Miracle-dz/UniFAR-FTUs huggingface dataset:
ZHOUPI and KERBEROS Mediate Embryo/Endosperm Separation by Promoting the Formation of an Extracuticular Sheath at the Embryo Surface

A cysteine-rich peptide, KERBEROS, acts downstream of the transcription factor ZHOUPI to modify the embryo-endosperm interface and mediate the separation of these two tissues during seed development. Arabidopsis thaliana seed development requires the concomitant development of two zygotic compartments, the embryo and the endosperm. Following fertilization, the endosperm expands and the embryo grows invasively through the endosperm, which breaks down. Here, we describe a structure we refer to as the embryo sheath that forms on the surface of the embryo as it starts to elongate. The sheath is deposited outside the embryonic cuticle and incorporates endosperm-derived material rich in extensin-like molecules. Sheath production is dependent upon the activity of ZHOUPI, an endosperm-specific transcription factor necessary for endosperm degradation, embryo growth, embryo-endosperm separation, and normal embryo cuticle formation. We show that the peptide KERBEROS, whose expression is ZHOUPI dependent, is necessary both for the formation of a normal embryo sheath and for embryo-endosperm separation. Finally, we show that the receptor-like kinases GSO1 and GSO2 are required for sheath deposition at the embryo surface but not for production of sheath material in the endosperm. We present a model in which sheath formation depends on the coordinated production of material in the endosperm and signaling within the embryo, highlighting the complex molecular interaction between these two tissues during early seed development.
Nanoimprint Lithography on curved surfaces prepared by fused deposition modelling

Fused deposition modelling (FDM) is an additive manufacturing technology commonly used for modelling, prototyping and production applications. The achievable surface roughness is one of its most limiting aspects. It is however of great interest to create well-defined (nanosized) patterns on the surface for functional applications such as optical effects, electronics or bio-medical devices. We used UV-curable polymers of different viscosities and flexible stamps made of poly(dimethylsiloxane) (PDMS) to perform Nanoimprint Lithography (NIL) on FDM-printed curved parts. Substrates with different roughness and curvature were prepared using a commercially available 3D printer. The nanoimprint results were characterized by optical light microscopy, profilometry and atomic force microscopy (AFM). Our experiments show promising results in creating well-defined microstructures on the 3D-printed parts.
Optogenetic Visualization of Presynaptic Tonic Inhibition of Cerebellar Parallel Fibers

Tonic inhibition was imaged in cerebellar granule cells of transgenic mice expressing the optogenetic chloride indicator, Clomeleon. Blockade of GABAA receptors substantially reduced chloride concentration in granule cells due to block of tonic inhibition. This indicates that tonic inhibition is a significant contributor to the resting chloride concentration of these cells. Tonic inhibition was observed not only in granule cell bodies, but also in their axons, the parallel fibers (PFs). This presynaptic tonic inhibition could be observed in slices both at room and physiological temperatures, as well as in vivo, and has many of the same properties as tonic inhibition measured in granule cell bodies. GABA application revealed that PFs possess at least two types of GABAA receptor: one high-affinity receptor that is activated by ambient GABA and causes a chloride influx that mediates tonic inhibition, and a second with a low affinity for GABA that causes a chloride efflux that excites PFs. Presynaptic tonic inhibition regulates glutamate release from PFs because GABAA receptor blockade enhanced both the frequency of spontaneous EPSCs and the amplitude of evoked EPSCs at the PF-Purkinje cell synapse. We conclude that tonic inhibition of PFs could play an important role in regulating information flow though cerebellar synaptic circuits. Such cross talk between phasic and tonic signaling could be a general mechanism for fine tuning of synaptic circuits. SIGNIFICANCE STATEMENT This paper demonstrates that an unconventional form of signaling, known as tonic inhibition, is found in presynaptic terminals and affects conventional synaptic communication. Our results establish the basic characteristics and mechanisms of presynaptic tonic inhibition and show that it occurs in vivo as well as in isolated brain tissue.
A Risk Classification Based Approach for Android Malware Detection

Existing Android malware detection approaches mostly have concentrated on superficial features such as requested or used permissions, which can’t reflect the essential differences between benign apps and malware. In this paper, we propose a quantitative calculation model of application risks based on the key observation that the essential differences between benign apps and malware actually lie in the way how permissions are used, or rather the way how their corresponding permission methods are used. Specifically, we employ a fine-grained analysis on Android application risks. We firstly classify application risks into five specific categories and then introduce comprehensive risk, which is computed based on the former five, to describe the overall risk of an application. Given that users’ risk preference and risk-bearing ability are naturally fuzzy, we design and implement a fuzzy logic system to calculate the comprehensive risk. On the basis of the quantitative calculation model, we propose a risk classification based approach for Android malware detection. The experiments show that our approach can achieve high accuracy with a low false positive rate using the RandomForest algorithm.
An unsupervised service annotation by review analysis

With the increase in popularity of review sites, users can write reviews on services that they have used in addition to reading reviews by other users. However, a number of reviews make it almost impossible for users to read all the reviews in detail. It is even more burdensome to compare multiple services. Thus, useful tools for extracting the unique features of services are necessary so that users can easily and intuitively understand the quality of services and compare them. In this study, we present an unsupervised method for extracting the unique and detailed features of services and the users' opinions on these features. By using the term frequency and inverse document frequency (TF-IDF) algorithm, our method can also extract in particular the praised or criticised features of a specific service. We conducted evaluations to show the validity of our method. In addition, we implemented an intuitive graphical user interface.
Growth of Pseudomonas taiwanensis VLB120∆C biofilms in the presence of n‐butanol

Biocatalytic processes often encounter problems due to toxic reactants and products, which reduce biocatalyst viability. Thus, robust organisms capable of tolerating or adapting towards such compounds are of high importance. This study systematically investigated the physiological response of Pseudomonas taiwanensis VLB120∆C biofilms when exposed to n‐butanol, one of the potential next generation biofuels as well as a toxic substance using microscopic and biochemical methods. Initially P. taiwanensis VLB120∆C biofilms did not show any observable growth in the presence of 3% butanol. Prolonged cultivation of 10 days led to biofilm adaptation, glucose and oxygen uptake doubled and consequently it was possible to quantify biomass. Complementing the medium with yeast extract and presumably reducing the metabolic burden caused by butanol exposure further increased the biomass yield. In course of cultivation cells reduced their size in the presence of n‐butanol which results in an enlarged surface‐to‐volume ratio and thus increased nutrient uptake. Finally, biofilm enhanced its extracellular polymeric substances (EPS) production when exposed to n‐butanol. The predominant response of these biofilms under n‐butanol stress are higher energy demand, increased biomass yield upon medium complements, larger surface‐to‐volume ratio and enhanced EPS production. Although we observed a distinct increase in biomass in the presence of 3% butanol it was not possible to cultivate P. taiwanensis VLB120∆C biofilms at higher n‐butanol concentrations. Thereby this study shows that biofilms are not per se tolerant against solvents, and need to adapt to toxic n‐butanol concentrations.
Perceived Surface Slant Is Systematically Biased in the Actively-Generated Optic Flow

Humans make systematic errors in the 3D interpretation of the optic flow in both passive and active vision. These systematic distortions can be predicted by a biologically-inspired model which disregards self-motion information resulting from head movements (Caudek, Fantoni, & Domini 2011). Here, we tested two predictions of this model: (1) A plane that is stationary in an earth-fixed reference frame will be perceived as changing its slant if the movement of the observer's head causes a variation of the optic flow; (2) a surface that rotates in an earth-fixed reference frame will be perceived to be stationary, if the surface rotation is appropriately yoked to the head movement so as to generate a variation of the surface slant but not of the optic flow. Both predictions were corroborated by two experiments in which observers judged the perceived slant of a random-dot planar surface during egomotion. We found qualitatively similar biases for monocular and binocular viewing of the simulated surfaces, although, in principle, the simultaneous presence of disparity and motion cues allows for a veridical recovery of surface slant.
An integrated approach of attention control of target human by nonverbal behaviors of robots in different viewing situations

A major challenge in HRI is to design a social robot that can attract a target human's attention to control his/her attention toward a particular direction in various social situations. If a robot would like to initiate an interaction with a person, it may turn its gaze to him/her for eye contact. However, it is not an easy task for the robot to make eye contact because such a turning action alone may not be enough to initiate an interaction in all situations, especially when the robot and the human are not facing each other or the human intensely attends to his/her task. In this paper, we propose a conceptual model of attention control with four phases: attention attraction, eye contact, attention avoidance, and attention shift. In order to initiate an attention control process, the robot first tries to gain the target participant's attention toward it through head turning, or head shaking action depending on the three viewing situations where the robot is captured in his/her field of view (central field of view, near peripheral field of view, and far peripheral field of view). After gaining her/his attention, the robot makes eye contact only with the target person through showing gaze awareness by blinking its eyes, and directs her/his attention toward an object by turning its eyes and head cues. Moreover, the robot can show attention to aversion behaviors if non-target persons look at it. We design a robot based on the proposed approach, and it is confirmed as effective to control the target participant's attention in experimental evaluation.
Monitoring tyrosine kinase inhibitor therapeutic responses with a panel of metabolic biomarkers in chronic myeloid leukemia patients

The aim of this study is to investigate the potential biomarkers associated with chronic myeloid leukemia (CML), reveal the metabolite changes related to the continuous phases of tyrosine kinase inhibitors (TKIs), and find the potential biomarkers associated with treatment effects. Fifty‐two patients with CML and 26 matched healthy people were enrolled as the discovery set. Another 194 randomly selected CML patients treated with TKI were chosen as the external validation set. Plasma samples from the patients and controls were profiled using the gas chromatography‐mass spectrometry‐based metabonomic approach. Multivariate and univariate statistical analyses were combined to select the differential metabolic features. The gas chromatography‐mass spectrometry‐based metabolomics showed a clear clustering and separation of metabolic patterns from healthy controls and pre‐ and post‐TKI treatment CML patients in the discovery set. We identified 9 metabolites that differentiated CML patients from healthy controls, including lactic acid, isoleucine, glycerol, glycine, myristic acid, d‐sorbitol, d‐galactose, d‐glucose, and myo‐inositol. Among the 9 markers, glycerol and myristic acid had the most significant association with TKI treatment effects in both discovery and external validation sets. In the receiver operating characteristic analysis, the combination of glycerol and myristic acid showed a better discrimination performance compared to a single biomarker. The results indicated that metabolic profiling has the potential for diagnosis of CML and the panel of biomarkers including myristic acid and glycerol could be useful in monitoring TKI therapeutic responses.
Dynamic and Physical Clustering of Gene Expression during Epidermal Barrier Formation in Differentiating Keratinocytes

The mammalian epidermis is a continually renewing structure that provides the interface between the organism and an innately hostile environment. The keratinocyte is its principal cell. Keratinocyte proteins form a physical epithelial barrier, protect against microbial damage, and prepare immune responses to danger. Epithelial immunity is disordered in many common diseases and disordered epithelial differentiation underlies many cancers. In order to identify the genes that mediate epithelial development we used a tissue model of the skin derived from primary human keratinocytes. We measured global gene expression in triplicate at five times over the ten days that the keratinocytes took to fully differentiate. We identified 1282 gene transcripts that significantly changed during differentiation (false discovery rate <0.01%). We robustly grouped these transcripts by K-means clustering into modules with distinct temporal expression patterns, shared regulatory motifs, and biological functions. We found a striking cluster of late expressed genes that form the structural and innate immune defences of the epithelial barrier. Gene Ontology analyses showed that undifferentiated keratinocytes were characterised by genes for motility and the adaptive immune response. We systematically identified calcium-binding genes, which may operate with the epidermal calcium gradient to control keratinocyte division during skin repair. The results provide multiple novel insights into keratinocyte biology, in particular providing a comprehensive list of known and previously unrecognised major components of the epidermal barrier. The findings provide a reference for subsequent understanding of how the barrier functions in health and disease.
A new species of Paralamyctes (Chilopoda: Lithobiomorpha: Henicopidae) from southern Chile

Paralamyctes wellingtonensis n. sp. occurs further south in Chile than its sister species, P. chilensis (Gervais in Walckenaer & Gervais, 1847). The new species, from Isla Wellington and Magallanes, is identified by distinctive female gonopods.
A comparison of sources of links for academic Web impact factor calculations

There has been much recent interest in extracting information from collections of Web links. One tool that has been used is Ingwersen’s Web impact factor. It has been demonstrated that several versions of this metric can produce results that correlate with research ratings of British universities showing that, despite being a measure of a purely Internet phenomenon, the results are susceptible to a wider interpretation. This paper addresses the question of which is the best possible domain to count backlinks from, if research is the focus of interest. WIFs for British universities calculated from several different source domains are compared, primarily the . edu, . ac.uk and . uk domains, and the entire Web. The results show that all four areas produce WIFs that correlate strongly with research ratings, but that none produce incontestably superior figures. It was also found that the WIF was less able to differentiate in more homogeneous subsets of universities, although positive results are still possible.
Mutations in COQ8B (ADCK4) found in patients with steroid‐resistant nephrotic syndrome alter COQ8B function

Mutations in COQ8B cause steroid‐resistant nephrotic syndrome with variable neurological involvement. In yeast, COQ8 encodes a protein required for coenzyme Q (CoQ) biosynthesis, whose precise role is not clear. Humans harbor two paralog genes: COQ8A and COQ8B (previously termed ADCK3 and ADCK4). We have found that COQ8B is a mitochondrial matrix protein peripherally associated with the inner membrane. COQ8B can complement a ΔCOQ8 yeast strain when its mitochondrial targeting sequence (MTS) is replaced by a yeast MTS. This model was employed to validate COQ8B mutations, and to establish genotype–phenotype correlations. All mutations affected respiratory growth, but there was no correlation between mutation type and the severity of the phenotype. In fact, contrary to the case of COQ2, where residual CoQ biosynthesis correlates with clinical severity, patients harboring hypomorphic COQ8B alleles did not display a different phenotype compared with those with null mutations. These data also suggest that the system is redundant, and that other proteins (probably COQ8A) may partially compensate for the absence of COQ8B. Finally, a COQ8B polymorphism, present in 50% of the European population (NM_024876.3:c.521A > G, p.His174Arg), affects stability of the protein and could represent a risk factor for secondary CoQ deficiencies or for other complex traits.
The Route of Antigen Entry Determines the Requirement for L-selectin during Immune Responses

L-selectin, an adhesion molecule constitutively expressed on leukocytes, is important for primary adhesion and extravasation of lymphocytes at specialized high endothelial venules within lymph nodes and other leukocytes at sites of inflammation. We have generated L-selectin–deficient mice by targeted disruption, and have confirmed a previously reported phenotype which includes strikingly impaired contact hypersensitivity (CHS) responses to reactive haptens (Tedder, T.F., D.A. Steeber, and P. Pizcueta. 1995. J. Exp. Med. 181:2259–2264; Xu, J.C., I.S. Grewal, G.P. Geba, and R.A. Flavell. 1996. 183:589–598.). Since the mechanism of this impairment has not been clarified, we sought to define the stage(s) at which the CHS response is affected in L-selectin–deficient mice. We show that epidermal Langerhans cells in L-selectin– deficient mice are normal in number, migrate to peripheral lymph nodes appropriately, and are functional in presenting allogeneic and haptenic antigens. Moreover, T cells, as well as neutrophil and monocyte effector populations, are fully capable of entry into the inflamed skin sites in the absence of L-selectin. Thus, antigen presentation and effector mechanisms are intact in L-selectin deficient mice. In contrast, virtually no antigen-specific T cells can be found within draining peripheral nodes after a contact challenge, suggesting that the defect resides primarily in the inability of antigen-specific T cells to home to and be activated in these nodes. Indeed, L-selectin–deficient mice mount completely normal CHS responses when alternate routes of immunization are used. These studies pinpoint the lesion in CHS to a discrete stage of the afferent limb of the response, clarify the role of L-selectin on effector populations, and illustrate the critical importance of the route of antigen entry to the successful execution of an immune response.
Modelling Emotional BDI Agents

Emotional-BDI agents are agents whose behaviour is guided not only by beliefs, desires and intentions, but also by the role of emotions in reasoning and decision-making. In this paper we introduce the logic EBDI for specifying Emotional-BDI agents in general and a special kind of Emotional-BDI agent under the effect of fear. The focus of this work is in the expressiveness of EBDI and on using it to establish some properties which agents under the effect of an emotion should exhibit.
Optimizing homeostatic cell renewal in hierarchical tissues

In order to maintain homeostasis, mature cells removed from the top compartment of hierarchical tissues have to be replenished by means of differentiation and self-renewal events happening in the more primitive compartments. As each cell division is associated with a risk of mutation, cell division patterns have to be optimized, in order to minimize or delay the risk of malignancy generation. Here we study this optimization problem, focusing on the role of division tree length, that is, the number of layers of cells activated in response to the loss of terminally differentiated cells, which is related to the balance between differentiation and self-renewal events in the compartments. Using both analytical methods and stochastic simulations in a metapopulation-style model, we find that shorter division trees are advantageous if the objective is to minimize the total number of one-hit mutants in the cell population. Longer division trees on the other hand minimize the accumulation of two-hit mutants, which is a more likely evolutionary goal given the key role played by tumor suppressor genes in cancer initiation. While division tree length is the most important property determining mutant accumulation, we also find that increasing the size of primitive compartments helps to delay two-hit mutant generation.
Accurate and Efficient Wireless Device Fingerprinting Using Channel State Information

Due to the loose authentication requirement between access points (APs) and clients, it is notoriously known that WLANs face long-standing threats such as rogue APs and network freeloading. Take the rogue AP problem as an example, unfortunately encryption alone does not provide authentication. APs need to be equipped with certificates that are trusted by clients ahead of time. This requires either the presence of PKI for APs or other forms of pre-established trust (e.g., distributing the certificates offline), none of which is widely used. Before any strong security solution is deployed, we still need a practical solution that can mitigate the problem. In this paper, we explore a non-cryptographic solution that is readily deployable today on end hosts (e.g., smartphones and laptops) without requiring any changes to the APs or the network infrastructure. The solution infers the Carrier Frequency Offsets (CFOs) of wireless devices from Channel State Information (CSI) as their hardware fingerprints without any special hardware requirement. CFO is attributed to the oscillator drift, which is a fundamental physical property that cannot be manipulated easily and remains fairly consistent over time but varies significantly across devices. The real experiments on 23 smartphones and 34 APs (with both identical and different brands) in different scenarios demonstrate that the detection rate could exceed 94%.