Miracle-dz/UniFAR-FTUs huggingface dataset:
Quality of service in an information-centric network

QoS provisioning is one of the key challenges facing current as well as future Internet architectures. Its dependency on content recognition does not allow a straightforward support of QoS in the IP, host-centric, model. In contrast, Information-Centric Networking (ICN) offers native content identification in the network, which can be exploited to develop a common, elegant, framework for supporting QoS-based delivery. Therefore, ICN may naturally overcome many of the cumbersome fixes and limitations of today's solutions. In this work, we exploit the flexibility in semantic representation offered by ICN to present a flexible and scalable ICN-based QoS model. Our model defines QoS requirements as information items that can be linked to the content at various aggregation levels, independent of the communication approach. Therefore, it can be applied uniformly to various network types and hierarchies. Furthermore, our model offers enhanced traffic treatment as well as resource utilization while significantly reducing the overhead on the network.
Circuit model for parameter study of Marx generators on megajoule machines

Sandia National Laboratories (SNL) is planning to redesign the pulsed power driver on Z, including the Marx generators, the intermediate-store water capacitors, the laser triggered switches and the pulse-forming lines to increase the energy delivered to a Z-pinch load. The present Marx system consists of 36 generators that store over 11 MJ of energy. Each generator contains sixty 1.30 /spl mu/F capacitors that are charged in bipolar fashion to 95 kV. The system erects to 5.7 MV when switched, and stores 366 kJ of energy. The 60-capacitors are configured as 12-capacitors to a row and 5-rows to a generator. A circuit model has been developed using MICROCAP to model one of the 36-Marx generators. The model contains the capacitors, inter-stage switches, ground resistors, trigger resistors, and the connection and internal inductance, capacitance, and resistance associated with the generator components. The paper describes the approach used to develop the model, presents the model, validates the model by comparing output to measured data, and shows how parasitic coupling can affect generator performance.
Development and Use of IgM/J‐Chain Fusion Proteins for Characterization of Immunoglobulin Superfamily Ligand‐Receptor Interactions

Discovery of binding partners for immunoglobulin molecules expressed by cells of the immune system is an important topic of current research. However, many ligand‐receptor interactions are of low affinity, and hence detection is refractory to most established protocols. We evaluated fusion proteins based on human IgM as high avidity probes to screen for ligand‐receptor binding. We describe methods for cloning, expression, and quantification of IgM fusion proteins with J‐chain. Furthermore, we outline protocols to assess binding of IgM fusion proteins to cells and to plate‐bound proteins. Compared to standard IgG‐fusion proteins, IgM + J chain increased binding of a test interaction, PD‐L1 to PD‐1, up to 1000‐fold. Curr. Protoc. Protein Sci. 75:19.24. 1‐19.24. 11. © 2014 by John Wiley & Sons, Inc.
High-Throughput Antibody Generation Using Multiplexed Immunization and Immunogen Array Analysis

In this work, the authors developed a new screening approach using multiplexed immunization and immunogen array analysis to improve the efficiency of antibody screening for high-throughput antibody generation. The immunogen array is based on a 96-well format in which different immunogens and negative as well as positive controls are immobilized in each well, thus making it possible to screen hundreds of antibody candidates simultaneously. To demonstrate this approach, a model of 4 mixed immunogens immunization was employed. In total, 675 antibody candidates were screened before and after established antibody hybridomas in parallel with immunogen arrays and enzyme-linked immunosorbent assay. The signal intensity, specificity, and cross-reactivity of produced antibody candidates were analyzed using a hierarchical cluster algorithm to track the characteristics of antibody candidates during antibody generation, which might reduce the number of false-positive and false-negative binding of antibodies. Moreover, 4 monoclonal antibodies that were produced successfully recognized their corresponding target antigens.
Reduced DICER1 Elicits an Interferon Response in Endometrial Cancer Cells

DICER1 is essential for the generation of mature miRNAs and other short noncoding RNAs. Several lines of investigation implicate DICER1 as a tumor suppressor. Reduced DICER1 levels and changes in miRNA abundance have been associated with aggressive tumor phenotypes. The global effects of reduced DICER1 on mRNA transcript abundance in tumor cells remain largely unknown. We used short hairpin RNA to stably knock down DICER1 in endometrial cancer cell lines to begin to determine how reduced DICER1 activity contributes to tumor phenotypes. DICER1 knockdown did not affect cell proliferation but caused enhanced cell migration and growth in soft agar. miRNA and mRNA profiling in KLE cells revealed overall decreases in miRNA levels and changes in the relative abundance of many mRNAs. One of the most striking changes in mRNA levels was the upregulation of IFN-stimulated genes (ISG), the majority of which lack known miRNA target sequences. IFNβ, a key upstream regulator of the IFN response, was significantly increased in DICER1 knockdowns in the AN3CA, Ishikawa, and KLE endometrial cancer cell lines and in the normal endometrial cell line EM-E6/E7/TERT. IFNβ secreted in media from KLE and EM-E6/E7/TERT shDcr cells was sufficient to activate an IFN response in HT29 cells. The reduced miRNA processing in DICER1 knockdowns was associated with increases in pre-miRNAs in the cytoplasm. Our findings suggest that elevated pre-miRNA levels trigger the IFN response to double-stranded RNA. We thus report a novel effect of reduced DICER1 function in cancer cells. Mol Cancer Res; 10(3); 316–25. ©2012 AACR.
The effect of matched filtering with programmable root raised cosine filter on error vector magnitude of M-QAM broadband over visible light

This paper investigates the Error Vector Magnitude (EVM) obtained using different parameters of Root Raised Cosine Filter (RRCF) for Visible Light Communication (VLC) front ends for M-QAM (M-ary Quadrature Amplitude Modulation) Broadband over Visible Light (BVL). The authors conducted a real measurement EVM using a modern modular PCI eXtensions for Instrumentation (PXI) measuring apparatus. This sophisticated measuring system is built by vector-signal generator RF VSG NI PXI-5670 and vector-signal analyzer RF VSA NI PXI-5660. BVL is a new research direction based essentially on VLC technology. Again, it is intended to utilize the visible spectrum of optical radiation as a communication direction to the end user (download) and to utilize the infra-red spectrum of optical radiation in the reverse communication direction (upload). This article studies the influence of roll-off factor (α) to the value EVM for 4QAM and 16QAM modulations for different power levels (0dBm, 5dBm, 10 dBm).
Guideline adherence in ectopic pregnancy management.

BACKGROUND Evidence-based guidelines have been issued for ectopic pregnancy (EP), covering both diagnostic and therapeutic management. In general, guidelines aim to reduce practice variation and to improve quality of care. To assess the guideline adherence in the management of EP, we developed guideline-based quality indicators and measured patient care in various hospitals. METHODS A panel of experts and clinicians developed quality indicators based on recommendations from the Dutch guideline on EP management, using the systematic RAND-modified Delphi method. With these indicators, patient care was assessed in six Dutch hospitals between January 2003 and December 2005. For each quality indicator, a ratio for guideline adherence was calculated. Overall adherence was reported, as well as adherence per hospital type, i.e. academic, teaching and non-teaching hospitals. RESULTS Out of 30 guideline-based recommendations, 12 quality indicators were selected covering procedural, structural and outcome aspects of care. For 317 women surgically treated for EP, these aspects were assessed. Overall adherence to the guideline was 75%. The highest adherence (98%) was observed for performing transvaginal sonography during the diagnostic workup. The lowest adherence (21%) was observed for performing salpingotomy in case of contra-lateral tubal pathology. Wide variance in adherence (0-100%) existed between academic, teaching and non-teaching hospitals. CONCLUSIONS The overall guideline adherence was reasonable, with ample room for improvement in various aspects of care. Further research should focus on the barriers for guideline dissemination and adherence, to further improve the management of EP.
Evidences of histologic thrombotic microangiopathy and the impact in renal outcomes of patients with IgA nephropathy

Introduction IgA nephropathy (IgAN) is the most common primary glomerulopathy worldwide. According to the Oxford Classification, changes in the kidney vascular compartment are not related with worse outcomes. This paper aims to assess the impact of thrombotic microangiopathy (TMA) in the outcomes of Brazilian patients with IgAN. Materials and Methods Analysis of clinical data and kidney biopsy findings from patients with IgAN to assess the impact of TMA on renal outcomes. Results The majority of the 118 patients included were females (54.3%); mean age of 33 years (25;43); hypertension and hematuria were observed in 67.8% and 89.8%, respectively. Median creatinine: 1.45mg/dL; eGFR: 48.8ml/min/1.73m2; 24-hour proteinuria: 2.01g; low serum C3: 12.5%. Regarding to Oxford Classification: M1: 76.3%; E1: 35.6%; S1: 70.3%; T1/T2: 38.3%; C1/C2: 28.8%. Average follow-up: 65 months. Histologic evidence of TMA were detected in 21 (17.8%) patients and those ones presented more frequently hypertension (100% vs. 61%, p <0.0001), hematuria (100% vs 87.6%, p=0.0001), worse creatinine levels (3.8 vs. 1.38 mg/dL, p=0.0001), eGFR (18 vs. 60 ml/min/1.73m2), p =0.0001), low serum C3 (28.5% vs. 10.4%, p =0.003), lower hemoglobin levels (10.6 vs. 12.7g/dL, p<0.001) and platelet counts (207,000 vs. 267,000, p=0.001). Biopsy findings of individuals with TMA revealed only greater proportions of E1 (68% vs. 32%, p = 0.002). Individuals with TMA were followed for less time (7 vs. 65 months, p<0.0001) since they progressed more frequently to chronic kidney disease (CKD) requiring renal replacement therapy (RRT) (71.4% vs. 21,6%, p<0.0001). Male sex, T1/T2, and TMA were independently associated with progression to CKD-RRT. Conclusions In this study patients with TMA had worse clinical manifestations and outcomes. In terms of histologic evidence, E1 distinguished patients with TMA from other patients. These findings indicate that vascular compartment may also be a prognostic marker in IgAN patients.
The Relation Between Injury of the Spinothalamocortical Tract and Central Pain in Chronic Patients With Mild Traumatic Brain Injury

Objectives:Little is known about the pathogenetic etiology of central pain in patients with traumatic brain injury (TBI). We investigated the relation between injury of the spinothalamocortical tract (STT) and chronic central pain in patients with mild TBI. Design:Retrospective survey. Participants:We recruited 40 consecutive chronic patients with mild TBI and 21 normal control subjects: 8 patients were excluded by the inclusion criteria and the remaining 32 patients were finally recruited. The patients were classified according to 2 groups based on the presence of central pain: the pain group (22 patients) and the nonpain group (10 patients). Methods:Diffusion tensor tractography for the STT was performed using the Functional Magnetic Resonance Imaging of the Brain Software Library. Values of fractional anisotropy (FA), mean diffusivity (MD), and tract volume of each STT were measured. Results:Lower FA value and tract volume were observed in the pain group than in the nonpain group and the control group (P < .05). By contrast, higher MD value was observed in the pain group than in the nonpain group and the control group (P < .05). However, no significant differences in all diffusion tensor imaging parameters were observed between the nonpain group and the control group (P > .05). Conclusions:Decreased FA and tract volume and increased MD of the STTs in the pain group appeared to indicate injury of the STT. As a result, we found that injury of the STT is related to the occurrence of central pain in patients with mild TBI. We believe that injury of the STT is a pathogenetic etiology of central pain following mild TBI.
Antiviral cytotoxic T cell response induced by in vivo priming with a free synthetic peptide

Induction in vivo of antiviral cytotoxic T cell response was achieved in a MHC class I-dependent fashion by immunizing mice three times with a free unmodified 15-mer peptide derived from the nucleoprotein of lymphocytic choriomeningitis virus in IFA. The effector T cells are CD8+, restricted to the class I Ld allele of the analyzed mouse strain, and are specific both at the level of secondary restimulation in vitro and at the effector T cell level. These results suggest that cocktails of viral peptides may be used as antiviral T cell vaccines.
Bis(pyrrolidin-1-yl)phosphinic (2,4-difluorobenzoyl)amide

The P atom in the title molecule, C15H20F2N3O2P, is in a distorted tetrahedral P(O)(N)(N)2 environment. The phosphoryl group and the NH unit adopt a syn orientation with respect to each other. An F atom at position 2 and an H atom at position 6 are found to occupy similar sites in a 0.70:0.30 ratio and were refined with fixed occupancies. The pyrrolidin-1-yl rings are disordered over two sets of sites, with site occupancies of 0.566 (6) and 0.434 (6), and were refined using a two-part model. In the crystal, hydrogen-bonded dimers linked by pairs of N—H⋯O(P) hydrogen bonds generate an R 2 2(8) ring motif.
A measurement approach based on micro-doppler maps for human motion analysis and detection

Human motion analysis is a task of increasing importance in several modern application fields, such as in medicine, avionics, security, and disaster recovery. It requires the application of sophisticated measurement techniques based on micro-Doppler effect, human walking modeling, cinematic simulation, image processing and measurements. In this paper, a novel and comprehensive measurement approach is proposed for the detection and analysis of human motion. The approach combines theoretical concepts and tools of micro-Doppler theory, image processing, and human modeling, in a original way. The attention is primarily focused on some measurement issues and implications that, if taken into account, can give an important enhancement to micro-Doppler-based future applications. Some simulation results concerning one specific issue of the measurement approach are finally provided and discussed.
New genotypic adaptability and stability analyses using Legendre polynomials and genotype-ideotype distances

Developing cultivars with superior performance in different cultivation environments is one of the main challenges of breeding programs. The current adaptability and stability analyses have limitations, especially when used with trials with genetic or statistical imbalances, heterogeneity of residual variances, and genetic covariance. Thus, adaptability and stability analyses based on mixed model approaches are an effective alternative in such cases. We propose a new methodology for genotypic adaptability and stability analyses, based on Legendre polynomials and genotype-ideotype distances aiming at greater precision when recommending cultivars. We applied the methodology to a set of common bean cultivars throughout a multi-environment trial. We used a set of 13 trials, where they were classified in unfavorable or favorable environments, depending on the average of the cultivars in these trials. The results showed that the methodology allows to predict the genotypic values of cultivars in environments where they were not evaluated with high accuracy values, therefore circumventing the imbalance of the experiments. From these values, it was possible to measure the genotypic adaptability according to ideotypes. The stability of the cultivars was quantified as the invariance of their behavior throughout the trials. The use of ideotypes based on real data allowed a better comparison of the performance of cultivars across environments.
Distorted face image segmentation in PCA with neural network

In this paper, we propose a new face image restoration method based on the features extracted from the noisy images given by the principal components of the noise covariance matrix. This technique deliberate the additive normal scattered degradation classic and use of a code shrinkage technique to remove noise from the images. The proposed work have been a large number of artificial neural networks and learning algorithms with PCA for distorted pixels to solve group face image feature extraction problems, most of them being adaptive in nature and well-suited for many real environments where adaptive approach is required as a well-known statistical technique for face feature extraction, data compression, multivariate data for serious of images.
Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories

The pandemic of SARS coronavirus 2 (SARS-CoV-2) has motivated an intensive analysis of its molecular epidemiology following its worldwide spread. To understand the early evolutionary events following its emergence, a dataset of 985 complete SARS-CoV-2 sequences was assembled. Variants showed a mean 5.5-9.5 nucleotide differences from each other, commensurate with a mid-range coronavirus substitution rate of 3×10−4 substitutions/site/year. Almost half of sequence changes were C->U transitions with an 8-fold base frequency normalised directional asymmetry between C->U and U->C substitutions. Elevated ratios were observed in other recently emerged coronaviruses (SARS-CoV and MERS-CoV) and to a decreasing degree in other human coronaviruses (HCoV-NL63, -OC43, -229E and -HKU1) proportionate to their increasing divergence. C->U transitions underpinned almost half of the amino acid differences between SARS-CoV-2 variants, and occurred preferentially in both 5’U/A and 3’U/A flanking sequence contexts comparable to favoured motifs of human APOBEC3 proteins. Marked base asymmetries observed in non-pandemic human coronaviruses (U>>A>G>>C) and low G+C contents may represent long term effects of prolonged C->U hypermutation in their hosts. Importance The evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short and long term evolution. Repeated cycles of mutation and reversion in favoured mutational hotspots and the widespread occurrence of amino acid changes with no adaptive value for the virus represents a quite different paradigm of virus sequence change from neutral and Darwinian evolutionary frameworks that are typically used in molecular epidemiology investigations.
GABI-Kat SimpleSearch: A Flanking Sequence Tag (FST) Database for the Identification of T-DNA Insertion Mutants in Arabidopsis Thaliana

SUMMARY GABI-Kat SimpleSearch is a database of flanking sequence tags (FSTs) of T-DNA mutagenized Arabidopsis thaliana lines that were generated by the GABI-Kat project. Sequences flanking the T-DNA insertion sites were aligned to the A.thaliana genome sequence, annotated with information about the FST, the insertion site and the line from which the FST was derived. A web interface permits text-based as well as sequence-based searches for relevant insertions. GABI-Kat SimpleSearch aims to help biologists to quickly find T-DNA insertion mutants for their research. AVAILABILITY http://www.mpiz-koeln.mpg. de/GABI-Kat/
Network coding scheme with multi-rate transmission in 802.11 DCF wireless networks

Recently network coding has been proven as a very promising technique to improve wireless network throughput. In multi-rate wireless networks, simply seeking more coding opportunities or coding more packets into one frame without exploiting multi-rate feature may lead to selecting low-rate links for transmission, and thus compromise the performance gain brought by network coding. In this paper, we aim at exploiting the potential benefits brought by both multi-rate and network coding. We carefully address the bottleneck problem in applying network coding to multi-rate networks, and propose an multi-rate COPE-like network coding scheme, which is called COPE-MR and employs the Multi-rate Rate Adaptation(MRA) algorithm. It implements COPE with some extension to allow it to work in multi-rate environment. Simulation experiments results based on NS-2 demonstrate that COPE-MR can significantly improve network performances in terms of both throughput and end-to-end delay in 802.11 DCF multi-rate environment, at a relatively low cost of signaling overhead.
Quantitative mutant analysis of viral quasispecies by chip-based matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry

RNA viruses exist as quasispecies, heterogeneous and dynamic mixtures of mutants having one or more consensus sequences. An adequate description of the genomic structure of such viral populations must include the consensus sequence(s) plus a quantitative assessment of sequence heterogeneities. For example, in quality control of live attenuated viral vaccines, the presence of even small quantities of mutants or revertants may indicate incomplete or unstable attenuation that may influence vaccine safety. Previously, we demonstrated the monitoring of oral poliovirus vaccine with the use of mutant analysis by PCR and restriction enzyme cleavage (MAPREC). In this report, we investigate genetic variation in live attenuated mumps virus vaccine by using both MAPREC and a platform (DNA MassArray) based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Mumps vaccines prepared from the Jeryl Lynn strain typically contain at least two distinct viral substrains, JL1 and JL2, which have been characterized by full length sequencing. We report the development of assays for characterizing sequence variants in these substrains and demonstrate their use in quantitative analysis of substrains and sequence variations in mixed virus cultures and mumps vaccines. The results obtained from both the MAPREC and MALDI-TOF methods showed excellent correlation. This suggests the potential utility of MALDI-TOF for routine quality control of live viral vaccines and for assessment of genetic stability and quantitative monitoring of genetic changes in other RNA viruses of clinical interest.