Miracle-dz/UniFAR-FTUs huggingface dataset:
The 3′-untranslated region of mRNAs as a site for ribozyme cleavage-dependent processing and control in bacteria

ABSTRACT Besides its primary informational role, the sequence of the mRNA (mRNA) including its 5′- and 3′- untranslated regions (UTRs), contains important features that are relevant for post-transcriptional and translational regulation of gene expression. In this work a number of bacterial twister motifs are characterized both in vitro and in vivo. The analysis of their genetic contexts shows that these motifs have the potential of being transcribed as part of polycistronic mRNAs, thus we suggest the involvement of bacterial twister motifs in the processing of mRNA. Our data show that the ribozyme-mediated cleavage of the bacterial 3′-UTR has major effects on gene expression. While the observed effects correlate weakly with the kinetic parameters of the ribozymes, they show dependence on motif-specific structural features and on mRNA stabilization properties of the secondary structures that remain on the 3′-UTR after ribozyme cleavage. Using these principles, novel artificial twister-based riboswitches are developed that exert their activity via ligand-dependent cleavage of the 3′-UTR and the removal of the protective intrinsic terminator. Our results provide insights into possible biological functions of these recently discovered and widespread catalytic RNA motifs and offer new tools for applications in biotechnology, synthetic biology and metabolic engineering.
The Study of High-Affinity TCRs Reveals Duality in T Cell Recognition of Antigen: Specificity and Degeneracy1

TCRs exhibit a high degree of Ag specificity, even though their affinity for the peptide/MHC ligand is in the micromolar range. To explore how Ag specificity is achieved, we studied murine T cells expressing high-affinity TCRs engineered by in vitro evolution for binding to hemoglobin peptide/class II complex (Hb/I-Ek). These TCRs were shown previously to maintain Ag specificity, despite having up to 800-fold higher affinity. We compared the response of the high-affinity TCRs and the low-affinity 3.L2 TCR toward a comprehensive set of peptides containing single substitutions at each TCR contact residue. This specificity analysis revealed that the increase in affinity resulted in a dramatic increase in the number of stimulatory peptides. The apparent discrepancy between observed degeneracy in the recognition of single amino acid-substituted Hb peptides and overall Ag specificity of the high-affinity TCRs was examined by generating chimeric peptides between the stimulatory Hb and nonstimulatory moth cytochrome c peptides. These experiments showed that MHC anchor residues significantly affected TCR recognition of peptide. The high-affinity TCRs allowed us to estimate the affinity, in the millimolar range, of immunologically relevant interactions of the TCR with peptide/MHC ligands that were previously unmeasurable because of their weak nature. Thus, through the study of high-affinity TCRs, we demonstrated that a TCR is more tolerant of single TCR contact residue substitutions than other peptide changes, revealing that recognition of Ag by T cells can exhibit both specificity and degeneracy.
Design of filterbanks using a fast optimization approach

An optimization approach is proposed which can be used to design all types of filter banks. The design problem is formulated as the iterative minimization of two quadratic functions consisting of the perfect reconstruction (PR) condition and the energy in the filters' stopband areas. By relaxing the frequency specifications on the filters' passband areas, the performance indexes are becoming quadratic functions and can be efficiently minimized. This might result in the presence of ripple inside the filter bank, but the output would be ripple-free provided that the PR conditions are satisfied. The performance of the proposed algorithm (available in [14]) is illustrated with four examples indicating that a good filter bank design can be obtained very fast.
Calculating eGFR using the MDRD equation.

Sir, In a recent paper, MacGregor et al . suggested that the recently developed IDMS-traceable Modification of Diet in Renal Disease (MDRD) equation should be used to calculate GFR from serum creatinine measurements.1 This equation was developed for use with creatinine results from measurement procedures with calibrations that are traceable to the isotope dilution gas chromatography mass spectroscopy (IDMS) creatinine reference method. Since most routine measurement procedures for serum creatinine have not been calibrated to be traceable to the IDMS reference method, the authors suggest that measurement-procedure-specific correction factors derived …
Title A study on cross-cultural and cross-dataset generalizability ofmusic mood regression models

The goal of music mood regression is to represent the emotional expression of music pieces as numerical values in a low-dimensional mood space and automatically predict those values for unseen music pieces. Existing studies on this topic usually train and test regression models using music datasets sampled from the same culture source, annotated by people with the same cultural background, or otherwise constructed by the same method. In this study, we explore whether and to what extent regression models trained with samples in one dataset can be applied to predicting valence and arousal values of samples in another dataset. Specifically, three datasets that differ in factors such as cultural backgrounds of stimuli (music) and subjects (annotators), stimulus types and annotation methods are evaluated and the results suggested that cross-cultural and cross-dataset predictions of both valence and arousal values could achieve comparable performance to within-dataset predictions. We also discuss how the generalizability of regression models can be affected by dataset characteristics. Findings of this study may provide valuable insights into music mood regression for nonWestern and other music where training data are scarce.
Interactions between the breast cancer-associated MUC1 mucins and C-type lectin characterized by optical tweezers

Carbohydrate–protein interactions govern many crucial processes in biological systems including cell recognition events. We have used the sensitive force probe optical tweezers to quantify the interactions occurring between MGL lectins and MUC1 carrying the cancer-associated glycan antigens mucins Tn and STn. Unbinding forces of 7.6±1.1 pN and 7.1±1.1 pN were determined for the MUC1(Tn)—MGL and MUC1(STn)—MGL interactions, at a force loading rate of ~40 pN/s. The interaction strength increased with increasing force loading rate, to 27.1±4.4 and 36.9±3.6 pN at a force loading rate of ~ 310 pN/s. No interactions were detected between MGL and MUC1(ST), a glycoform of MUC1 also expressed by breast carcinoma cells. Interestingly, this glycan (ST) can be found on proteins expressed by normal cells, although in this case not on MUC1. Additionally, GalNAc decorated polyethylene glycol displayed similar rupture forces as observed for MUC1(Tn) and MUC1(STn) when forced to unbind from MGL, indicating that GalNAc is an essential group in these interactions. Since the STn glycan decoration is more frequently found on the surface of carcinomas than the Tn glycan, the binding of MUC1 carrying STn to MGL may be more physiologically relevant and may be in part responsible for some of the characteristics of STn expressing tumours.
Political Parties, World Demand, and Unemployment: Domestic and International Sources of Economic Activity

This article replicates and extends earlier work on the politics of macroeconomic policy by considering political effects on unemployment in 14 western industrial nations between 1960 and 1983. Changes of party control of government display broadly the expected effects, namely that unemployment falls under left-wing governments and rises under right-wing governments. However, the principal conclusions of this article are that partisan effects on unemployment in open economies (that is, economies heavily dependent on trade with other countries) can only be satisfactorily estimated relative to the constraint imposed by the level of world economic activity, and that in addition to politicians' strategic incentives, political institutions and economic regime constraints also determine whether partisan effects on unemployment will be sustained, transitory, or absent. With respect to the latter, on the whole no effects are found where no such effects were promised by the new government before taking office; where one-party or dominant-partner coalitions form, the effect on unemployment is transitory, whereas where broad coalitions form, it is sustained or absent. Finally, ceteris paribus, any partisan effects are more likely where governments secure parliamentary majorities.
Cardiomyocyte cytokinesis score: a potential method for cardiomyocyte proliferation

One of the most important indicators of myocardial regeneration is cardiomyocyte proliferation. However, it is difficult to distinguish cardiomyocytes in the regenerating stage from binucleated or multinucleated myocytes by conventional morphometric techniques. As cell cycle progression (CCP) scores have been successfully applied to the evaluation of the proliferation of cancer cells, we sought to establish a multi‐gene score to evaluate cardiomyocyte proliferation in this study. Given the disturbances of nuclear division without cell division that occurs in cardiomyocytes, ten cytokinesis‐correlated genes (Anln, Aurkb, Cenpa, Kif4, Kif23, Prc1, RhoA, Spin1, TACC2, and CDC42) were chosen to establish the cardiomyocyte cytokinesis score (CC‐Score). The expression levels of these genes in H9C2 rat cardiomyoblast cells, the proliferation of which were stimulated or inhibited, were detected using qRT‐PCR. To confirm the feasibility of the CC‐Score system, four conventional methods for evaluating cardiomyocyte proliferation, including the MTT assay, BrdU assay, immunofluorescence, and flow cytometry analysis, were used in each group. The results of the CC‐Score in the assessment of the proliferation of H9C2 cells were consistent with those of four commonly used proliferative assay methods. We conclude that the CC‐Score can be used to assess the proliferation status of H9C2 cells, and suggest that the CC‐Score may be a potential method for the assessment of cardiomyocyte proliferation in myocardial regeneration. However, validation studies utilizing primary cultured rat cardiomyocytes and heart tissue are warranted.
Space-time codes and concatenated channel codes for wireless communications

Following a brief historical perspective on channel coding, an introduction to space-time block codes is given. The various space-time codes considered are then concatenated with a range of channel codecs, such as convolutional and block-based turbo codes as well as conventional and turbo trellis codes. The associated estimated complexity issues and memory requirements are also considered. These discussions are followed by a performance study of various space-time and channel-coded transceivers. Our aim is first to identify a space-time code/channel code combination constituting a good engineering tradeoff in terms of its effective throughput, bit-error-rate performance, and estimated complexity. Specifically, the issue of bit-to-symbol mapping is addressed in the context of convolutional codes (CCs) and convolutional coding as well as Bose-Chaudhuri-Hocquenghem coding-based turbo codes in conjunction with an attractive unity-rate space-time code and multilevel modulation is detailed. It is concluded that over the nondispersive or narrow-band fading channels, the best performance versus complexity tradeoff is constituted by Alamouti's twin-antenna block space-time code concatenated with turbo convolutional codes. Further comparisons with space-time trellis codes result in similar conclusions.
A Duration Model For Defaultable Bonds

I extend recent theoretical work on duration and derive an improved model for the risk-adjusted duration of corporate bonds. My ex-ante risk-adjusted duration is the sum of the bond's Fisher-Weil duration and the duration of the potential expected delay in recovery caused by the default option. My main conclusion is that failing to adjust duration for default is costly for high-yield bonds, especially those with a shorter time to maturity. For investment-grade bonds, this cost is trivial for all maturities. 2003 The Southern Finance Association and the Southwestern Finance Association.
Accurate, Noninvasive Detection of Helicobacter pylori DNA from Stool Samples: Potential Usefulness for Monitoring Treatment

ABSTRACT A novel DNA assay demonstrating sensitive and accurate detection of Helicobacter pylori from stool samples is reported. Moreover, in three individuals tested for therapeutic response, the assay showed the disappearance of H. pylori DNA during treatment. Thus, this noninvasive molecular biology-based assay has the potential to be a powerful diagnostic tool given its ability to specifically identify H. pylori DNA.
The Varieties of Democracy

Professor Beteille was formerly the Chair of the Indian Council of Social Science Research, and was made National Research Professor in 2006 and Corresponding Fellow of the British Academy in 1992. He is an Honorary Fellow of the Royal Anthropological Institute. His research and writings have focused on social inequality, especially the relationship between caste, class, and power, and also explored the theme of inequality in agrarian social structures arising from the ownership, control, and use of land. His later writings have focused on institutions and processes.
miR-142-3p is a key regulator of IL-1β-dependent synaptopathy in neuroinflammation.

MicroRNAs (miRNA) play an important role in posttranscriptional gene regulation of several physiological and pathological processes. In multiple sclerosis (MS), a chronic inflammatory and degenerative disease of the CNS, and in its mouse model, the experimental autoimmune encephalomyelitis (EAE), miRNA dysregulation has been mainly related to immune system dysfunction and white matter pathology. However, little is known about their role in grey matter pathology. Here, we explored miRNA involvement in the inflammation-driven alterations of synaptic structure and function, collectively known as synaptopathy, a neuropathological process contributing to excitotoxic neurodegeneration in MS/EAE. Particularly, we observed that miR-142-3p is increased in the cerebrospinal fluid (CSF) of patients with active MS and in EAE brains. We propose miR-142-3p as a molecular mediator of the IL-1β-dependent down-regulation of the glial glutamate-aspartate transporter (GLAST), which causes an enhancement of the glutamatergic transmission in the EAE cerebellum. The synaptic abnormalities mediated by IL-1β and the clinical and neuropathological manifestations of EAE disappeared in miR-142 knock-out mice. Furthermore, we observed that in vivo miR-142-3p inhibition, either by a preventive and local treatment or by a therapeutic and systemic strategy, abolished IL-1β- and GLAST-dependent synaptopathy in EAE wild-type mice. Consistently, miR-142-3p was responsible for the glutamatergic synaptic alterations caused by CSF of patients with MS, and CSF levels of miR-142-3p correlated with prospective MS disease progression. Our findings highlight miR-142-3p as key molecular player in IL-1β-mediated synaptic dysfunction possibly leading to excitotoxic damage in both EAE and MS diseases. Inhibition of miR-142-3p could be neuroprotective in MS. SIGNIFICANCE STATEMENT Current studies suggest the role of glutamate excitotoxicity in the development and progression of MS and of its mouse model EAE. The molecular mechanisms linking inflammation and synaptic alterations in MS/EAE are still unknown. Here, we identified miR-142-3p as a determinant molecular actor in inflammation-dependent synaptopathy typical of both MS and EAE. miR-142-3p was up-regulated in the cerebrospinal fluid of MS patients and in EAE brains. Inhibition of miR-142-3p, locally in EAE brain and in a MS chimeric in vitro model, recovered glutamatergic synaptic enhancement typical of EAE/MS. We proved that miR-142-3p promoted the IL-1β-dependent glutamate dysfunction by targeting GLAST, a crucial glial transporter involved in glutamate homeostasis. Finally, we suggest miR-142-3p as a negative prognostic factor in RRMS patients.
Strategic planning of regional development in higher education

Purpose – This study seeks to show how higher education institutions can plan regional strategies to increase their external impact on the environment.Design/methodology/approach – The balanced scorecard approach is used to provide a general framework to communicate the strategy.Findings – The approach is useful in accomplishing the strategic themes and objectives.Practical implications – The study presents an example of how higher educational institutions are able to plan their joint regional strategy.Originality/value – This study contributes to the knowledge and practice of strategic planning in the network of educational institutions. The findings of this study are useful to administrators of educational institutions aiming to plan a regional strategy and improve the external impact of institutions.
A new type of robust tracking control of robot manipulators based on generalized SP-D control scheme

This paper is concerned with a new type of robust tracking control scheme for robot manipulators using SP-D (saturated proportional and differential) feedback loops. The control scheme based on quasi-natural potential is generalized from set-point regulation to trajectory tracking by exploiting an effective auxiliary variable with positional and velocity errors. Without any uncertainties in the manipulator model, the tracking SP-D control scheme ensures globally asymptotic stability. In the presence of parametric model uncertainties, the proposed robust tracking controller is able to guarantee globally uniformly ultimate boundedness. Experimental results on the SICE standard manipulator show theoretical effectiveness of the robust tracking SP-D control.
Cyberspace, globalization and empire

The article proposes that the framework of media imperialism is appropriate for the study of US dominance of information and communication technology (ICT) industries in the period 1975–2000. Early media imperialism theories focused on US television exports at a time when such exports were set to decline in many local markets. Covert influences such as ownership, business models, professional values, content formatting, audience preferences, cultural hybrids and technologies, were insufficiently considered. In particular, the earlier focus on television and content may have distracted attention from the emergence of microprocessor-based computer networking technologies, their significance for the development of ICT industries, and the profound influence these have exerted on US economic and foreign policies. This article documents the continuing dominance of US corporate power, of US-based transnational corporations (TNCs) and, among them, of ICT industries, within the global economy. It charts US dominance of most spheres of computing and telecommunications at the turn of the 21st century. With specific reference to intelligence estimates of future global trends it assesses the significance of the ‘Asian challenge’, specifically the challenge of Asian ICT activity to the prospects of a continuation of US hegemony.
Options on Realized Variance in Log-OU Models

Abstract We study the pricing of options on realized variance in a general class of Log-OU (Ornstein–Ühlenbeck) stochastic volatility models. The class includes several important models proposed in the literature. Having as common feature the log-normal law of instantaneous variance, the application of standard Fourier–Laplace transform methods is not feasible. We derive extensions of Asian pricing methods, to obtain bounds, in particular, a very tight lower bound for options on realized variance.
Visual Acuity and Contrast Sensitivity Testing for Sports Vision

Abstract: The building blocks of effective sports vision are visual acuity and contrast sensitivity. Proper measurement of these spatial vision attributes is necessary for repeatability in the clinic or in the laboratory. The most repeatable method of testing visual acuity is with logMAR charts-either the Bailey-Lovie chart or the Early Treatment Diabetic Retinopathy Study chart. The Pelli-Robson and the Mars are the most repeatable contrast sensitivity tests. Athletes may or may not demonstrate superior visual acuity and contrast sensitivity compared with age-matched nonathlete populations, and the optical quality of their eyes may be similar. Dynamic visual acuity in athletes and their performance are typically superior to those of nonathletes. How these differences relate to on-field performance is not known. Other changes to the visual system because of refractive surgery or contact lens wear may increase higher order aberrations and reduce low-contrast visual acuity. The ability to improve already-normal visual acuity is unclear although contrast sensitivity can improve with fast-paced video games. Tinted contact lenses help reduce discomfort glare and speed up adaptation but do not have an appreciable effect on visual acuity and contrast sensitivity. Conclusion: The use of valid and repeatable visual acuity and contrast sensitivity tests is essential for measuring the differences in visual performance among athletes and nonathletes. The development of a standardized dynamic visual acuity test is needed as are well-controlled scientific studies to evaluate the benefits of sports vision training
Price Expectations and Supply Response

Price in agricultural supply equations is usually the expected price. In general, models of agricultural supply response assume that their representation of producer expectations is correct. If this assumption is wrong, the supply response parameter will have embodied within it an estimate of the expected price distortion, biasing the estimated parameter. Furthermore, no effort has been made in existing models to allow for heterogeneous price expectations. In almost every supply model, one price estimate is used to represent the price expectations of hundreds or thousands of producers, which could masks a wide range behavior among heterogenous producers. Rather than assuming the model’s representation of producer expectations is correct, the goal of this paper is to use revealed producer behavior to assist in the estimation of producer’s expected prices. To explicitly address producers’ formation of the expected price, this study jointly estimates the supply equation and the price expectation equation. The empirical application is a pooled time-series cross-section data analysis of U.S. wheat and corn supply data at the county level.
A Dataset for Benchmarking Image-Based Localization

A novel dataset for benchmarking image-based localization is presented. With increasing research interests in visual place recognition and localization, several datasets have been published in the past few years. One of the evident limitations of existing datasets is that precise ground truth camera poses of query images are not available in a meaningful 3D metric system. This is in part due to the underlying 3D models of these datasets are reconstructed from Structure from Motion methods. So far little attention has been paid to metric evaluations of localization accuracy. In this paper we address the problem of whether state-of-the-art visual localization techniques can be applied to tasks with demanding accuracy requirements. We acquired training data for a large indoor environment with cameras and a LiDAR scanner. In addition, we collected over 2000 query images with cell phone cameras. Using LiDAR point clouds as a reference, we employed a semi-automatic approach to estimate the 6 degrees of freedom camera poses precisely in the world coordinate system. The proposed dataset enables us to quantitatively assess the performance of various algorithms using a fair and intuitive metric.