Miracle-dz/UniFAR-FTUs huggingface dataset:
Bidirectional promoters link cAMP signaling with irreversible differentiation through promoter-associated non-coding RNA (pancRNA) expression in PC12 cells

Abstract Bidirectional promoters are the major source of gene activation-associated noncoding RNA (ncRNA). PC12 cells offer an interesting model for understanding the mechanism underlying bidirectional promoter-mediated cell cycle control. Nerve growth factor (NGF)-stimulated PC12 cells elongate neurites, and are in a reversible cell-cycle-arrested state. In contrast, these cells irreversibly differentiate and cannot re-enter the normal cell cycle after NGF plus cAMP treatment. In this study, using directional RNA-seq, we found that bidirectional promoters for protein-coding genes with promoter-associated ncRNA (pancRNA) were enriched for cAMP response element consensus sequences, and were preferred targets for transcriptional regulation by the transcription factors in the cAMP-dependent pathway. A spindle-formation-associated gene, Nusap1 and pancNusap1 were among the most strictly co-transcribed pancRNA–mRNA pairs. This pancRNA–mRNA pair was specifically repressed in irreversibly differentiated PC12 cells. Knockdown (KD) and overexpression experiments showed that pancNusap1 positively regulated the Nusap1 expression in a sequence-specific manner, which was accompanied by histone acetylation at the Nusap1 promoter. Furthermore, pancNusap1 KD recapitulated the effects of cAMP on cell cycle arrest. Thus, we conclude that pancRNA-mediated histone acetylation contributes to the establishment of the cAMP-induced transcription state of the Nusap1 locus and contributes to the irreversible cell cycle exit for terminal differentiation of PC12 cells.
Flickr-tag prediction using multi-modal fusion and meta information

We present our evaluation and analysis on Yahoo! Large-scale Flickr-tag Image Classification dataset. Our evaluations show that combining multi-features and different classification models, the MAP of tag prediction can be significantly improve over ordinary linear classification. Further analysis shows that some tags are given not because of the visual content but the meta information of images. Our experiments show that we can make more accurate prediction on certain tags using meta information without any training process, compared with visual content based classifiers. Combine the meta information, multi-features and multi-models fusion, we achieve significantly better performance than simple linear classification. We also evaluate the performance of various mid-level feature, and the results suggest that "Concept Bank" feature may be a promising direction for the task.
Detrital Clay Coats, Clay Minerals, and Pyrite: A Modern Shallow-Core Analogue For Ancient and Deeply Buried Estuarine Sandstones

The spatial distribution of clay minerals and authigenic-clay-coated sand grains in ancient and deeply buried petroleum reservoirs, which can enhance or degrade reservoir quality, is poorly understood. Authigenic clay coats are reported to originate from the thermally driven recrystallization of detrital clay coats or through in situ growth from the authigenic alteration of precursor and early-diagenetic minerals during burial diagenesis. To help predict the spatial distribution of authigenic clay coats and clay minerals in estuarine sandstones, this study provides the first modern-analogue study, using the Ravenglass Estuary, UK, which integrates the distribution patterns of lithofacies, Fe-sulfide, and precursor detrital-clay-coats and clay-minerals. X-ray-diffraction-determined mineralogy and the extent of detrital clay-coat coverage of sediment in twenty-three one-meter cores was established, at an unprecedented high resolution. The output from this study shows that detrital clay mineral distribution patterns are controlled principally by the physical sorting of clay minerals by grain size. Chlorite is most abundant in coarsergrained sediment (e.g., low-amplitude dunes), whereas illite is most abundant in finer-grained sub-environments (e.g., mud flats). Kaolinite abundance is relatively homogeneous, whereas smectite abundance is negligible in the Ravenglass Estuary. This study has shown that distribution patterns of detrital-clay-coats and clay-minerals are controlled by processes active during deposition and bio-sediment interaction in the top few millimeters in the primary deposition environment. In the Ravenglass Estuary, distribution patterns of detrital-clay-coats and clay-minerals have not been overprinted by the postdepositional processes of sediment bioturbation or mechanical infiltration. Optimum detritalclay-coat coverage and clay mineralogy, which might serve as a precursor to porosity-preserving authigenic clay coats in deeply buried sandstone reservoirs, is likely to occur in low-amplitude dunes in the inner estuary and central basin. Furthermore, bioturbation in low-amplitude dunes has reduced Fe-sulfide growth due to oxidization, meaning that iron remains available for the formation of authigenic Fe-bearing clay minerals, such as chlorite, that can lead to enhanced reservoir quality in deeply buried sandstones.
A cluster based minimum battery cost AODV routing using multipath route for zigbee

IEEE 802.15. 4 standard is uniquely designed for low data rate wireless personal area networks (LR-WPANs). The IEEE 802.15. 4 targets the applications such as industrial, agricultural, vehicular, residential, medical sensors and actuators which have more relaxed throughput requirements. ZigBee is a wireless technology based on IEEE 802.15. 4. ZigBee routing uses ad hoc on-demand distance vector (AODV) routing protocol. In this paper we present an improved version of AODV called multipath energy aware AODV routing (ME-AODV), which utilizes the topology of network to divide it into one or more logical clusters and restricts the flooding of route request outside the cluster. The mesh links created at the time of cluster formation are used to decrease the routing path. ME-AODV uses nodes of the same cluster to share routing information, which significantly reduces the route path discovery. Since ZigBee routing is based on shortest-hop count, which causes overuse of a small set of nodes hence decreasing node as well as network lifetime. We also propose a mix of ad hoc on-demand multipath distance vector routing (AOMDV) and minimal-battery cost routing (MBCR) as an extension to AODV to increase the lifetime of network. The simulations have been performed using IEEE 802.15. 4, ns-2 module.
Signaling pathways in phagocytosis

Phagocytosis is an uptake of large particles governed by the actin‐based cytoskeleton. Binding of particles to specific cell surface receptors is the first step of phagocytosis. In higher Eucaryota, the receptors able to mediate phagocytosis are expressed almost exclusively in macrophages, neutrophils, and monocytes, conferring immunodefence properties to these cells. Receptor clustering is thought to occur upon particle binding, that in turn generates a phagocytic signal. Several pathways of phagocytic signal transduction have been identified, including the activation of tyrosine kinases and (or) serine/threonine kinase C in pivotal roles. Kinase activation leads to phosphorylation of the receptors and other proteins, recruited at the sites of phagocytosis. Monomeric GTPases of the Rho and ARF families are likely to be engaged downstream of activated receptors. The GTPases, in cooperation with phosphatidylinositol 4‐phosphate 5‐kinase and phosphatidylinositol 3‐kinase lipid modifying enzymes, can modulate locally the assembly of the submembranous actin filament system leading to particle internalization. BioEssays 21:422–431, 1999. © 1999 John Wiley & Sons, Inc.
Del (9q) AML: clinical and cytological characteristics and prognostic implications

Del (9q) is a recurrent cytogenetic abnormality in acute myeloid leukaemia (AML). We report an analysis of 81 patients with del(9q) as a diagnostic karyotypic abnormality entered into the Medical Research Council AML trials 10, 11 and 12. Patients were divided into three groups: (i) Sole del (9q), 21 patients; (ii) Del(9q) in association with t(8;21), 29 patients; (iii) Del(9q) in association with other cytogenetic abnormalities, 31 patients. Sole del(9q) was associated with a characteristic bone marrow phenotype at diagnosis: a single Auer rod was found in all cases examined. There was also an association with erythroid dysplasia (74%) and granylocytic lineage vacuolation (90%). The incidence of all three of these features was significantly higher (P < 0·05) in the sole del(9q) group compared with control cases lacking del(9q). The overall survival (OS) of all 81 patients was compared with a control group of 1738 patients with normal cytogenetics entered in the same trials over the period of investigation. The 5‐year OS for patients with del(9q) was 45%, compared with 35% for the control group (P = 0·09). Patients with del(9q) in association with t(8;21) had a 5‐year OS of 75%, which was significantly better than the groups with either sole del(9q) (40%) and del(9q) with other abnormalities (26%; P = 0·008). Karyotyping indicated a common area of deletion in the region 9q21–22, which was present in 94% of cases. It is likely that the deletion of single or multiple tumour suppressor genes located in this region may underlie the pathogenesis of del (9q) AML.
AND/OR Search for Marginal MAP

Mixed inference such as the marginal MAP query (some variables marginalized by summation and others by maximization) is key to many prediction and decision models. It is known to be extremely hard; the problem is NPPP-complete while the decision problem for MAP is only NP-complete and the summation problem is #P-complete. Consequently, approximation anytime schemes are essential. In this paper, we show that the framework of heuristic AND/OR search, which exploits conditional independence in the graphical model, coupled with variational-based mini-bucket heuristics can be extended to this task and yield powerful state-of-the-art schemes. Specifically, we explore the complementary properties of best-first search for reducing the number of conditional sums and providing time-improving upper bounds, with depth-first search for rapidly generating and improving solutions and lower bounds. We show empirically that a class of solvers that interleaves depth-first with best-first schemes emerges as the most competitive anytime scheme.
Robots as embodied beings - interactionally sensitive body movements in interactions among autistic children and a robot

The general context of the work presented in this paper is assistive robotics with our long-term aim to support children with autism. This paper is part of an investigation into what ways and to what extent a robot can assume the role of a social mediator - encouraging autistic children to interact with the robot, with each other and with co-present adults. The article provides a case study evaluation of segments of trials where four children with autism interacted with a robot as well as with each other. It focuses primarily on the ways in which the autistic children were found to skilfully orientate and reorientate their bodies in a way that was sensitive to the activities of the adult (such as requests and adjustments to the robot), the robot (its position and movement) and another child. Results are presented using an analysis of interaction informed by conversation analytic principles. The analysis showed how the children exhibited interaction skills where the robot served as a salient object mediating joint attention with other children.
Swarm Observation of Field‐Aligned Currents Associated With Multiple Auroral Arc Systems

Auroral arcs occur in regions of upward field‐aligned currents (FACs); however, the relation is not one to one, since kinetic energy of the current‐carrying electrons is also important in the production of auroral luminosity. Multiple auroral arc systems provide an opportunity to study the relation between FACs and auroral brightness in detail. In this study, we have identified two types of FAC configurations in multiple parallel arc systems using ground‐based optical data from the Time History of Events and Macroscale Interactions during Substorms all‐sky imagers, magnetometers and electric field instruments on board the Swarm satellites. In “unipolar FAC” events, each arc is an intensification within a broad, unipolar current sheet and downward return currents occur outside of this broad sheet. In “multipolar FAC” events, multiple arc systems represent a collection of multiple up/down current pairs. By collecting 17 events with unipolar FAC and 12 events with multipolar FACs, we find that (1) unipolar FAC events occur most frequently between 20 and 21 magnetic local time and multipolar FAC events tend to occur around local midnight and within 1 h after substorm onset. (2) Arcs in unipolar FAC systems have a typical width of 10–20 km and a spacing of 25–50 km. Arcs in multipolar FAC systems are wider and more separated. (3) Upward currents with more arcs embedded have larger intensities and widths. (4) Electric fields are strong and highly structured on the edges of multiple arc system with unipolar FAC. The fact that arcs with unipolar FAC are much more highly structured than the associated currents suggests that arc multiplicity is indicative not of a structured generator deep in the magnetosphere, but rather of the magnetosphere‐ionosphere coupling process.
Common acute lymphocytic leukemia antigen is identical to neutral endopeptidase

We purified CALLA from human kidney and isolated a cDNA clone reactive with two oligonucleotide probes corresponding to two distinct peptides. The amino acid sequence translated from the CALLA cDNA revealed 100% identity with that of human neutral endopeptidase (NEP, enkephalinase). The distribution of CALLA antigen and NEP in normal tissues are similar.
Modelling and Path Planning of Snake Robot in cluttered environment

Studying snake robot locomotion in a cluttered environment has been a complicated and computationally expensive task. This is because the motion model is discontinuous due to the physical contact with obstacles, and the contact force cannot be determined solely by contact positions. We present a unique mathematical model of the robot interacting with obstacles in which the contact forces are mapped on the basis of a viscous friction model. Also a motion planning strategy has been introduced which helps deriving the simplest path that ensures sufficient number of contacts of the robot with the obstacles required to reach a goal position. Numerical simulations and experimental results are presented to validate the theoretical approach.
Proportional Fairness-Based Beamforming and Signal Splitting for MISO-SWIPT Systems

The problem of proportional fairness-based beamforming and power splitting is investigated for simultaneous wireless information and power transferring systems. Due to the non-convexity of the formulated problem, a suboptimal solution is proposed based on the classical zero-forcing beamforming (ZFBF) and maximal ratio transmission techniques. To overcome the limitation of the ZFBF technique, a successive approximation-based algorithm is proposed. Simulation results verify the effectiveness of the proposed algorithms.
Miniaturized coaxial cylindrical cavity filters based on sub-wavelength metamaterial loaded resonator

This paper presents analysis, design and simulation of a novel sub-wavelength metamaterial resonator and its application in designing miniaturized filters. The presented sub-wavelength resonator is a coaxial cylindrical cavity in which a combination of an ordinary dielectric material and a metamaterial layer has been inserted. The general dispersion relation for such a resonator is formulated. Using this general formula and considering the sub-wavelength scenario, the approximate dispersion relation is extracted. Based on this approximate dispersion relation and through the use of an anisotropic μ negative (MNG) layer, it is shown that this configuration may in principal exhibit an arbitrary low resonant frequency for a fixed dimension. In comparison with miniaturized rectangular cavities and also miniaturized one-dimensional resonators, the above mentioned resonator provides the possibility of selecting a distinct mode of operation and also a further degree of freedom in the approximate dispersion relation which brings more flexibility in designing miniaturized resonators. As an example design and simulation of a miniaturized coaxial cavity resonator together with the complete design of the anisotropic MNG layer are presented. The resultant cavity diameter is shortened by approximately 69% in comparison with theoretical minimum dimensions of a cylindrical cavity resonator of the same height. Finally based on the designed miniaturized resonator a miniaturized filter with the center frequency of 5.85GHz and the bandwidth of 20MHz is designed and simulated.
An Online Social-Networking Enabled Telehealth System for Seniors - A Case Study

The past decade has seen healthcare costs rising faster than government expenditure in most developed countries. Various telehealth solutions have been proposed to make healthcare services more efficient and cost-effective. However, existing telehealth systems are focused on treating diseases instead of preventing them, suffer from high initial costs, lack extensibility, and do not address the social and psychological needs of patients. To address these shortcomings, we have employed a user-centred approach and leveraged Web 2.0 technologies to develop Healthcare4Life (HC4L), an online telehealth system targeted at seniors. In this paper, we report the results of a 6-week user study involving 43 seniors aged 60 and above. The results indicate that seniors welcome the opportunity of using online tools for managing their health, and that they are able to use such tools effectively. Functionalities should be tailored towards individual needs (health conditions). Users have strong opinions about the type of information they would like to submit and share. Social networking functionalities are desired, but should have a clear purpose such as social games or exchanging information, rather than broadcasting emotions and opinions. The study suggests that the system positively changes the attitude of users towards their health management, i.e. users realise that their health is not controlled by health professionals, but that they have the power to positively affect their well-being.
Statistical modeling of lake ice phenology: issues and implications

Numerous studies suggest the utility of lake ice phenology as an index of climate variability and change (e.g., PALECKI & BARRY 1986, SCHINDLER et al. 1990, RoBERTSON et al. 1992, WYNNE & LILLESAND 1993, AssEL & ROBERTSON 1995, ANDERSON et al. 1996, WYNNE et al. 1998). Interest in lake ice phenology as a proxy stems from numerous factors, including the following: (l) the magnitude of temperature increases predicted by global warming scenarios is predicted to be greatest in the midto high latitudes in winter and early spring, (2) some lake ice records commence prior to the onset of recorded temperatures, (3) lakes that freeze are often numerous in areas with a relative paucity of meteorological stations (PALECKI & BARRY 1986), and (4) lake ice can be detected from the space-borne sensors from which substantial archival data are available (MASLANIK & BARRY 1987, WYNNE & LILLESAND 1993, WYNNE et al. 1998). The use of climate proxies stems primarily from inherent constraints o n the use of direct temperature (or other) measurements such as short records, changes in instrumentation or protocol over time, insufficient measurement density, urban heat islands, ete. In addition, however, climate indicators are an integra! part of the "fingerprint method," the sui te of observations of both direct and proxy climate variables used to analyze observed climatic variability and change in the context of various global warming scenarios. MAUNDER (1992) defines the fingerprint method as "identification of an observed multivariate signal with a structure unique to the predicted enhanced greenhouse effect. " While the fingerprint method is not without critics (e.g., SCHNEIDER 1994), it is still part and parcel of state-of-the-art dimate change detection. Records of lake ice formation and breakup are thus important in studies of climate variability and change. However, like the direct measurements they supplement or replace, al! proxy measures have inherent limitations that impinge on inference. This is as true for lake ice phenology as for other proxies. In this paper, we highlight some of the more important issues for consideration. Issues to be discussed include the following: (l) changes in observers and protocols at both particular lakes and among lakes, (2) the spatial dependence of the data, (3) the length and range of longitudinal data, (4) years in which lakes do not freeze, (5) the effects of morphology, (6) the effects of other climatic variables besides temperature, (7) high interannual variability, and (8) anomalous events such as volcanic eruptions or EI Nifios.
Histotripsy of VX-2 tumor implanted in a renal rabbit model.

INTRODUCTION Histotripsy is an extracorporeal focused ultrasound (US) technology that uses controlled cavitation to induce nonthermal mechanical tissue fractionation. Feasibility of histotripsy ablation of normal renal tissue in an in vivo rabbit model has previously been demonstrated. Our specific objective in this study was to characterize the histologic effects of histotripsy on VX-2 tumor implanted in the kidneys of an in vivo rabbit model. METHODS VX-2 tumor was implanted below the renal capsule in 15 New Zealand white rabbits. Two weeks after implantation, tumors were localized with diagnostic US imaging. Targeted volumes within the observed tumor were treated with short (3 micros) pulses of 1 MHz acoustic energy at a repetition frequency of 300 Hz. Twenty tumors were treated with histotripsy and 7 served as tumor controls. Three normal kidneys were also treated with histotripsy. Kidneys and lungs were harvested, grossly inspected, and processed for histopathologic analysis. RESULTS Real-time US imaging confirmed presence of cavitation during all histotripsy treatments. Examination of tumor and kidney specimens revealed 100% tumor growth with an average tumor diameter of 7 mm (range 2-12). In 16 of 20 tumors treated with histotripsy, acellular zones of debris and finely disrupted cellular architecture were present on histology. Kidneys harvested 24 hours after treatment revealed an extensive inflammatory reaction. CONCLUSIONS Transcutaneous application of histotripsy to implanted VX-2 tumor in rabbit kidney produced fractionation of malignant tissue. These findings support the further study and development of histotripsy for potential oncologic application.
Crystal Structure of Bombyx mori Lipoprotein 6: Comparative Structural Analysis of the 30-kDa Lipoprotein Family

The 30-kDa lipoprotein (LP) family of mulberry silkworm comprises major hemolymph proteins specific to the fifth instar larvae. The family consists of 46 members, 24 of which are referred to as typical 30-kDa LPs. To date, two crystal structures of 30-kDa LPs from Bombyx mori have been described (Bmlp3 and Bmlp7). Here, we present the crystal structure of Bmlp6, another 30-kDa LP member. Bmlp6 is comprised of two domains characteristic of this family, the VHS-type N-terminal domain and β-trefoil C-terminal domain. The structures of the three 30-kDa LPs have been compared and a number of differences are noted, including loop conformation, the surface electrostatic potential, and the potential binding cavities. We discuss the observed structural differences in the light of the potential different roles of the particular 30-kDa LP members in silkworm physiology.