Miracle-dz/UniFAR-FTUs huggingface dataset:
miR2Disease: a manually curated database for microRNA deregulation in human disease

‘miR2Disease’, a manually curated database, aims at providing a comprehensive resource of microRNA deregulation in various human diseases. The current version of miR2Disease documents 1939 curated relationships between 299 human microRNAs and 94 human diseases by reviewing more than 600 published papers. Around one-seventh of the microRNA–disease relationships represent the pathogenic roles of deregulated microRNA in human disease. Each entry in the miR2Disease contains detailed information on a microRNA–disease relationship, including a microRNA ID, the disease name, a brief description of the microRNA–disease relationship, an expression pattern of the microRNA, the detection method for microRNA expression, experimentally verified target gene(s) of the microRNA and a literature reference. miR2Disease provides a user-friendly interface for a convenient retrieval of each entry by microRNA ID, disease name, or target gene. In addition, miR2Disease offers a submission page that allows researchers to submit established microRNA–disease relationships that are not documented. Once approved by the submission review committee, the submitted records will be included in the database. miR2Disease is freely available at http://www.miR2Disease. org.
An Empirical Taxonomy of Structures of Work Organizations.

The taxonomy of structures of work organizations presented is based on three previously established empirical dimensions: structuring of activities, concentration of authority, and line control of workflow. On the basis of a sample of 52 organizations in the English Midlands, clusters of organizations on these three dimensions are examined and a sevenfold classification of organization structures is developed. These are identified as full bureaucracy, nascent full bureaucracy, work flow bureaucracy, nascent workflow bureaucracy, preworkflow bureaucracy, personnel bureaucracy, and implicitly structured organizations, their characteristic contextual features as to size, technology, dependence on other organizations, and ownership are demonstrated, and a possible developmental sequence is suggested. The results indicate that the concept of a single bureaucratic type is no longer useful, since bureaucracy takes different forms in different settings.
Neuromuscular recruitment related to stimulus presentation and task instruction during the anti‐saccade task

The contextual control of movement requires the transformation of sensory information into appropriate actions, guided by task‐appropriate rules. Previous conceptualizations of the sensorimotor transformations underlying anti‐saccades (look away from a stimulus) have suggested that stimulus location is first registered and subsequently transformed into its mirror location before being relayed to the motor periphery. Here, by recording neck muscle activity in monkeys performing anti‐saccades, we demonstrate that stimulus presentation induces a transient recruitment of the neck muscle synergy used to turn the head in the wrong direction, even though subjects subsequently looked away from the stimulus correctly. Such stimulus‐driven aspects of recruitment developed essentially at reflexive latencies (∼60–70 ms after stimulus presentation), and persisted at modest eccentricities regardless of head‐restraint. Prior to stimulus presentation, neck muscle activity also reflected whether the animals were preparing for an anti‐saccade or a pro‐saccade (look toward a stimulus). Neck muscle activity prior to erroneous anti‐saccades also resembled that observed prior to pro‐saccades. These results emphasize a parallel nature to the sensorimotor transformations underlying the anti‐saccade task, suggesting that the top‐down and bottom‐up processes engaged in this task influence the motor periphery. The bottom‐up aspects of neck muscle recruitment also fit within the context of recent results from the limb‐movement literature, showing that stimulus‐driven activation of muscle synergies may be a generalizing strategy in inertial‐laden systems.
Learning and Transformation in the Context of Hawaiian Traditional Ecological Knowledge

Traditional ecological knowledge is a potentially powerful medium in which to teach environmental education and has the potential for influencing transformative learning. Although many educators agree that one of the focuses of environmental education is adult transformation, this has not been extensively explored in the context of Hawaiian environmental knowledge. Specifically, there has been very little work done in immersion courses where nonnative and part-native students learn from local and indigenous experts. The purpose of this study is to explore the possibility of transformative learning in this context. This article investigates student responses to the course curriculum and instructional methodologies of an undergraduate, introductory immersion course on Hawaiian environmental knowledge. The article also explores one student’s transformation through her participation in the course and describes the conditions that were met to catalyze that transformation.
Coded multicast fronthauling and edge caching for multi-connectivity transmission in fog radio access networks

This work studies the advantages of coded multicasting for the downlink of a Fog Radio Access Network (F-RAN) system equipped with a multicast fronthaul link. In this system, a control unit (CU) in the baseband processing unit (BBU) pool is connected to distributed edge nodes (ENs) through a multicast fronthaul link of finite capacity, and the ENs have baseband processing and caching capabilities. Each user equipment (UE) requests a file in a content library which is available at the CU, and the requested files are served by the closest ENs based on the cached contents and on the information received on the multicast fronthaul link. The performance of coded multicast fronthauling is investigated in terms of the delivery latency of the requested contents under the assumption of pipelined transmission on the fronthaul and edge links and of single-user encoding and decoding strategies based on the hard transfer of files on the fronthaul links. Extensive numerical results are provided to validate the advantages of the coded multicasting scheme compared to uncoded unicast and multicast strategies.
HUBCODE: hub-based forwarding using network coding in delay tolerant networks

Most people-centric delay tolerant networks have been shown to exhibit power-law behavior. Analysis of the temporal connectivity graph of such networks reveals the existence of hubs, a fraction of the nodes, which are collectively connected to the rest of the nodes. In this paper, we propose a novel forwarding strategy called HubCode, which seeks to use the hubs as message relays. The hubs employ random linear network coding to encode multiple messages addressed to the same destination, thus reducing the forwarding overheads. Further, the use of the hubs as relays ensures that most messages are delivered to the destinations. Two versions of HubCode are presented, with each scheme exhibiting contrasting behavior in terms of the computational costs and routing overheads. We formulate a mathematical model for message delivery delay and present a closed-form expression for the same. We validate our model and demonstrate the efficacy of our solutions in comparison with other forwarding schemes by simulating a large-scale vehicular delay tolerant network using empirically collected movement traces of a city-wide public transport network. Under pragmatic assumptions, which account for short contact durations between nodes, our schemes outperform comparable strategies by more than 20%. Copyright © 2011 John Wiley & Sons, Ltd.
Development of exposed die large body to die size ratio wafer level package technology

Traditionally fan out wafer level package technology has been associated with lower power, smaller body sizes (typically <; 8 mm × 8 mm), small body-to-die size area ratios (<;2) and fine pitch BGAs (0.4 mm or less). This work extends this technology to larger body sizes up to 13 mm × 13 mm, higher powers, > 5 W, and larger body-to-die size area ratios up to 10.5. It is shown that such packages can be readily manufactured in a 300 mm wafer format with yields exceeding 99% and final package warpage <; 75 um. Further, data is presented showing that 10 mm × 10 mm packages with a body to die area ratio of 6.25 are compatible with moisture sensitivity level 1, and easily pass 2000 temperature cycle (-55C to 125C air to air) and 288 hr uHAST. That is to say they have reliability that is compatible with that required for all storage and communications applications. Larger package sizes, up to 13 mm × 13 mm, and body-to-die area ratios, > 10, have also been demonstrated. However, failures in extended temperature cycle were found in these larger packages. All of the failures were due to pre-identified package design flaws that violated well established rules. This indicates if such packages were designed with no rule violations then they would meet the reliability requirements needed for communications and storage applications.
Long-range projections coordinate distributed brain-wide neural activity with a specific spatiotemporal profile

Significance What makes the brain tick? A simple yet challenging question that has captivated our minds for centuries. This sentiment was fittingly reflected in the launch of The BRAIN Initiative 3 years ago, spurred by the rapid advancement of noninvasive brain imaging and neuronal mapping technologies that have advanced our understanding of neural networks, which are central to brain functions and behavior. Here, we study the patterns of large-scale brain-wide interactions mediated by thalamo-cortical networks through optogenetics and functional MRI. We found that the thalamus can recruit long-range cortical and subcortical networks and initiate their interactions in a spatiotemporally specific manner. This finding provides a fresh impetus to study the mysteries of the brain. One challenge in contemporary neuroscience is to achieve an integrated understanding of the large-scale brain-wide interactions, particularly the spatiotemporal patterns of neural activity that give rise to functions and behavior. At present, little is known about the spatiotemporal properties of long-range neuronal networks. We examined brain-wide neural activity patterns elicited by stimulating ventral posteromedial (VPM) thalamo-cortical excitatory neurons through combined optogenetic stimulation and functional MRI (fMRI). We detected robust optogenetically evoked fMRI activation bilaterally in primary visual, somatosensory, and auditory cortices at low (1 Hz) but not high frequencies (5–40 Hz). Subsequent electrophysiological recordings indicated interactions over long temporal windows across thalamo-cortical, cortico-cortical, and interhemispheric callosal projections at low frequencies. We further observed enhanced visually evoked fMRI activation during and after VPM stimulation in the superior colliculus, indicating that visual processing was subcortically modulated by low-frequency activity originating from VPM. Stimulating posteromedial complex thalamo-cortical excitatory neurons also evoked brain-wide blood-oxygenation-level–dependent activation, although with a distinct spatiotemporal profile. Our results directly demonstrate that low-frequency activity governs large-scale, brain-wide connectivity and interactions through long-range excitatory projections to coordinate the functional integration of remote brain regions. This low-frequency phenomenon contributes to the neural basis of long-range functional connectivity as measured by resting-state fMRI.
ILP with Noise and Fixed Example Size: A Bayesian Approach

Current inductive logic programming systems are limited in their handling of noise, as they employ a greedy covering approach to constructing the hypothesis one clause at a time. This approach also causes di(cid:14)culty in learning recursive predicates. Additionally, many current systems have an implicit expectation that the cardinality of the positive and negative examples re(cid:13)ect the \proportion" of the concept to the instance space. A framework for learning from noisy data and (cid:12)xed example size is presented. A Bayesian heuristic for (cid:12)nding the most probable hypothesis in this general framework is derived. This approach evaluates a hypothesis as a whole rather than one clause at a time. The heuristic, which has nice theoretical properties, is incorporated in an ILP system, Lime. Experimental results show that Lime handles noise better than FOIL and PROGOL. It is able to learn recursive de(cid:12)nitions from noisy data on which other systems do not perform well. Lime is also capable of learning from only positive data and also from only negative data.
CCM: Low cost dynamic data exchange to emulate RAM on NAND flash

In embedded systems, it brings great benefits to use NAND flash for dynamic data exchange like using RAM, since RAM is usually expensive and consumes much energy. However, the major hardware limitations of NAND flash make it difficult to directly and dynamically read\write\erase on NAND flash. Traditional virtual memory systems are all based on flash translation layer and file system, which lead to frequently flash read\write\erase and more RAM requirement. To address this problem, we propose a Comet Circle Model (CCM) to emulate RAM for low cost embedded systems in this paper. CCM dynamically makes the distribution of valid pages in NAND flash follow a fixed function through integrating its physical page-level mapping and circularly write-back techniques. As a result, CCM can select a block without valid pages to write data almost every time in data writing, which avoids data moving among blocks. Both theoretical analysis and experimental results show that the data moving times and erase counts of CCM closely reach the theoretical lower bounds.
The ERF 11 Transcription Factor Promotes Internode Elongation by Activating Gibberellin Biosynthesis and Signaling 1 [ OPEN ]

Department of Biology, Duke University, Durham, North Carolina 27705 (X.Z., Z.-L.Z., L.T., J.P., E.A.N., T.-p.S.); RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan (J.Y., Y.K.); Department of Cell and Systems Biology, University of Toronto, Ontario M5S 3B2, Canada (S.L., D.D., P.M.); Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario M5S 3B2, Canada (D.D.); and State Key Laboratory of Genetic Engineering and Fudan Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (K.Q.)
Role of AP-1 in Developmentally Regulated Lysosomal Trafficking in Trypanosoma brucei

ABSTRACT African trypanosomes are the causative agents of human trypanosomiasis (sleeping sickness). The pathogenic stage of the parasite has unique adaptations to life in the bloodstream of the mammalian host, including upregulation of endocytic and lysosomal activities. We investigated stage-specific requirements for cytoplasmic adaptor/clathrin machinery in post-Golgi apparatus biosynthetic sorting to the lysosome using RNA interference silencing of the Tbμ1 subunit of adaptor complex 1 (AP-1), in conjunction with immunolocalization, kinetic analyses of reporter transport, and quantitative endocytosis assays. Tbμ1 silencing was lethal in both stages, indicating a critical function(s) for the AP-1 machinery. Transport of soluble and membrane-bound secretory cargoes was Tbμ1 independent in both stages. In procyclic parasites, trafficking of the lysosomal membrane protein, p67, was disrupted, leading to cell surface mislocalization. The lysosomal protease trypanopain was also secreted, suggesting a transmembrane-sorting receptor for this soluble hydrolase. In bloodstream trypanosomes, both p67 and trypanopain trafficking were unaffected by Tbμ1 silencing, suggesting that AP-1 is not necessary for biosynthetic lysosomal trafficking. Endocytosis in bloodstream cells was also unaffected, indicating that AP-1 does not function at the flagellar pocket. These results indicate that post-Golgi apparatus sorting to the lysosome is critically dependent on the AP-1/clathrin machinery in procyclic trypanosomes but that this machinery is not necessary in bloodstream parasites. We propose a simple model for stage-specific default secretory trafficking in trypanosomes that is consistent with the behavior of other soluble and glycosylphosphatidylinositol-anchored cargos and which is influenced by upregulation of endocytosis in bloodstream parasites as an adaptation to life in the mammalian bloodstream.
The Teaching-Family Model: A Replicable System of Care

SUMMARY For nearly 30 years, the Teaching-Family technology of treatment, staff training, and program evaluation has been faithfully applied within diverse human service agencies throughout the country. The model serves as a means to organize and orient child care agencies and direct care providers, to provide a common ground for dealing with youngsters in residential treatment settings. The philosophy of care derives from the natural strengths of families bolstered by knowledge able, accessible, and helpful support staff. The Teaching-Family Model was developed over a 20 year period through the collaborative efforts of NIMH, the Achievement Place Research Project at the University of Kansas, and several community-based group homes in Kansas. Within the Teaching-Family model of residential treatment for difficult youth, problem behaviors are dealt with by creating supportive family-style home environments staffed by professional teaching-parents serving 6 to 8 residents. The homes are typically affiliated with local social service agencies that provide Teaching-Family Model training, consultation, and evaluation services. Agencies providing Teaching-Family services undergo routine consumer-based and onsite evaluations, carried out by the National Teaching-Family Association to assure that treatment, training, and evaluation services are being implemented faithfully.
Multiuser MISO Beamforming for Simultaneous Wireless Information and Power Transfer

This paper studies a multiuser multiple-input single-output (MISO) broadcast simultaneous wireless information and power transfer (SWIPT) system, where a multi-antenna access point (AP) sends wireless information and energy simultaneously via spatial multiplexing to multiple single-antenna receivers each of which implements information decoding (ID) or energy harvesting (EH). We aim to maximize the weighted sum-power transferred to all EH receivers subject to given minimum signal-to-interference-and-noise ratio (SINR) constraints at different ID receivers. In particular, we consider two types of ID receivers (referred to as Type I and Type II, respectively) without or with the capability of cancelling the interference from (a priori known) energy signals. For each type of ID receivers, we formulate the joint information and energy transmit beamforming design as a nonconvex quadratically constrained quadratic program (QCQP). First, we obtain the globally optimal solutions for our formulated QCQPs by applying an optimization technique so-called semidefinite relaxation (SDR). It is shown via SDR that under the condition of independently distributed user channels, no dedicated energy beam is used for the case of Type I ID receivers to achieve the optimal solution; while for the case of Type II ID receivers, employing no more than one energy beam is optimal. Next, we establish a new form of the celebrated uplink-downlink duality for our studied downlink beamforming problems, and thereby develop alternative algorithms to obtain the same optimal solutions as by SDR. Finally, numerical results are provided to evaluate the performance of proposed optimal beamforming designs for MISO SWIPT systems.
Fast Solvers for Models of Fluid Flow with Spectral Elements

Title of dissertation: FAST SOLVERS FOR MODELS OF FLUID FLOW WITH SPECTRAL ELEMENTS P. Aaron Lott, Doctor of Philosophy, 2008 Dissertation directed by: Professor Howard Elman Department of Computer Science Institute for Advanced Computer Studies & Associate Research Professor Anil Deane Institute for Physical Sciences and Technology We introduce a preconditioning technique based on Domain Decomposition and the Fast Diagonalization Method that can be applied to tensor product based discretizations of the steady convection-diffusion and the linearized Navier-Stokes equations. The method is based on iterative substructuring where fast diagonalization is used to efficiently eliminate the interior degrees of freedom and subsidiary subdomain solves. We demonstrate the effectiveness of this preconditioner in numerical simulations using a spectral element discretization. This work extends the use of Fast Diagonalization to steady convection-diffusion systems. We also extend the “least-squares commutator” preconditioner, originally developed for the finite element method [19], to a matrix-free spectral element framework. We show that these two advances, when used together, allow for efficient computation of steady-state solutions the the incompressible Navier-Stokes equations using high-order spectral element discretizations. FAST SOLVERS FOR MODELS OF FLUID FLOW WITH SPECTRAL ELEMENTS
N-Cadherin Inhibits Schwann Cell Migration on Astrocytes

Astrocytes exclude Schwann cells (SCs) from the central nervous system (CNS) at peripheral nerve entry zones and restrict their migration after transplantation into the CNS. We have modeled the interactions between SCs, astrocytes, and fibroblasts in vitro. Astrocytes and SCs in vitro form separate territories, with sharp boundaries between them. SCs migrate poorly when placed on astrocyte monolayers, but migrate well on various other surfaces such as laminin (LN) and skin fibroblasts. Interactions between individual SCs and astrocytes result in long-lasting adhesive contacts during which the SC is unable to migrate away from the astrocyte. In contrast, SC interactions with fibroblasts are much shorter with less arrest of migration. SCs adhere strongly to astrocytes and other SCs, but less well to substrates that promote migration, such as LN and fibroblasts. SC-astrocyte and SC-SC adhesion is mediated by the calcium-dependent cell adhesion molecule N-cadherin. Inhibition of N-cadherin function by calcium withdrawal, peptides containing the classical cadherin cell adhesion recognition sequence His-Ala-Val, or antibodies directed against this sequence inhibit SC adhesion and increase SC migration on astrocytes. We suggest that N-cadherin-mediated adhesion to astrocytes inhibits the widespread migration of SCs in CNS tissue.
Minimum reading fluency necessary for comprehension among second‐grade students

The current study examined the relationship between oral reading fluency (ORF) and reading comprehension for students in second grade. A total of 84 participants were randomly assigned to oneoffourconditionsthatinvolvedreadingagrade-appropriatepassagewitheither0%,10%,20%, or 30% scrambled words and answering subsequent comprehension questions. The correlation coefficient between ORF and the number of comprehension questions correctly answered was r = . 54. Receiver operating characteristics were then used to empirically derive a minimum ORF score necessary for comprehension, indicating that when these students read 63 words correct per minute they successfully comprehended what they read. Finally, the diagnostic accuracy of the derived criterion of 63 words read correctly per minute was tested and resulted in overall correct classification of . 80. C