the broad distributi.
A dural lymphatic vascular system that drains brain interstitial fluid and macromolecules

Lymphatic circulation extends throughout most of the body and contributes to tissue homeostasis and function by facilitating the clearance of excess fluid and macromolecules from the interstitium (Secker and Harvey, 2015). However, the central nervous system (CNS) is considered to lack lymphatic vasculature, which has raised long-standing questions about how cerebral interstitial fluid (ISF) is cleared of waste products (Iliff and Nedergaard, 2013). The exchange of compounds is limited by the blood–brain barrier, which functions as a diffusion barrier between the brain and circulating blood. Therefore, the transvascular clearance of most compounds is dependent on specific active transporter mechanisms (Zlokovic, 2011). In addition, the brain has adapted to use a unique paravascular route in which fluids may freely exchange between the brain ISF and the cerebrospinal fluid (CSF) along glial “lymphatic” (glymphatic) routes without crossing the tightly regulated endothelial cell (EC) layer (Iliff et al., 2012; Xie et al., 2013). Downstream of the glymphatic system, the majority of the CSF is considered to drain into the venous circulation through arachnoid granulations. Still, several studies have found that a substantial proportion of the CSF is also drained into extracranial lymphatic vessels and LNs (Koh et al., 2005). However, the mechanisms of CSF entry into the extracranial lymphatic compartment are unclear. The visualization of lymphatic vessels has been markedly facilitated over the last decade by the identification of specific lymphatic EC markers, such as prospero homeobox protein 1 (PROX1) transcription factor, a master regulator in the program specifying the lymphatic EC fate (Hong et al., 2002), vascular endothelial growth factor receptor 3 (VEGFR3), a lymphangiogenic tyrosine kinase receptor (Secker and Harvey, 2015), chemokine (C-C motif) ligand 21 (CCL21), a chemokine secreted by lymphatic ECs which facilitates the migration of dendritic cells into LNs (Liao and von der Weid, 2015), lymphatic vessel endothelial hyaluronan CORRESPONDENCE Kari Alitalo: kari.alitalo@helsinki.fi
Dual function of MIPS1 as a metabolic enzyme and transcriptional regulator

Because regulation of its activity is instrumental either to support cell proliferation and growth or to promote cell death, the universal myo-inositol phosphate synthase (MIPS), responsible for myo-inositol biosynthesis, is a critical enzyme of primary metabolism. Surprisingly, we found this enzyme to be imported in the nucleus and to interact with the histone methyltransferases ATXR5 and ATXR6, raising the question of whether MIPS1 has a function in transcriptional regulation. Here, we demonstrate that MIPS1 binds directly to its promoter to stimulate its own expression by locally inhibiting the spreading of ATXR5/6-dependent heterochromatin marks coming from a transposable element. Furthermore, on activation of pathogen response, MIPS1 expression is reduced epigenetically, providing evidence for a complex regulatory mechanism acting at the transcriptional level. Thus, in plants, MIPS1 appears to have evolved as a protein that connects cellular metabolism, pathogen response and chromatin remodeling.
A clickstream-based collaborative filtering recommendation model for e-commerce

In recent years, clickstream-based collaborative filtering (CCF) recommendation models have received much attention mainly due to their scalability. The common CCF recommendation models are Markov models, sequential association rules, association rules, and clustering. The models have shown the trade-off relationship between precision and recall in performance. To address the trade-off relationship, some study has combined two or more different models or applied multi-order models. The increase of recommendation effectiveness by these models is also at best marginal. To increase recall while minimizing the loss of precision and therefore to increase overall performance measured by the F value, we build a sequentially applied model (SAM) by applying the individual models in tandem in an order determined through a learning process. We evaluated SAM over the individual models with Web usage data, and the result is promising.
A customized design of DRAM controller for on-chip 3D DRAM stacking

To address the “memory wall” challenge, on-chip memory stacking has been proposed as a promising solution. The stacking memory adopts three-dimensional (3D) IC technology, which leverages through-silicon-vias (TSVs) to connect layers, to dramatically reduce the access latency and improve the bandwidth without the constraint of I/O pins. To demonstrate the feasibility of 3D memory stacking, this paper introduces a customized 3D Double-Data-Rate (DDR) SDRAM controller design, which communicates with DRAM layers by TSVs. In addition, we propose a parallel access policy to further improve the performance. The 3D DDR controller is integrated in a 3D stacking System-on-Chip (SoC) architecture, where a high-bandwidth 3D DRAM chip is stacked on the top. The 3D SoC is divided into two logic layers with each having an area of 2.5 × 5.0mm2, with a 3-layer 2Gb DRAM stacking. The whole chip has been fabricated in Chartered 130nm low-power process and Tezzaron's 3D bonding technology. The simulation result shows that the on-chip DRAM controller can run as fast as 133MHz and provide 4.25GB/s data bandwidth in a single channel and 8.5GB/s with parallel access policy.
Morphological disparity opposes latitudinal diversity gradient in lacertid lizards

While global variation in taxonomic diversity is strongly linked to latitude, the extent to which morphological disparity follows geographical gradients is less well known. We estimated patterns of lineage diversification, morphological disparity and rates of phenotypic evolution in the Old World lizard family Lacertidae, which displays a nearly inverse latitudinal diversity gradient with decreasing species richness towards the tropics. We found that lacertids exhibit relatively constant rates of lineage accumulation over time, although the majority of morphological variation appears to have originated during recent divergence events, resulting in increased partitioning of disparity within subclades. Among subclades, tropical arboreal taxa exhibited the fastest rates of shape change while temperate European taxa were the slowest, resulting in an inverse relationship between latitudinal diversity and rates of phenotypic evolution. This pattern demonstrates a compelling counterexample to the ecological opportunity theory of diversification, suggesting an uncoupling of the processes generating species diversity and morphological differentiation across spatial scales.