Miracle-dz/UniFAR-FTUs huggingface dataset:
Insufficient levels of NFIII and its low affinity for the origin of adenovirus type 12 (Ad12) DNA replication contribute to the abortive infection of BHK21 hamster cells by Ad12

Human adenovirus type 12 (Ad12) induces undifferentiated sarcomas in neonate Syrian hamsters and hence presents a suitable model for studies of the molecular mechanism of viral oncogenesis. Since we submit that an understanding of the early steps in the interaction between Ad12 and hamster cells might shed light on the initiation of malignant transformation, the abortive infection of BHK21 hamster cells with Ad12 has been investigated in detail. Ad12 replication in these cells is blocked in early stages, while Ad2 can replicate to moderate titers. Early Ad12 genes are expressed in BHK21 hamster cells, but there is a total block in Ad12 DNA replication and late gene transcription. The Ad5-transformed hamster cell line BHK297-C131, with the left terminus of Ad5 DNA chromosomally integrated and constitutively expressed, allows limited levels of Ad12 DNA replication and late transcription, probably through Ad5 E1 functions, but not the translation of late Ad12 gene products. We have now investigated the capacities of binding of nuclear proteins NFI and NFIII from permissive human KB cells, nonpermissive hamster BHK21 cells, and complementing BHK297-C131 cells to the origin of replication (ori) of Ad2 or Ad12 DNA. The electrophoretic mobility shift assay has been used to assess these binding reactions. The data support the notions that NFIII of BHK21 cells has a lower affinity for the ori of Ad12 DNA than for the ori of Ad2 DNA and that the levels of NFIII in BHK21 cells are markedly reduced compared with the levels in the permissive human KB cells or the complementing BHK297-C131 hamster cells. These deficiencies are contributing factors for the abortive infection of BHK21 hamster cells with Ad12. The lack of sufficient levels of NFIII in BHK21 cells is also consistent with the decreased replication capacity of Ad2 in hamster compared with human cell lines.
Cytoplasmic N-Terminal Protein Acetylation Is Required for Efficient Photosynthesis in Arabidopsis Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012377.

The Arabidopsis atmak3-1 mutant was identified on the basis of a decreased effective quantum yield of photosystem II. In atmak3-1, the synthesis of the plastome-encoded photosystem II core proteins D1 and CP47 is affected, resulting in a decrease in the abundance of thylakoid multiprotein complexes. DNA array–based mRNA analysis indicated that extraplastid functions also are altered. The mutation responsible was localized to AtMAK3, which encodes a homolog of the yeast protein Mak3p. In yeast, Mak3p, together with Mak10p and Mak31p, forms the N-terminal acetyltransferase complex C (NatC). The cytoplasmic AtMAK3 protein can functionally replace Mak3p, Mak10p, and Mak31p in acetylating N termini of endogenous proteins and the L-A virus Gag protein. This result, together with the finding that knockout of the Arabidopsis MAK10 homolog does not result in obvious physiological effects, indicates that AtMAK3 function does not require NatC complex formation, as it does in yeast. We suggest that N-acetylation of certain chloroplast precursor protein(s) is necessary for the efficient accumulation of the mature protein(s) in chloroplasts.
Stochastic Model Predictive Controller for the Integration of Building Use and Temperature Regulation

The aim of a modern Building Automation System (BAS) is to enhance interactive control strategies for energy efficiency and user comfort. In this context, we develop a novel control algorithm that uses a stochastic building occupancy model to improve mean energy efficiency while minimizing expected discomfort. We compare by simulation our Stochastic Model Predictive Control (SMPC) strategy to the standard heating control method to empirically demonstrate a 4.3% reduction in energy use and 38.3% reduction in expected discomfort.
Extraction of feature lines on triangulated surfaces using morphological operators

Triangle meshes are a popular representation of surfaces in computer graphics. Our aim is to detect feature on such surfaces. Feature regions distinguish themselves by high curvature. We are using discrete curvature analysis on triangle meshes to obtain curvature values in every vertex of a mesh. These values are then thresholded resulting in a so called binary feature vector. By adapting morphological operators to triangle meshes, noise and artifacts can be removed from the feature. We introduce an operator that determines the skeleton of the feature region. This skeleton can then be converted into a graph representing the desired feature. Therefore a description of the surface’s geometrical characteristics is constructed.
Reservation-based Network-on-Chip Timing Models for Large-scale Architectural Simulation

Architectural simulation is an essential tool when it comes to evaluating the design of future many-core chips. However, reproducing all the components of such complex systems precisely would require unreasonable amounts of computing power. Hence, a trade off between accuracy and compute time is needed. For this reason most state-of-the-art tools do not have accurate models for the networks-on-chip, and rely on timing models that permit fast-simulation. Generally, these models are very simplistic and disregard contention for the use of network resources. As the number of nodes in the network-on-chip grows, fluctuations with contention and other parameters can considerably affect the accuracy of such models. In this paper we present and evaluate a collection of timing models based on a reservation scheme which consider the contention for the use of network resources. These models provide results quickly while being more accurate than simple no-contention approaches.
Odd-Char Multivariate Hidden Field Equations

We present a multivariate version of Hidden Field Equations (HFE) over a nite eld of odd characteristic, with an extra embedding modi er. Combining these known ideas makes our new MPKC (multivariate public key cryptosystem) more e cient and scalable than any other extant multivariate encryption scheme. Switching to odd characteristics in HFE-like schemes a ects how an attacker can make use of eld equations. Extensive empirical tests (using magma-2.14, the best commercially available F4 implementation) suggests that our new construction is indeed secure against algebraic attacks using Grobner Basis algorithms. The embedding serves both to narrow down choices of pre-images and to guard against a possible Kipnis-Shamir type (rank) attack. We may hence reasonably argue that for practical sizes, prior attacks take exponential time. We demonstrate that our construction is in fact e cient by implementing practical-sized examples of our odd-char HFE with 3 variables ( THFE ) over F31. To be precise, our preliminary THFE implementation is 15× 20× the speed of RSA-1024.
Computer-aided software engineering (CASE): technology for improving software development productivity

Today, system developers are challenged to produce complex, high quality software to support explosive demand for new and revised computer applications. This challenge is complicated by severe resource constraints, forcing management to deploy new technologies, methods and procedures to manage this increasingly complex environment. Often the methods, procedures and technologies are not integrated. Therefore, they achieve less than desired improvements in productivity, or force management to make tradeoff decisions between software quality and developer efficiency.Computer-Aided Software Engineering (CASE) helps system developers meet their challenge by providing a new generation of integrated system development tools which provides an automated environment in which to design and implement system projects. CASE technology enables system developers to improve both quality and efficiency, resulting in a net improvement in maintenance and development productivity.The objectives of this paper are to provide the reader with sufficient information about CASE technology to develop an evaluation and implementation strategy for utilizing CASE to improve systems development productivity.
Variability in Testing for Antineutrophil Cytoplasmic Antibodies: A Survey of Participants in the College of American Pathologists Proficiency Testing Program.

CONTEXT -Variability in testing for antineutrophil cytoplasmic antibodies (ANCAs) contributes to confusion and controversy related to testing for vasculitis and other ANCA-associated diseases. OBJECTIVES -To survey laboratory testing practices regarding ANCA testing and to investigate differences in testing algorithms. DESIGN -Supplemental questions were sent to the 333 laboratories participating in the College of American Pathologists proficiency testing program for ANCA as part of the Special Immunology S2 Survey. RESULTS -A total of 315 laboratories submitted responses to the supplemental questions. Only 88 of 315 participants (28%) reported using a combination of indirect immunofluorescence (IFA) and enzyme immunoassay (EIA) techniques as recommended by current guidelines, with a few additional labs using IFA and multiplex bead assay as an acceptable alternative to EIA. Other labs reported using only IFA, EIA, or multiplex bead assays. CONCLUSIONS -A wide variety of testing algorithms are in use for ANCA testing despite evidence to suggest that a combination of IFA and EIA testing provides the most comprehensive information. Laboratories should inform clinicians clearly about testing practices and utility of testing in specific disease states.
Real-Time Stereo Vision Based Fingertip Detection and Tracking

Fingertip detection and tracking is the foundation of many hand-based natural Human Computer Interaction (HCI) applications. Previous methods either can hardly provide a natural way of interaction, or are too complex to be adopted in practical systems. In this paper, we propose a real-time stereo vision-based fingertip detection and tracking method that works very well in real environment. Our method can get the accurate fingertip position regardless the finger shape for the single finger. Fingertip detection is formulated as a graph theory problem, and can be solved easily given the 2D finger skeleton image. The accurate 3D location of the fingertip can be obtained based on stereo vision. To achieve the robustness against noise and occlusion, Kalman filter is applied to smooth the trajectory of fingertip. Our method is simple yet effective, and can run in real-time on a normal PC. Keywords-fingertip detection; finger tracking; stereo vision; finger segmentation; finger skeleton; trajectory; Kalman filter
Nerve growth factor withdrawal-induced cell death in neuronal PC12 cells resembles that in sympathetic neurons

Previous studies have shown that in neuronal cells the developmental phenomenon of programmed cell death is an active process, requiring synthesis of both RNA and protein. This presumably reflects a requirement for novel gene products to effect cell death. It is shown here that the death of nerve growth factor-deprived neuronal PC12 cells occurs at the same rate as that of rat sympathetic neurons and, like rat sympathetic neurons, involves new transcription and translation. In nerve growth factor-deprived neuronal PC12 cells, a decline in metabolic activity, assessed by uptake of [3H]2-deoxyglucose, precedes the decline in cell number, assessed by counts of trypan blue-excluding cells. Both declines are prevented by actinomycin D and anisomycin. In contrast, the death of nonneuronal (chromaffin-like) PC12 cells is not inhibited by transcription or translation inhibitors and thus does not require new protein synthesis. DNA fragmentation by internucleosomal cleavage does not appear to be a consistent or significant aspect of cell death in sympathetic neurons, neuronal PC12 cells, or nonneuronal PC12 cells, notwithstanding that the putative nuclease inhibitor aurintricarboxylic acid protects sympathetic neurons, as well as neuronal and nonneuronal PC12 cells, from death induced by trophic factor removal. Both phenotypic classes of PC12 cells respond to aurintricarboxylic acid with similar dose-response characteristics. Our results indicate that programmed cell death in neuronal PC12 cells, but not in nonneuronal PC12 cells, resembles programmed cell death in sympathetic neurons in significant mechanistic aspects: time course, role of new protein synthesis, and lack of a significant degree of DNA fragmentation.
Misunderstanding and misrepresentation: a reply to Hutchison and Schagen

In this journal, I previously published a paper discussing how to conduct an analysis based on a cluster sample. In that paper, I outlined several widely adopted alternative approaches, and pointed out that such approaches are anyway not needed for population figures, and not possible for non-probability samples (Gorard 2007). Thus, I queried the prevalence and relevance of complex approaches such as multi-level modelling (MLM) for most real-life analyses. I illustrated the lack of substantive difference in the results obtained via MLM and other approaches in a number of recent studies. And I repeated my challenge (from Gorard 2003a) for those advocating the use of MLM to find and publish a real study in which the policy or practice implications of the research would differ depending on whether MLM or a sensible alternative was used. Instead of taking up this challenge, Hutchison and Schagen (2008) responded with a paper that misrepresents (and even misquotes) what I said, in an attempt to defend their favoured technique of MLM. In my reply to them here, I hope to establish their misunderstanding of this important topic. This might lead readers to imagine that this will be a highly technical paper about a statistical issue. It is not. I also hope to establish their misrepresentation of my paper. The issue is one of wider and greater concern than the surface argument about whether MLM is of any great value. It is about the kind of intellectual processes we are prepared to endorse as a field.1 This paper deals first with areas in which we agree, and then areas in which Hutchison and Schagen (2008) simply restate their position, before turning to the more substantive consideration of why it is not necessary or appropriate to use MLM in most real analytical situations.
Water Vapor Tomography With Two Microwave Radiometers

The present study shows how two microwave radiometers can be used to derive a 2-D water vapor field by means of a tomographic technique. For this purpose, synthetic measurements are simulated with a radiative transfer model applied to water vapor fields. These fields are obtained from a Large Eddy Simulation model, producing realistic atmospheric boundary layer structures. To derive the water vapor field from the microwave measurements, an iterative procedure based on the optimal estimation technique is used. The synthetic measurements are calculated for various measurement geometries. The comparison of the measurement geometries from one versus two radiometers shows that the standard deviation obtained from measurements with the two radiometers is smaller by 15%, and the degrees of freedom for signal are simultaneously larger by 61%. For deriving the best possible water vapor field, the spatial distribution of the measurement angles and the angular resolution of the scan are important. The angles are optimally distributed when most measurements originate from regions with a high variability in the water vapor field.
Fast and Accurate TIS Testing Method for Wireless User Equipment With RSS Reporting

A fast and accurate total isotropic sensitivity (TIS) testing method for wireless user equipment based on radiated sensitivity measurement and received signal strength (RSS) reporting is proposed in this paper. Innovative techniques for avoiding the effects of RSS reporting errors on TIS accuracy and reducing the total TIS measurement time are presented and incorporated into the testing procedures. The proposed method is suitable for receiver sensitivity testing of single input, single output radio systems having RSS reporting such as cellular communication, WiFi, and Bluetooth systems.
Efficient kernel calculation for multirelational data

Today, most of the data in business applications is stored in relational database systems or in data warehouses built on top of relational database systems. Often, for more data is available than can be processed by standard learning algorithms in reasonable time. This paper presents an extension to kernel algorithms that makes use of the more compact relational representation of data instead of the usual attribute-value representation to significantly speed up the kernel calculation.
Application of inter-simple sequence repeats to insect cell lines: Identification at the clonal andtissue-specific level

SummaryInter-simple sequence repeat (ISSR) primers designed to anneal to microsatellites were used to obtain deoxyribonucleic acid (DNA) fingerprint profiles to distinguish among 16 established insect cell lines derived from an assortment of lepidopteran, dipteran, and coleopteran species. Three different levels of cell line comparison were made: (1) between parents and their clones, (2) among cell lines derived from different tissues from the same species, and (3) among cell lines derived from different insect species. Of the 16 repeat oligonucleotide primers used in this study, nine primers generated several unique markers to distinguish between parental cell lines and their clones. Four of the 16 primers also generated DNA profiles with a number of unique bands, enabling the distinction among cell lines derived from specific tissues from the same species. In addition, ISSR-generated DNA profiles provided the greatest number of unique markers to distinguish easily among insect cell lines derived from different species.
The bolometric light curves and physical parameters of stripped-envelope supernovae

The optical and optical/near-infrared pseudobolometric light curves of 84 stripped-envelope supernovae (SNe) are constructed using a consistent method and a standard cosmology. The light curves are analysed to derive temporal characteristics and peak luminosity L_p, enabling the construction of a luminosity function. Subsequently, the mass of ^(56)Ni synthesised in the explosion, along with the ratio of ejecta mass to ejecta kinetic energy, are found. Analysis shows that host-galaxy extinction is an important factor in accurately determining luminosity values as it is significantly greater than Galactic extinction in most cases. It is found that broad-lined SNe Ic (SNe Ic-BL) and gamma-ray burst SNe are the most luminous subtypes with a combined median L_p, in erg s^(−1), of log(L_p) = 42.99 compared to 42.51 for SNe Ic, 42.50 for SNe Ib, and 42.36 for SNe IIb. It is also found that SNe Ic-BL synthesise approximately twice the amount of ^(56)Ni compared with SNe Ic, Ib, and IIb, with median M_(Ni) = 0.34, 0.16, 0.14, and 0.11 M_⊙, respectively. SNe Ic-BL, and to a lesser extent SNe Ic, typically rise from L_p/2 to L_p more quickly than SNe Ib/IIb; consequently, their light curves are not as broad.
Spherical matching for temporal correspondence of non-rigid surfaces

This paper introduces spherical matching to estimate dense temporal correspondence of non-rigid surfaces with genus-zero topology. The spherical domain gives a consistent 1D parameterization of non-rigid surfaces for matching. Non-rigid 3D surface correspondence is formulated as the recovery of a bijective mapping between two surfaces in the 2D domain. Formulating matching as a 2D bijection guarantees a continuous one-to-one surface correspondence without overfolding. This overcomes limitations of direct estimation of non-rigid surface correspondence in the 3D domain. A multiple resolution coarse-to-fine algorithm is introduced to robustly estimate the dense correspondence which minimizes the disparity in shape and appearance between two surfaces. Spherical matching is applied to derive the temporal correspondence between non-rigid surfaces reconstructed at successive frames from multiple view video sequences of people. Dense surface correspondence is recovered across complete motion sequences for both textured and uniform regions, without the requirement for a prior model of human shape or kinematics structure for tracking
Credit-Scheduled Delay-Bounded Congestion Control for Datacenters

Small RTTs (~tens of microseconds), bursty flow arrivals, and a large number of concurrent flows (thousands) in datacenters bring fundamental challenges to congestion control as they either force a flow to send at most one packet per RTT or induce a large queue build-up. The widespread use of shallow buffered switches also makes the problem more challenging with hosts generating many flows in bursts. In addition, as link speeds increase, algorithms that gradually probe for bandwidth take a long time to reach the fair-share. An ideal datacenter congestion control must provide 1) zero data loss, 2) fast convergence, 3) low buffer occupancy, and 4) high utilization. However, these requirements present conflicting goals. This paper presents a new radical approach, called ExpressPass, an end-to-end credit-scheduled, delay-bounded congestion control for datacenters. ExpressPass uses credit packets to control congestion even before sending data packets, which enables us to achieve bounded delay and fast convergence. It gracefully handles bursty flow arrivals. We implement ExpressPass using commodity switches and provide evaluations using testbed experiments and simulations. ExpressPass converges up to 80 times faster than DCTCP in 10 Gbps links, and the gap increases as link speeds become faster. It greatly improves performance under heavy incast workloads and significantly reduces the flow completion times, especially, for small and medium size flows compared to RCP, DCTCP, HULL, and DX under realistic workloads.
Abundant distribution of TARP γ‐8 in synaptic and extrasynaptic surface of hippocampal neurons and its major role in AMPA receptor expression on spines and dendrites

Transmembrane α‐amino‐3‐hydroxyl‐5‐isoxazolepropionate (AMPA) receptor regulatory proteins (TARPs) play pivotal roles in AMPA receptor trafficking and gating. Here we examined cellular and subcellular distribution of TARP γ‐8 in the mouse brain. Immunoblot and immunofluorescence revealed the highest concentration of γ‐8 in the hippocampus. Immunogold electron microscopy demonstrated dense distribution of γ‐8 on the synaptic and extrasynaptic surface of hippocampal neurons with very low intracellular labeling. Of the neuronal surface, γ‐8 was distributed at the highest level on asymmetrical synapses of pyramidal cells and interneurons, whereas their symmetrical synapses selectively lacked immunogold labeling. Then, the role of γ‐8 in AMPA receptor expression was pursued in the hippocampus using mutant mice defective in the γ‐8 gene. In the mutant cornu ammonis (CA)1 region, synaptic and extrasynaptic AMPA receptors on dendrites and spines were severely reduced to 35–37% of control levels, whereas reduction was mild for extrasynaptic receptors on somata (74%) and no significant decrease was seen for intracellular receptors within spines. In the mutant CA3 region, synaptic AMPA receptors were reduced mildly at asymmetrical synapses in the stratum radiatum (67% of control level), and showed no significant decrease at mossy fiber–CA3 synapses. Therefore, γ‐8 is abundantly distributed on hippocampal excitatory synapses and extrasynaptic membranes, and plays an important role in increasing the number of synaptic and extrasynaptic AMPA receptors on dendrites and spines, particularly, in the CA1 region. Variable degrees of reduction further suggest that other TARPs may also mediate this function at different potencies depending on hippocampal subregions, input sources and neuronal compartments.