Miracle-dz/UniFAR-FTUs huggingface dataset:
The mechanism of mRNA activation

During translation initiation, messenger RNA molecules must be identified and activated for loading into a ribosome. In this rate-limiting step, the heterotrimeric protein eukaryotic initiation factor eIF4F must recognize and productively interact with the 7-methylguanosine cap at the 5’ end of the messenger RNA and subsequently activate the message. Despite its fundamental, regulatory role in gene expression, the molecular events underlying cap recognition and messenger RNA activation remain mysterious. Here, we generate a unique, single-molecule fluorescence imaging system to interrogate the dynamics with which eIF4F discriminates productive and non-productive locations on full-length, native messenger RNA molecules. At the single-molecule level, we observe stochastic sampling of eIF4F along the length of the messenger RNA and identify allosteric communication between the eIF4F subunits which ultimately drive cap-recognition and subsequent activation of the message. Our experiments uncover novel functions for each subunit of eIF4F and we conclude by presenting a model for messenger RNA activation which precisely defines the composition of the activated message. This model provides a general framework for understanding how messenger RNA molecules may be discriminated from one another, and how other RNA-binding proteins may control the efficiency of translation initiation.
Fast evolution of SARS-CoV-2 BA.2.86 to JN.1 under heavy immune pressure

While the BA.2. 86 variant demonstrated significant antigenic drift and enhanced ACE2 binding affinity, its ability to evade humoral immunity was relatively moderate compared to dominant strains like EG.5 and HK.3. However, the emergence of a new subvariant, JN.1 (BA.2.86.1.1), which possesses an additional spike mutation, L455S, compared to BA.2. 86, showed a markedly increased prevalence in Europe and North America, especially in France. Here, we found that L455S of JN.1 significantly enhances immune evasion capabilities at the expense of reduced ACE2 binding affinity. This mutation enables JN.1 to effectively evade Class 1 neutralizing antibodies, offsetting BA.2. 86’s susceptibility and thus allowing it to outcompete both its precursor BA.2. 86 and the prevailing variants HV.1 (XBB.1.5+L452R+F456L) and JD.1. 1 (XBB.1.5+L455F+F456L+A475V) in terms of humoral immune evasion. The rapid evolution from BA.2. 86 to JN.1, similar to the earlier transition from BA.2. 75 to CH.1. 1, highlights the importance of closely monitoring strains with high ACE2 binding affinity and distinct antigenicity, despite their temporarily unremarkable immune evasion capabilities. Such strains could survive and transmit at low levels, since their large antigenic distance to dominant strains allow them to target distinct populations and accumulate immune-evasive mutations rapidly, often at the cost of receptor binding affinity.
Integrative multiomics analysis of neointima proliferation in human saphenous vein: implications for bypass graft disease

Introduction Human saphenous veins (SV) are widely used as grafts in coronary artery bypass (CABG) surgery but often fail due to neointima proliferation (NP). NP involves complex interplay between vascular smooth muscle cells (VSMC) and fibroblasts. Little is known, however, regarding the transcriptomic and proteomic dynamics of NP. Here, we performed multi-omics analysis in an ex vivo tissue culture model of NP in human SV procured for CABG surgery. Methods and results Histological examination demonstrated significant elastin degradation and NP (indicated by increased neointima area and neointima/media ratio) in SV subjected to tissue culture. Analysis of data from 73 patients suggest that the process of SV adaptation and NP may differ according to sex and body mass index. RNA sequencing confirmed upregulation of pro-inflammatory and proliferation-related genes during NP and identified novel processes, including increased cellular stress and DNA damage responses, which may reflect tissue trauma associated with SV harvesting. Proteomic analysis identified upregulated extracellular matrix-related and coagulation/thrombosis proteins and downregulated metabolic proteins. Spatial transcriptomics detected transdifferentiating VSMC in the intima on the day of harvesting and highlighted dynamic alterations in fibroblast and VSMC phenotype and behavior during NP. Specifically, we identified new cell subpopulations contributing to NP, including SPP1+, LGALS3+ VSMC and MMP2+, MMP14+ fibroblasts. Conclusion Dynamic alterations of gene and protein expression occur during NP in human SV. Identification of the human-specific molecular and cellular mechanisms may provide novel insight into SV bypass graft disease.
Calibrating Bayesian decoders of neural spiking activity

Accurately decoding external variables from observations of neural activity is a major challenge in systems neuroscience. Bayesian decoders, that provide probabilistic estimates, are some of the most widely used. Here we show how, in many common settings, the probabilistic predictions made by traditional Bayesian decoders are overconfident. That is, the estimates for the decoded stimulus or movement variables are more certain than they should be. We then show how Bayesian decoding with latent variables, taking account of low-dimensional shared variability in the observations, can improve calibration, although additional correction for overconfidence is still needed. We examine: 1) decoding the direction of grating stimuli from spike recordings in primary visual cortex in monkeys, 2) decoding movement direction from recordings in primary motor cortex in monkeys, 3) decoding natural images from multi-region recordings in mice, and 4) decoding position from hippocampal recordings in rats. For each setting we characterize the overconfidence, and we describe a possible method to correct miscalibration post-hoc. Properly calibrated Bayesian decoders may alter theoretical results on probabilistic population coding and lead to brain machine interfaces that more accurately reflect confidence levels when identifying external variables. Significance Statement Bayesian decoding is a statistical technique for making probabilistic predictions about external stimuli or movements based on recordings of neural activity. These predictions may be useful for robust brain machine interfaces or for understanding perceptual or behavioral confidence. However, the probabilities produced by these models do not always match the observed outcomes. Just as a weather forecast predicting a 50% chance of rain may not accurately correspond to an outcome of rain 50% of the time, Bayesian decoders of neural activity can be miscalibrated as well. Here we identify and measure miscalibration of Bayesian decoders for neural spiking activity in a range of experimental settings. We compare multiple statistical models and demonstrate how overconfidence can be corrected.
Raman microscopy of cryofixed biological specimens for high-resolution and high-sensitivity chemical imaging

Raman microscopy is an emerging molecular imaging technology, yet its signal-to-noise-ratio (SNR) in measurements of biological specimens is severely limited due to the small cross-section of Raman scattering. Here, we present Raman imaging techniques of cryofixed specimens to overcome SNR limitations by enabling long exposure of specimens under highly stabilized low-temperature conditions. The observation of frozen specimens in a cryostat at a constant low temperature immediately after rapid freezing enabled the improvement of SNR and significantly enhanced spatial and spectral resolution. We also confirmed that the cryofixation can preserve physicochemical states of specimens by observing alkyne-labeled coenzyme Q in cytosol and hemeproteins in acute ischemic myocardium, which cannot be done by fixation using chemical reagents. Finally, we applied the technique for multiplex Raman imaging of label-free endogenous molecules and alkyne-tagged molecules in cryofixed HeLa cells, demonstrating its capability of high-content imaging of complex biological phenomena while maintaining physiological conditions.
Lateral extrusion along the Altyn Tagh Fault, Qilian Shan (NE Tibet): insight from a 3D crustal budget

The lithospheric strike‐slip Altyn Tagh Fault has accommodated hundreds of kilometres of displacement between the Qaidam and Tarim blocks since its Eocene reactivation. However, the way the deformation is accommodated in the Qilian Shan and further east remains uncertain. Based on 360 km of north‐eastward migration of the relatively rigid Qaidam block along the Altyn Tagh Fault and 3D isovolumetric balancing of the crustal deformation within the Altyn Tagh Fault–Qilian Shan system, we demonstrate that 250 ± 28 km (43.8–49.4%) of N20E directed crustal shortening and an additional ~250–370 km of eastward motion of the Qilian Shan crust must be accounted for by strike‐slip faulting in the Qilian Shan and crustal thickening in the Qinling area, as well as by extension in the adjoining North China block graben systems.
Hydrothermal Activity at Slow-Spreading Mid-Ocean Ridges: Evidence from Chlorine in Basalt

Hydrothermal activity can be traced by the chlorine (Cl) concentrations of erupted mid-ocean ridge basalts, if their magmas assimilated hydrothermally altered, Cl-rich crust. In contrast to fast-spreading ridges, this process is not observed so far at slow-spreading ridges, due to their intrinsically lower basaltic Cl contents (<200 ppm). This study involves the development of a new, high precise (<2 ppm SD) technique to measure Cl by electron microprobe, which is applied to basaltic glasses and mineral melt-inclusions from the southern Mid-Atlantic Ridge, the Red Sea Rift and the Gakkel Ridge (all <3.5 cm/yr). Addition of hydrothermal Cl is determined by comparing Cl with major and trace element concentrations. Chemical thermobarometry is used to obtain depth information on hydrothermal circulation. Cl data is compared to geological settings (e.g. hydrothermal sites, volcanoes, faults) to examine their relationships and to assess basaltic Cl as prospection tool for hydrothermal vents.
Soil organic carbon dynamics and its influence on the soil erodibility factor.

The effect of erosion and erosion control measures on changes in the amount of organic matter in soil was studied. We investigated the influence of organic matter inputs into the soil on surface runoff, soil erosion and soil erodibility (K-factor), including the monitoring of carbon dynamics, as a result of torrential rains. The research was conducted on experimental plots in Třebsin site. Erosion leads to soil carbon loss and subsequently to increasing concentrations of carbon in sediments (enrichment ratio). We can conclude from the results that the input of organic matter into the soil (especially farmyard manure) significantly contributes to a decrease in surface runoff and soil loss and also to a reduction of carbon leaching into sediments; so it contributes to carbon sequestration into the soil.
LA POBLACIÓN RURAL EN CATALUNYA: ENTRE EL DECLIVE Y LA REVITALIZACIÓN 1

This article focuses on recent population trends (1981-2001) in rural Catalonia (Spain). The first part reveals demographic revitalisation in certain rural areas, but there is also some evidence of demographic decline in others. The second part examines rural migration, the main cause of actual demographic change. Migration analysis is used as a means of investigating the social, economic and functional factors which explain the new dynamics of population in these areas. Conclusions point to various special characteristics that are apparent in revitalised rural areas and a number of reasons why it is not possible to export this experience of success to municipalities that are currently depressed. Finally, there is a discussion of the role that urban actors are playing in the transformation or rural areas and of the possible future dangers or their excessive influence.
A sea ice free summer Arctic within 30 years?

September 2008 followed 2007 as the second sequential year with an extreme summer Arctic sea ice extent minimum. Although such a sea ice loss was not indicated until much later in the century in the Intergovernmental Panel on Climate Change 4th Assessment Report, many models show an accelerating decline in the summer minimum sea ice extent during the 21st century. Using the observed 2007/2008 September sea ice extents as a starting point, we predict an expected value for a nearly sea ice free Arctic in September by the year 2037. The first quartile of the distribution for the timing of September sea ice loss will be reached by 2028. Our analysis is based on projections from six IPCC models, selected subject to an observational constraints. Uncertainty in the timing of a sea ice free Arctic in September is determined based on both within‐model contributions from natural variability and between‐model differences.
Data modeling and querying for video databases (Video veri tabanları için veri modelleme ve sorgulama)

DATA MODELING AND QUERYING FOR VIDEO DATABASES Mehmet Emin Donderler Ph.D. in Computer Engineering Supervisors: Assoc. Prof. Dr. Ozgur Ulusoy and Asst. Prof. Dr. Uǧur Gudukbay July, 2002 With the advances in information technology, the amount of multimedia data captured, produced and stored is increasing rapidly. As a consequence, multimedia content is widely used for many applications in today’s world, and hence, a need for organizing this data and accessing it from repositories with vast amount of information has been a driving stimulus both commercially and academically. In compliance with this inevitable trend, first image and especially later video database management systems have attracted a great deal of attention since traditional database systems are not suitable to be used for multimedia data. In this thesis, a novel architecture for a video database system is proposed. The architecture is original in that it provides full support for spatio-temporal queries that contain any combination of spatial, temporal, object-appearance, external-predicate, trajectory-projection and similarity-based object-trajectory conditions by a rule-based system built on a knowledge-base, while utilizing an object-relational database to respond to semantic (keyword, event/activity and category-based) and low-level (color, shape and texture) video queries. Research results obtained from this thesis work have been realized by a prototype video database management system, which we call BilVideo. Its tools, Fact-Extractor and Video-Annotator, its Web-based visual query interface and its SQL-like textual query language are presented. Moreover, the query processor of BilVideo and our spatio-temporal query processing strategy are also discussed.
Climate envelopes of mire complex types in fennoscandia

Abstract. Peatlands are characteristic features of the Fennoscandian landscape, about one‐quarter of the land surface being classified as peatland. The aim of this work was to determine the extent to which the distribution of four main mire complex types (aapa mire, blanket bog, palsa mire, raised bog) can be modelled on the basis of climatological parameters. Additionally, the relative importance of different climatological variables in influencing the distribution of different mire complex types was scrutinized using the variation partitioning method. Variation partitioning is a novel statistical approach that provides deeper understanding of the importance of different explanatory variable groups for geographical patterns than traditional regression methods. The variation in the distribution of mire complex types was decomposed into independent and joint effects of temperature, precipitation and spatial variables. The distributional limits of aapa mires, palsa mires and raised bogs were primarily associated with thermal factors, whereas moisture regime also played an obvious role for blanket bogs. A considerable amount of variation in the distribution of mire complex types was accounted for by the joint effects of explanatory variables and may thus be causally related to two or all three groups of variables. Although the present distribution of mire complex types corresponded well to the contemporary climate in Fennoscandia, our results indicate that the climate envelopes of palsa mires are narrow. Thus, they can be expected to be extremely sensitive to changes in future climatic conditions.
INVESTIGATION OF NON-PARAMETRIC STABILITY METHODS IN 28 BREAD WHEAT GENOTYPES IN SOME TROPICAL REGIONS OF IRAN

"This study was conducted to investigate the interaction effects of genotype and environment and environmental effects, adaptation and stability of bread wheat (Triticum aestivum) yield with different genetic structure and selection of stable and productive genotypes in twenty-eight bread wheat genotypes in a randomized complete block design with four replications is evaluated in Ahvaz, Dezful, Darab, Iranshahr, Zabol and Khorramabad stations for two years (94-95 and 95-96), comparison of non-parametric stability methods and the use of non-parametric tests have been the objectives of this study. The results of ANOVA composite analysis of variance at the level of meaningful 1% probability indicate that different genotypes react in different environments. Based on the results of two non-parametric statistics, Nassar and Huhn and, genotypes 16, 25, 27, 15 with low values were selected as the most stable genotypes. In the two stability criteria and, the genotypes with the lowest value are known as the most stable genotypes, genotypes 15, 16, 27 were identified as the most stable genotypes. High correlation of s statistic with grain yield and other non-parametric stability methods do not have a positive correlation with mean yield, which indicates a static concept, Thennarasu (1995) used four stability parameters to analyze the nonparametric stability. Examination of criteria, and show that genotype 27 is introduced as a stable genotype in all four criteria. TOP measurement was associated with high performance Stability, results of PC principal component analysis and correlation analysis Statistical and non-parametric stability performance showed that only ranking methods are useful for simultaneous selection for high performance and stability .
Turkish Validity And Reliability Study of The Social Behavior Scale for Preschool Children

This study was conducted to perform the validity and reliability analyses of the Social Behavior Scale for Preschool Children (SBS). The data were obtained as a result of the evaluation of the social behaviors of 315 children aged between 4 and 6, who were attending 6 independent kindergartens affiliated to the Ministry of National Education in Kirikkale, by 20 teachers. In testing the validity of the scale, the expert opinion was obtained for content validity, exploratory and confirmatory factor analysis was performed, and the significance of the difference between the test scores of the groups, the face validity and characteristics of which were known, was checked for construct validity. For testing the reliability of the scale, the internal consistency coefficient and the test-retest reliability coefficient were calculated for each age group and each dimension of the scale. It was concluded that the sample included in the study was adequate for the structural equation method. In the study, it was determined from the exploratory factor analysis and the confirmatory factor analysis that 15 items were gathered under 3 factors. In the reliability analysis of the scale, the total Cronbach’s alpha coefficient value was found to be 0.745. The Social Behavior Scale for Preschool Children is a valid and reliable scale for Turkish children.
Effect of Evidence Based Practices Guideline Intervention on Daily Living Problems of Children Suffering from Attention Deficit Hyperactivity Disorder and Their Mothers' Stressors

: Attention-deficit hyperactivity disorder (ADHD) is the most commonly diagnosed behavioral disorders in children. It is clinically characterized by hyperactivity, impulsivity and inattention. These symptoms often continue into adulthood and may lead to an increase of family conflict, poor occupational performance and academic failures throughout adult life. Aim: The aim of the current study was to evaluate the effect of evidence based practices guidelines intervention on daily living problems of children suffering from attention deficit hyperactivity disorder and their mothers' stressors. This aim achieved through; assessing daily living problems of children suffering from ADHD, assessing mothers' knowledge regarding ADHD and their daily stressors experienced by them as a result of having children with ADHD, implementing and disseminating evidence based practices guidelines regarding ADHD for mothers to overcome daily living problems of their children suffering from ADHD and alleviate the mothers' daily stressors. Design: A quasi-experimental study was utilized. Setting: This study was conducted at Children Out-patient Clinic at the Psychiatric Medical Center affiliated to Ain Shams University Hospitals. Sample: The study involved a purposive sample of 40 school age children with ADHD and their accompanying mothers. Tools: 1. Pre-designed Questionnaire Format; to assess characteristics of the studied mothers & their children and assess mothers' knowledge regarding ADHD. 2. Connors Parent Questionnaire to assess features of emotional distress, aggressive behaviors, academic difficulties, hyperactivity and impulsivity (daily problems) of children suffering from ADHD as reported by their mothers. 3. Vanderbilt Parent Assessment Scale to assess level of impairment of children with ADHD through their mothers. 4. Disruptive Behavior Stress Inventory to assess mothers' potential stressors experienced as a result of having a child who displays behavioral difficulties. Results of the current study revealed that there was improvement in the total mean score of satisfactory mothers' knowledge regarding ADHD post guidelines intervention. Also, there was improvement in total mean score of children's daily living problems as reported by their mothers post guidelines intervention. Conclusion: Evidence based practices guidelines intervention has a positive effect on daily living problems of children suffering from ADHD, alleviate mothers' daily stressors and psychological constraints as a result of having child with ADHD. This study recommended that evidence based practices guidelines can be applied more widely for all mothers having children with ADHD as one of the nursing interventions aiming to overcome daily living problems of their children and alleviate level of mothers' stress.
Nursing Students, Practicing, Attitude about Menstrual Hygienic Care at El-Nasr Health Insurance Hospital

: menstruation is a natural process, it is linked with several misconceptions and practices, which sometimes result into adverse health outcomes. Hygiene-related practices of women during menstruation are of considerable importance. The aim of this study is to assess female students’ knowledge and attitude regarding menstruation, observe general wellbeing of female student and investigating the relationship between current knowledge of female students about menstruation and menstrual hygienic practices. A descriptive research design was utilized to fulfill the aims of the study. The sample consist of 200 nursing student at El-Nasr Insurance Health Hospital in Helwan City. The researcher met the students through studying day in break time to illustrate the nature of study and gather data. The result revealed that the majority of nursing students has a poor knowledge and attitude of menstruation hygiene. So this study recommends to spot attention on reproductive system hygienic care as a part of fixed curriculum in infection control.