Miracle-dz/UniFAR-FTUs huggingface dataset:
Specific Sequence Features, Recognized by the SMN Complex, Identify snRNAs and Determine Their Fate as snRNPs

ABSTRACT The survival of motor neurons (SMN) complex is essential for the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) as it binds to and delivers Sm proteins for assembly of Sm cores on the abundant small nuclear RNAs (snRNAs). Using the conserved snRNAs encoded by the lymphotropic Herpesvirus saimiri (HVS), we determined the specific sequence and structural features of RNAs for binding to the SMN complex and for Sm core assembly. We show that the minimal SMN complex-binding domain in snRNAs, except U1, is comprised of an Sm site (AUUUUUG) and an adjacent 3′ stem-loop. The adenosine and the first and third uridines of the Sm site are particularly critical for binding of the SMN complex, which directly contacts the backbone phosphates of these uridines. The specific sequence of the adjacent stem (7 to 12 base pairs)-loop (4 to 17 nucleotides) is not important for SMN complex binding, but it must be located within a short distance of the 3′ end of the RNA for an Sm core to assemble. Importantly, these defining characteristics are discerned by the SMN complex and not by the Sm proteins, which can bind to and assemble on an Sm site sequence alone. These findings demonstrate that the SMN complex is the identifier, as well as assembler, of the abundant class of snRNAs in cells because it is able to recognize an snRNP code that they contain.
A device for stent designing in emodynamic surgery room

Quantitative angiography has becoming largely used in interventional cardiology mainly because of its positive impact in terms of patients survival indexes and life quality. Such a tecnique is performed with a laparoscopic procedure and cures coronary stenoses with the installation of a medical stent. Benefits from the treatment are immediately perceived by patients. Furthermore laparoscopy avoids the potential problems related to the complexity of an open-heart surgery procedure. Stent positioning is guided by using contrast liquid and angiographic X-Rays images. The operator looks at angiographic images to estimate the dimensions of the stent to be installed. With the described procedure physicians may have difficulties in optimally estimating the stenosis size in order to choose the most appropriate stent because they have no absolute reference on the angiographer screens. In this paper we present an innovative device able to assist the physicians pre-implant analysis and thus supporting him for an optimal stent choice.
The hippocampus, medial prefrontal cortex, and selective memory retrieval: Evidence from a rodent model of the retrieval‐induced forgetting effect

Inhibition is an important component of many cognitive functions, including memory. For example, the retrieval‐induced forgetting (RIF) effect occurs when extra practice with some items from a study list inhibits the retrieval of the nonpracticed items relative to a baseline condition that does not involve extra practice. Although counterintuitive, the RIF phenomenon may be important for resolving interference by inhibiting potentially competing retrieval targets. Neuroimaging studies suggest that the hippocampus and prefrontal cortex are involved in the RIF effect, but controlled lesion studies have not yet been performed. We developed a rodent model of the RIF training procedure and trained control rats and rats with temporary inactivation of the hippocampus or medial prefrontal cortex (mPFC). Rats were trained on a list of odor cues, presented in cups of digging medium with a buried reward, followed by additional practice trials with a subset of the cues. We then tested the rats' memories for the cues and their association with reward by presenting them with unbaited cups containing the test odorants and measuring how long they persisted in digging. Control rats exhibited a robust RIF effect in which memory for the nonpracticed odors was significantly inhibited. Thus, extra practice with some odor cues inhibited memory for the others, relative to a baseline condition that involved an identical amount of training. Inactivation of either the hippocampus or the mPFC blocked the RIF effect. We also constructed a computational model of a representational learning circuit to simulate the RIF effect. We show in this model that “sideband suppression” of similar memory representations can reproduce the RIF effect and that alteration of the suppression parameters and learning rate can reproduce the lesion effects seen in our rats. Our results suggest that the RIF effect is widespread and that inhibitory processes are an important feature of memory function. © 2014 Wiley Periodicals, Inc.
Normative data of the Brazilian elderly in Logical Memory subtest of WMS-R

Avaliação Psicológica, 2017, 16(1), 11-18 ABSTRACT The aim of this study was to establish normative data for the Brazilian elderly population in the Logical Memory (LM) subtest of the Wechsler Memory Scale, revised version (WMS-R) and investigate the ability of scores in this subtest (immediate and delayed recall) to discriminate the elderly with and without depressive symptoms. The sample consisted of 334 elderly participants. Participants answered a sociodemographic and health questionnaire, the MMSE, the GDS-15, and the LM subtest. Data were analyzed by descriptive statistics, Student’s t test, multiple linear regression, univariate analysis, and discriminant analysis. Age, education, and depressive symptoms significantly influenced all the scores of LM. Normative data were available according to three age groups, three levels of education, sex, and presence or absence of depressive symptoms. Results are in agreement with the literature, demonstrating the importance of establishing reference standards in accordance with sociodemographic and cultural characteristics.
Plant Genome Size Estimation by Flow Cytometry: Inter-laboratory Comparison

Flow cytometry is a convenient and rapid method that has been used extensively for estimation of nuclear genome size in plants. In contrast to general expectations, results obtained in different laboratories showed some striking discrepancies. The aim of this joint experiment was to test the reliability and reproducibility of methods. Care was taken to avoid a bias due to the quantity of DNA in the nucleus, the procedure for nuclei isolation or the type of instrument. Nuclear DNA content was estimated in nine plant species representing a typical range of genome size (2C = approx. 03-30 pg DNA). Each of the four laboratories involved in this study used a different buffer and/or procedure for nuclei isolation. Two laboratories used arc lamp-based instruments while the other two used laser-based instruments. The results obtained after nuclei staining with propidium iodide (a DNA intercalator) agreed well with those obtained using Feulgen densitometry. On the other hand, results obtained after staining with DAPI (binding preferentially to AT-rich regions) did not agree with those obtained using Feulgen densitometry. Small, but statistically significant, differences were found between data obtained with individual instruments. Differences between the same type of instruments were negligible, while larger differences were observed between lamp- and laserbased instruments. Ratios of fluorescence intensity obtained by laser instruments were higher than those obtained by lamp-based cytometers or by Feulgen densitometry. The results obtained in this study demonstrate that flow cytometry with DNA intercalators is a reliable method for estimation of nuclear genome size in plants. However, the study confirmed an urgent need for an agreement on standards. Given the small but systematic differences between different types of flow cytometers, analysis of very small differences in genome size should be made in the same laboratory and using the same instrument. © 1998 Annals of Botany Company
Elevated Atmospheric CO 2 Affects Ectomycorrhizal Species Abundance and Increases Sporocarp Production under Field Conditions

Anthropogenic activities during the last century have increased levels of atmospheric CO2. Forest net primary productivity increases in response to elevated CO2, altering the quantity and quality of carbon supplied to the rhizosphere. Ectomycorrhizal fungi form obligate symbiotic associations with the fine roots of trees that mediate improved scavenging for nutrients in exchange for a carbohydrate supply. Understanding how the community structure of ectomycorrhizal fungi is altered by climate change is important to further our understanding of ecosystem function. Betula pendula and Fagus sylvatica were grown in an elevated CO2 atmosphere delivered using free air carbon dioxide enrichment (FACE) under field conditions in the U.K., and Picea abies was grown under elevated CO2 in glass domes in the Czech Republic. We used morphotyping and sequencing of the internal transcribed spacer region of the fungal ribosomal operon to study ectomycorrhizal OPEN ACCESS Forests 2015, 5 1257 community structure. Under FACE, un-colonised roots tips increased in abundance for Fagus sylvatica, and during 2006, sporocarp biomass of Peziza badia significantly increased. In domes, ectomycorrhizal community composition shifted from short-distance and smooth medium-distance to contact exploration types. Supply and competition for carbon belowground can influence ectomycorrhizal community structure with the potential to alter ecosystem function.
A framework for comparing Web-based learning environments

As notions such as the information revolution and knowledge-based economies become increasingly realistic, there is considerable pressure on academic, corporate and governmental decision makers to improve both the accessibility and the quality of learning opportunities that they provide to those they serve. Many are turning to World Wide Web-based technologies as part of the solution. A Web-based learning environment is a networked computer application that enables people to learn from a distance. Learners can be physically separated from teachers and from each other, and they can participate in the learning environment at their convenience. Choosing which Web-based learning environment to adopt is an important decision as it often involves a substantial investment for organizations and signi cantly impacts how people will learn. In order to better understand how people learn and the possibilities for Web-based learning environments to support learning, we review the relevant educational theory. We also review the human-computer interaction literature to better understand how people can e ectively use software. Intuitive and ad-hoc comparisons between competing products are not likely to lead to adopting the optimal Web-based learning environment for a particular organization. Therefore, we propose a comparison framework for Web-based learning environments which is based primarily on educational theory and human-computer interaction research. The comparison framework consists of a large number of comparison dimensions covering a broad range of issues relevant to the adoption of a Web-based learning environment. The comparison framework serves two main audiences. The primary audience consists of decision makers of organizations considering
Mislocalization of Perceived Saccade Target Position Induced by Perisaccadic Visual Stimulation

The perceptual localization of objects flashed at the time of a saccade often shows large spatial distortions. These perisaccadic mislocalizations exhibit different spatial patterns depending on the experimental condition. In darkness, when only extraretinal information is available, mislocalization is spatially uniform. In light and when visual references are available, mislocalization is directed toward the saccade target, resembling a compression of visual space. These patterns are derived from measurements of the absolute perceived position of the flashed object in egocentric space. Here, we report that also the perceived location of the saccade target is altered when an object is flashed perisaccadically. The mislocalization of the target depends on the presentation time of the flashed object and is directed toward the position of the flash. The resulting compression of the relative distance between target and flash is similar in darkness and in light and can also be found during fixation. When the localization of the flashed object is described relative to the perceived location of the saccade target, spatial compression becomes similar in many experimental conditions. We therefore suggest that perisaccadic compression relies on an encoding of relative spatial locations of objects rather than on localizations in egocentric space.
Quantum Theory of Neutrino Spin-Light in Matter

The quantum theory of the spin light of neutrino ($SL\nu$) exactly accounting for the effect of the background matter is developed. The $SL\nu$ rate and power, and also the emitted photon's energy are obtained for the different values of the neutrino momentum and density of matter. The spatial distribution of the radiation power and the dependence of the emitted photon's energy on the direction of radiation are studied. It is also shown that, in a wide range of the neutrino momentum and densities of matter, the $SL\nu$ radiation is characterized by nearly total circular polarization. Conditions for the effective neutrino spin-light radiation in the electron plasma are discussed.
Global Climate and Infectious Disease: The Cholera Paradigm*

The origin of cholera has been elusive, even though scientific evidence clearly shows it is a waterborne disease. However, standard bacteriological procedures for isolation of the cholera vibrio from environmental samples, including water, between epidemics generally were unsuccessful. Vibrio cholerae, a marine vibrio, requiring salt for growth, enters into a dormant, viable but nonculturable stage when conditions are unfavorable for growth and reproduction. The association of Vibrio cholerae with plankton, notably copepods, provides further evidence for the environmental origin of cholera, as well as an explanation for the sporadic and erratic occurrence of cholera epidemics. On a global scale, cholera epidemics can now be related to climate and climatic events, such as El Niño, as well as the global distribution of the plankton host. Remote sensing, with the use of satellite imagery, offers the potential for predicting conditions conducive to cholera outbreaks or epidemics.
Efficient Testing of Recovery Code Using Fault Injection

A critical part of developing a reliable software system is testing its recovery code. This code is traditionally difficult to test in the lab, and, in the field, it rarely gets to run; yet, when it does run, it must execute flawlessly in order to recover the system from failure. In this article, we present a library-level fault injection engine that enables the productive use of fault injection for software testing. We describe automated techniques for reliably identifying errors that applications may encounter when interacting with their environment, for automatically identifying high-value injection targets in program binaries, and for producing efficient injection test scenarios. We present a framework for writing precise triggers that inject desired faults, in the form of error return codes and corresponding side effects, at the boundary between applications and libraries. These techniques are embodied in LFI, a new fault injection engine we are distributing http://lfi.epfl. ch. This article includes a report of our initial experience using LFI. Most notably, LFI found 12 serious, previously unreported bugs in the MySQL database server, Git version control system, BIND name server, Pidgin IM client, and PBFT replication system with no developer assistance and no access to source code. LFI also increased recovery-code coverage from virtually zero up to 60% entirely automatically without requiring new tests or human involvement.
Efficient reversible image watermarking by using dynamical prediction-error expansion

Reversible watermarking is a special watermarking technique which allows one to extract both the hidden data and the exact original signal from the watermarked content. In this paper, a recently introduced reversible image watermarking method based on prediction-error expansion is further investigated and improved. Instead of taking the pixels with small prediction-error as embedding pixels (i.e., the pixels that carry watermark bits), we propose to select these pixels in a dynamical way. In fact, we can pre-calculate the embedding distortion for each possible choice of embedding pixels, and determine the one with minimal distortion. We see that, with this choice of embedding pixels, the distortion is reduced comparing with the original method, and thus, the proposed approach has a better performance. In addition, experimental results show that the novel method outperforms some state-of-the-art algorithms.
Damp Mergers: Recent Gaseous Mergers without Significant Globular Cluster Formation?

Here we test the idea that new globular clusters (GCs) are formed in the same gaseous ("wet") mergers or interactions that give rise to the young stellar populations seen in the central regions of many early-type galaxies. We compare mean GC colors with the age of the central galaxy starburst. The red GC subpopulation reveals remarkably constant mean colors independent of galaxy age. A scenario in which the red GC subpopulation is a combination of old and new GCs (formed in the same event as the central galaxy starburst) cannot be ruled out, although this would require an age-metallicity relation for the newly formed GCs that is steeper than the Galactic relation. However, the data are also well described by a scenario in which most red GCs are old, and few, if any, are formed in recent gaseous mergers. This is consistent with the old ages inferred from some spectroscopic studies of GCs in external systems. The event that induced the central galaxy starburst may have therefore involved insufficient gas mass for significant GC formation. We term such gas-poor events "damp" mergers.
Generalized Cauchy identities, trees and multidimensional Brownian motions. Part I: bijective proof of generalized Cauchy identities

In this series of articles we study connections between combinatorics of multidimensional generalizations of the Cauchy identity and continuous objects such as multidimensional Brownian motions and Brownian bridges. In Part I of the series we present a bijective proof of the multidimensional generalizations of the Cauchy identity. Our bijection uses oriented planar trees equipped with some linear orders.
A shape-based object class model for knowledge transfer

Object class models trained on hundreds or thousands of images have shown to enable robust detection. Transferring knowledge from such models to new object classes trained from a few or even as little as one training instance however is still in its infancy. This paper designs a shape-based model that allows to easily and explicitly transfer knowledge on three different levels: transfer of individual parts' shape and appearance information, transfer of local symmetry between parts, and transfer of part topology. Due to the factorized form of the model, knowledge can either be transferred for the complete model or just partial knowledge corresponding to certain aspects of the model. The experiments clearly demonstrate that the proposed model is competitive with the state-of-the-art and enables both full and partial knowledge transfer.
Intestinal permeability in a patient with liver cirrhosis

Liver cirrhosis is a worldwide public health problem, and patients with this disease are at high risk of developing complications, bacterial translocation from the intestinal lumen to the mesenteric nodes, and systemic circulation, resulting in the development of severe complications related to high mortality rate. The intestinal barrier is a structure with a physical and biochemical activity to maintain balance between the external environment, including bacteria and their products, and the internal environment. Patients with liver cirrhosis develop a series of alterations in different components of the intestinal barrier directly associated with the severity of liver disease that finally increased intestinal permeability. A “leaky gut” is an effect produced by damaged intestinal barrier; alterations in the function of tight junction proteins are related to bacterial translocation and their products. Instead, increasing serum proinflammatory cytokines and hemodynamics modification, which results in the appearance of complications of liver cirrhosis such as hepatic encephalopathy, variceal hemorrhage, bacterial spontaneous peritonitis, and hepatorenal syndrome. The intestinal microbiota plays a fundamental role in maintaining the proper function of the intestinal barrier; bacterial overgrowth and dysbiosis are two phenomena often present in people with liver cirrhosis favoring bacterial translocation. Increased intestinal permeability has an important role in the genesis of these complications, and treating it could be the base for prevention and partial treatment of these complications.
The effects of hormonotherapy administered concurrent radiotherapy and trastuzumab on cardiac toxicity in rats.

OBJECTIVE This experimental study aims to investigate whether radiotherapy (RT) plus trastuzumab (T) followed by subsequent hormonotherapy increase the cumulative toxic effect on cardiac functions in rats. METHODS A total of 70 Wistar-Albino female rats with a mean weight 213 ± 27 g were randomly divided into equal seven groups. The first group (C) underwent no procedure. The second group (RT) underwent the whole thoracic radiation including heart. The third group (T) was administered T through tail vein alone. The fourth group (RT+T+Tx) was administered T initially and the whole thoracic radiation at two hours, followed by tamoxifen at one week. The fifth group (RT+T+Le) was administered T and then underwent thoracic radiation, followed by letrozole. The sixth group (T+RT+An) was administered T and then underwent thoracic radiation, followed by anastrazole. The seventh group (T+RT+Ex) was administered T and then underwent thoracic radiation, followed by exemestane at one week. Hormonotherapy was administered to the rats in the Group 5, 6 and 7, as indicated in the Group 4. Radiation therapy was administered following T treatment at two hours as a single 12 Gy fraction. After the rats were sedated under anesthesia and sacrificed at 24 weeks, cardiac tissues were removed. Serial sections obtained following paraffin blockage were stained and the ratio of myocardial fibrosis was assessed. According to statistical analyses by the one-way ANOVA test and Tukey HSD test, a significant difference between test components. RESULTS At the end of the study, no loss and adverse effects were seen in any group. There was a statistically significant difference among atrium, ventricle and aorta (p<0.001). The mean value of fibrosis scores increased in the rats which underwent RT. In the assessment of atrium, a significant difference was found between RT group and RT+T+An group and also T group and RT+T+Fe group (p<0.001). In the assessment of ventricule, a statistically significant difference was observed among RT, RT+T+An and RT+T+Ex. In the assessment of aorta, the scores of RT group was significantly higher than RT+T+An and RT+T+Ex. A statistically significant difference was observed among these groups (p<0.001). CONCLUSION Our study results suggested that there was no significant additional cardiotoxicity of adjuvant hormonotherapy following concomitant RT and T treatment, compared to RT in terms of cardiac fibrosis.