Miracle-dz/UniFAR-FTUs huggingface dataset:
The Polymerase η Translesion Synthesis DNA Polymerase Acts Independently of the Mismatch Repair System To Limit Mutagenesis Caused by 7,8-Dihydro-8-Oxoguanine in Yeast

ABSTRACT Reactive oxygen species are ubiquitous mutagens that have been linked to both disease and aging. The most studied oxidative lesion is 7,8-dihydro-8-oxoguanine (GO), which is often miscoded during DNA replication, resulting specifically in GC → TA transversions. In yeast, the mismatch repair (MMR) system repairs GO·A mismatches generated during DNA replication, and the polymerase η (Polη) translesion synthesis DNA polymerase additionally promotes error-free bypass of GO lesions. It has been suggested that Polη limits GO-associated mutagenesis exclusively through its participation in the filling of MMR-generated gaps that contain GO lesions. In the experiments reported here, the SUP4-o forward-mutation assay was used to monitor GC → TA mutation rates in strains defective in MMR (Msh2 or Msh6) and/or in Polη activity. The results clearly demonstrate that Polη can function independently of the MMR system to prevent GO-associated mutations, presumably through preferential insertion of cytosine opposite replication-blocking GO lesions. Furthermore, the Polη-dependent bypass of GO lesions is more efficient on the lagging strand of replication and requires an interaction with proliferating cell nuclear antigen. These studies establish a new paradigm for the prevention of GO-associated mutagenesis in eukaryotes.
A linear method for the retrieval of sun-induced chlorophyll fluorescence from GOME-2 and SCIAMACHY data

Abstract. Global retrievals of near-infrared sun-induced chlorophyll fluorescence (SIF) have been achieved in the last few years by means of a number of space-borne atmospheric spectrometers. Here, we present a new retrieval method for medium spectral resolution instruments such as the Global Ozone Monitoring Experiment-2 (GOME-2) and the SCanning Imaging Absorption SpectroMeter for Atmospheric CHartographY (SCIAMACHY). Building upon the previous work by Guanter et al. (2013) and Joiner et al. (2013), our approach provides a solution for the selection of the number of free parameters. In particular, a backward elimination algorithm is applied to optimize the number of coefficients to fit, which reduces also the retrieval noise and selects the number of state vector elements automatically. A sensitivity analysis with simulated spectra has been utilized to evaluate the performance of our retrieval approach. The method has also been applied to estimate SIF at 740 nm from real spectra from GOME-2 and for the first time, from SCIAMACHY. We find a good correspondence of the absolute SIF values and the spatial patterns from the two sensors, which suggests the robustness of the proposed retrieval method. In addition, we compare our results to existing SIF data sets, examine uncertainties and use our GOME-2 retrievals to show empirically the relatively low sensitivity of the SIF retrieval to cloud contamination.
Brain Circulation during Panic Attack: A Transcranial Doppler Study with Clomipramine Challenge

Introduction. Cerebral blood flow has been well studied in patients with panic disorder, but only few studies analyzed the mechanisms underlying the onset of a panic attack. The aim of the present study was to monitor the cerebral hemodynamics modifications during a panic attack. Materials and Methods. 10 panic disorder patients with recent onset, fully drug naïve, were compared to 13 patients with panic disorder with a previous history of treatment and to 14 controls. A continuous bilateral monitoring of mean flow velocities in right and left middle cerebral arteries was performed by transcranial Doppler. Clomipramine was chosen as challenge. Results. Eight out of 10 patients drug naïve and 6 control subjects out of 13 had a full blown panic attack during the test, whereas none of the patients with a history of treatment panicked. The occurrence of a panic attack was accompanied by a rapid decrease of flow velocities in both right and left middle cerebral arteries. Discussion. The bilateral acute decrease of mean flow velocity during a panic attack suggests the vasoconstriction of the microcirculation of deep brain structures perfused by middle cerebral arteries and involved in the so-called “fear circuitry,” thus suggesting that cerebral homeostatic dysfunctions seem to have a key role in the onset of a panic attack.
Statistical quantification of brain shape deformation with homologous brain shape modeling

Brain shape is deformed regionally by kinds of cerebral diseases and the degree of progress. Therefore quantitative evaluation of the deformation using MR images is effective for diagnosis of cerebral diseases. We proposed a homologous brain shape modeling deformation for quantitative evaluation of the brain shape using sulcal-distribution index (SDI) in MR images. So in this paper, we propose the homologous brain shape modeling. And we find the availability of the homologous brain shape modeling by investigating relationship between the movement distance with the homologous brain shape modeling and gray matter (GM) density of voxel based morphometry (VBM). This study employed nine male and two female and investigate a difference between male group and female group. The experimental results showed that the relationship between the homologous brain shape modeling and VBM was found from the same detection significant difference.
A Globally Optimal Algorithm for Robust TV-L1 Range Image Integration

Robust integration of range images is an important task for building high-quality 3D models. Since range images, and in particular range maps from stereo vision, may have a substantial amount of outliers, any integration approach aiming at high-quality models needs an increased level of robustness. Additionally, a certain level of regularization is required to obtain smooth surfaces. Computational efficiency and global convergence are further preferable properties. The contribution of this paper is a unified framework to solve all these issues. Our method is based on minimizing an energy functional consisting of a total variation (TV) regularization force and an L1 data fidelity term. We present a novel and efficient numerical scheme, which combines the duality principle for the TV term with a point-wise optimization step. We demonstrate the superior performance of our algorithm on the well-known Middlebury multi-view database and additionally on real-world multi-view images.
Allele-Specific Down-Regulation of RPTOR Expression Induced by Retinoids Contributes to Climate Adaptations

The mechanistic target of rapamycin (MTOR) pathway regulates cell growth, energy homeostasis, apoptosis, and immune response. The regulatory associated protein of MTOR encoded by the RPTOR gene is a key component of this pathway. A previous survey of candidate genes found that RPTOR contains multiple SNPs with strong correlations between allele frequencies and climate variables, consistent with the action of selective pressures that vary across environments. Using data from a recent genome scan for selection signals, we honed in on a SNP (rs11868112) 26 kb upstream to the transcription start site of RPTOR that exhibits the strongest association with temperature variables. Transcription factor motif scanning and mining of recently mapped transcription factor binding sites identified a binding site for POU class 2 homeobox 1 (POU2F1) spanning the SNP and an adjacent retinoid acid receptor (RAR) binding site. Using expression quantification, chromatin immunoprecipitation (ChIP), and reporter gene assays, we demonstrate that POU2F1 and RARA do bind upstream of the RPTOR gene to regulate its expression in response to retinoids; this regulation is affected by the allele status at rs11868112 with the derived allele resulting in lower expression levels. We propose a model in which the derived allele influences thermogenesis or immune response by altering MTOR pathway activity and thereby increasing fitness in colder climates. Our results show that signatures of genetic adaptations can identify variants with functional effects, consistent with the idea that selection signals may be used for SNP annotation.
Dynamic bandwidth reservation scheduling for the integrated wireless access of H.263 videoconference traffic with voice and e-mail packet traffic

A medium access control (MAC) protocol for wireless multimedia communications is presented and investigated. We explore, via an extensive simulation study, the performance of the protocol when integrating voice, H.263 variable bit rate (VBR) video and bursty e-mail data packet traffic over a wireless picocellular system of high capacity. Our scheme achieves high aggregate channel throughput in all examined cases of traffic loads, while satisfying the quality of service (QoS) requirements of each traffic type.
Strategies for minimising errors in hierarchical web categorisation

On the Web, browsing and searching categories is a popular method of finding documents. Two well-known category-based search systems are the Yahoo! ~and DMOZ hierarchies, which are maintained by experts who assign documents to categories. However, manual categorisation by experts is costly, subjective, and not scalable with the increasing volumes of data that must be processed. Several methods have been investigated for effective automatic text categorisation. These include selection of categorisation methods, selection of pre-categorised training samples, use of hierachies, and selection of document fragments or features. In this paper, we further investigate categorisation into Web hierarchies and the role of hierarchical information in improving categorisation effectiveness. We introduce new strategies to reduce errors in hierarchical categorisation. In particular, we propose novel techniques that shift the assignment into higher level categories when lower level assignment is uncertain. Our results show that absolute error rates can be reduced by over 2%.
Finding Similar Users in Facebook

Online social networks are rapidly asserting themselves as popular services on the Web. A central point is to determine whether two distinct users can be considered similar, a crucial concept with interesting consequences on the possibility to accomplish targeted actions like, for example, political and social aggregations or commercial promotions. In this chapter we propose an approach in order to estimate the similarity of two users based on the knowledge of social ties (i.e., common friends and groups of users) existing among users, and the analysis of activities (i.e., social events) in which users are involved. For each of these indicators, we draw a local measure of user similarity which takes into account only their joint behaviours. After this, we consider the whole network of relationships among users along with local values of similarities and combine them to obtain a global measure of similarity. Such a computation is carried out by applying the Katz coefficient, a popular parameter introduced in Social Science research. Finally, similarity values produced for each social activity are merged into a unique value of similarity by applying linear regression.
Further evidence that DDHD2 gene mutations cause autosomal recessive hereditary spastic paraplegia with thin corpus callosum

A. Magariello*, L. Citrigno*, S. Zuchner, M. Gonzalez, A. Patitucci, V. Sofia, F. L. Conforti, I. Pappalardo, R. Mazzei, C. Ungaro, M. Zappia and M. Muglia Institute of Neurological Sciences, National Research Council, Mangone (CS), Italy; Department of Human Genetics and Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA; and Dipartimento G.F. Ingrassia Sezione di Neuroscienze Universit a di Catania, Catania, Italy
Delirium superimposed on dementia: a survey of delirium specialists shows a lack of consensus in clinical practice and research studies

ABSTRACT Background: Despite advances in delirium knowledge and the publication of best practice guidelines, uncertainties exist regarding assessment of Delirium Superimposed on Dementia (DSD). An international survey of delirium specialists was undertaken to evaluate current practice. Methods: Invitations to participate in an online survey were distributed by email among members of four international delirium associations with additional publication on their websites. The survey covered the assessment and diagnosis of DSD in clinical practice and research studies. Questions were structured around current practice and attitudes. Results: The 205 responders were mostly confident that they could detect DSD with 60% rating their confidence at 7 or above on a likert scale of 0 (none) to 10 (excellent). Seventy-six percent felt that Dementia with Lewy Bodies (DLB) was the most challenging dementia subtype in which to diagnose DSD. Several scales were used to assess for the presence of DSD including the Confusion Assessment Method (CAM) (54%), DSM-5 criteria (25%) and CAM-ICU (15%). Responders stated that attention (71%), fluctuation in cognitive status (65%), and arousability (41%) were the most clinically useful features to assess when diagnosing DSD. Motor fluctuations were also deemed important but 61% had no specific test to monitor these. Conclusions: The largest survey of DSD practice to date demonstrates that despite good levels of confidence in recognizing DSD, there exists a lack of consensus concerning assessment and diagnosis globally. These findings suggest the need for the development of more research leading to precise diagnostic criteria and comprehensive guidelines regarding the assessment and diagnosis of DSD.
Coupling degree model of technological innovation networks: Based on organizational learning capability and network embeddedness capability

Based on the analysis of coupling relationship of the enterprise organizational learning capability and network embeddedness capability in technological innovation networks, coupling degree evaluation model was set up by means of synergetics theory in this paper. Then, the model was used to evaluate the coupling degree of technological innovation networks including H enterprise,which was the core in that technological innovation networks, on its organizational learning capability and network embeddedness capability. The empirical results shows that: the relation between organizational learning capability and network embeddedness capability is in the middle coupling state and the moderate coupling synergy statel.
Q-Parametrization and an SDP for H∞-optimal Decentralized Control

Abstract We consider the problem of finding decentralized controllers to optimize an H ∞ -norm. This can be cast as a convex optimization problem when certain conditions are satisfied, but it is an infinite-dimensional problem that still cannot be addressed with existing methods. We use Q -parametrization to approach the original problem with a sequence of finite-dimensional problems. A method is discussed to solve the resulting finite-dimensional approximated convex problem. It is then shown how this problem can be cast as a semidefinite program and generally solved much more efficiently.
XED: Exposing On-Die Error Detection Information for Strong Memory Reliability

Large-granularity memory failures continue to be a critical impediment to system reliability. To make matters worse, as DRAM scales to smaller nodes, the frequency of unreliable bits in DRAM chips continues to increase. To mitigate such scaling-related failures, memory vendors are planning to equip existing DRAM chips with On-Die ECC. For maintaining compatibility with memory standards, On-Die ECC is kept invisible from the memory controller. This paper explores how to design high reliability memory systems in presence of On-Die ECC. We show that if On-Die ECC is not exposed to the memory system, having a 9-chip ECC-DIMM (implementing SECDED) provides almost no reliability benefits compared to an 8-chip non-ECC DIMM. We also show that if the error detection of On-Die ECC can be exposed to the memory controller, then Chipkill-level reliability can be achieved even with a 9-chip ECC-DIMM. To this end, we propose eXposed On-Die Error Detection (XED), which exposes the On-Die error detection information without requiring changes to the memory standards or consuming bandwidth overheads. When the On-Die ECC detects an error, XED transmits a pre-defined “catch-word” instead of the corrected data value. On receiving the catch-word, the memory controller uses the parity stored in the 9-chip of the ECC-DIMM to correct the faulty chip (similar to RAID-3). Our studies show that XED provides Chipkill-level reliability (172× higher than SECDED), while incurring negligible overheads, with a 21% lower execution time than Chipkill. We also show that XED can enable Chipkill systems to provide Double-Chipkill level reliability while avoiding the associated storage, performance, and power overheads.
A TGFβ-Smad4-Fgf6 signaling cascade controls myogenic differentiation and myoblast fusion during tongue development

The tongue is a muscular organ and plays a crucial role in speech, deglutition and taste. Despite the important physiological functions of the tongue, little is known about the regulatory mechanisms of tongue muscle development. TGFβ family members play important roles in regulating myogenesis, but the functional significance of Smad-dependent TGFβ signaling in regulating tongue skeletal muscle development remains unclear. In this study, we have investigated Smad4-mediated TGFβ signaling in the development of occipital somite-derived myogenic progenitors during tongue morphogenesis through tissue-specific inactivation of Smad4 (using Myf5-Cre;Smad4flox/flox mice). During the initiation of tongue development, cranial neural crest (CNC) cells occupy the tongue buds before myogenic progenitors migrate into the tongue primordium, suggesting that CNC cells play an instructive role in guiding tongue muscle development. Moreover, ablation of Smad4 results in defects in myogenic terminal differentiation and myoblast fusion. Despite compromised muscle differentiation, tendon formation appears unaffected in the tongue of Myf5-Cre;Smad4flox/flox mice, suggesting that the differentiation and maintenance of CNC-derived tendon cells are independent of Smad4-mediated signaling in myogenic cells in the tongue. Furthermore, loss of Smad4 results in a significant reduction in expression of several members of the FGF family, including Fgf6 and Fgfr4. Exogenous Fgf6 partially rescues the tongue myoblast fusion defect of Myf5-Cre;Smad4flox/flox mice. Taken together, our study demonstrates that a TGFβ-Smad4-Fgf6 signaling cascade plays a crucial role in myogenic cell fate determination and lineage progression during tongue myogenesis.
Energy Efficiency vs. Economic Cost of Cellular Networks under Co-channel Interference

In this paper we analyze the efficiency of cellular network designs, by taking into account the co-channel interference among cells, different amounts of available bandwidths, and frequency reuse. A realistic power consumption model is considered for the energy efficiency analysis, and for the economic analysis it is employed a model in which the total cost is composed by three factors: spectrum license, energy and infrastructure costs. Our results show that different conclusions can be obtained according to the focus of the network design: energy efficiency or total costs. Assuming an economic point of view, the most cost efficient solutions can be obtained when the number of base stations and the available bandwidth are the factors to be balanced, as the infrastructure cost and the spectrum license costs correspond to the most relevant fraction of the total costs. However, considering the energy efficiency anlysis, it can be more beneficial to employ a higher system bandwidth and balance the number of base stations and the reuse of frequencies in order to minimize the required transmit power.
Effect of magnetic nanoparticles on apoptosis and cell cycle induced by wogonin in Raji cells

Traditional Chinese medicine is gradually becoming a new source of anticancer drugs. One such example is wogonin, which is cytotoxic to various cancer cell lines in vitro. However, due to its low water solubility, wogonin is restricted to clinical administration. Recently, the application of drug-coated magnetic nanoparticles (MNPs) to increase water solubility of the drug and to enhance its chemotherapeutic efficiency has attracted much attention. In this study, wogonin was conjugated with the drug delivery system of MNPs by mechanical absorption polymerization to fabricate wogonin-loaded MNPs. It was demonstrated that MNPs could strengthen wogonin-induced cell inhibition, apoptosis, and cell cycle arrest in Raji cells by methylthiazol tetrazolium assay, flow cytometer assay, and nuclear 4′,6-diamidino-2-phenylindole staining. Furthermore, the molecular mechanisms of these phenomena were explored by western blot, in which the protein levels of caspase 8 and caspase 3 were increased significantly while those of survivin and cyclin E were decreased significantly in wogonin-MNPs group. These findings suggest that the combination of wogonin and MNPs provides a promising strategy for lymphoma therapy.
Another Generalization of the Reed-Muller Codes

The punctured binary Reed-Muller code is cyclic and was generalized into the punctured generalized Reed-Muller code over $\gf(q)$ in the literature. The major objective of this paper is to present another generalization of the punctured binary Reed-Muller code. Another objective is to construct a family of reversible cyclic codes that are related to the newly generalized Reed-Muller codes.
Plastic Deformation Clusters with High Kinetic Energy in Metallic Glass

Although localized atomic rearrangements have been considered to be the underlying mechanism of plastic deformation in metallic glass, the nucleation and evolution of such plasticity events are still elusive. With the aid of molecular dynamics analysis, this study revealed that a series of localized atomic rearrangement events would occur in metallic glass as demonstrated by the formation of high-kinetic-energy clusters. It was found that atomic clusters of average sizes of 1 to 2 nm nucleate during elastic deformation, and become prevailing after yielding. The cores of these clusters contain several high-velocity atoms, which drive the local structural change and accommodate plastic strain. The nucleation and evolution of the local plasticity events are shown clearly by the strong dynamic signature, attributed to the spontaneous structural reshuffling after crossing an energy barrier.
A Comparison of Rheology Data for Radioactive and Stimulant Savannah River Site Waste

This document reviews radioactive and simulant rheology data on SRS waste slurries. Simulant sludge slurries have been prepared at Optima: Tank 51 for Sludge Batch 1A (SB1A) and trimmed for Sludge Batch 1B (SB1B), at USC-Columbia: Tank 8 and Tank 40 for Sludge Batch 2 (SB2), and at Clemson Environmental Technology Laboratory (CETL): SB2, Sludge Batch 3 (SB3), and several generic simulants. Various radioactive waste tank slurry samples have been analyzed for rheology in the SRTC Shielded Cells during the past 25 years. More recently, some rheological measurements have been made on the DWPF qualification samples for new sludge batches or on special samples pulled to help with resolution of processing issues. This document attempts to make comparisons of rheological data for systems where there were both some radioactive slurry data and some potentially similar simulant slurry data. The Approach section describes the basic data types encountered, e.g. sludges, Sludge Receipt and Adjustment Tank (SRAT) products, and Slurry Mix Evaporator (SME) products. The last are equivalent to melter feeds. This is followed by a discussion of rheometry and the Bingham Plastic fluid model. This model has been used to reduce rheological data on SRS waste slurries over the past twentymore » years. « less