Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants of the Tetrahymena ribozyme.

J1/2 of the Tetrahymena ribozyme, a sequence of three A residues, connects the RNA-binding site to the catalytic core. Addition or deletion of bases from J1/2 improves turnover and substrate specificity in the site-specific endonuclease reaction catalyzed by this ribozyme: G2CCCUCUA5 (S) + G in-equilibrium G2CCCUCU (P) + GA5. These paradoxical enhancements are caused by decreased affinity of the ribozyme for S and P [Young, B. , Herschlag, D. , & Cech, T.R. (1991) Cell 67, 1007]. An additional property of these mutant ribozymes, decreased fidelity of RNA cleavage, is now analyzed. (Fidelity is the ability to cleave at the correct phosphodiester bond within a particular RNA substrate.) Introduction of deoxy residues to give "chimeric" ribo/deoxyribooligonucleotides changes the positions of incorrect cleavage. Previous work indicated that S is bound to the ribozyme by both base pairing and teritary interactions involving 2'-hydroxyl groups of S. The data herein strongly suggest that the P1 duplex, which consists of S base-paired with the 5' exon binding site of the ribozyme, can dock into tertiary interactions in different registers; different 2'-hydroxyl groups of S plug into tertiary contacts with the ribozyme in the different registers. It is concluded that the mutations decrease fidelity by increasing the probability of docking out of register relative to docking in the normal register, thereby giving cleavage at different positions along S. These data also show that the contribution of J1/2 to the teritiary interactions is indirect, not direct. Thus, a structural role of the nonconserved J1/2 is indicated: this sequence positions S to optimize tertiary binding interactions and to ensure cleavage at the phosphodiester bond corresponding to the 5' splice site. Substitution of sulfur for the nonbridging pro-RP oxygen atom at the normal cleavage site has no effect on (kcat/Km)S but decreases the fraction of cleavage at the normal site in reactions catalyzed by the -3A mutant ribozyme, which has all three A residues of J1/2 removed. Thus, the ribozyme chooses where to cleave S after rate-limiting binding of S, indicating that docking can change after binding and suggesting that the ribozyme could act processively. Indeed, it is shown that the +2A ribozyme cleaves at one position along an RNA substrate and then, before releasing that RNA product, cleaves it again. (ABSTRACT TRUNCATED AT 400 WORDS)
Mediator-dependent secondary injury after unilateral blunt thoracic trauma.

The pathophysiologic sequence leading to respiratory failure after chest trauma can be an inevitable consequence of the primary injury or a secondary, mediator-driven inflammatory process. To distinguish between these alternatives, a simple cross-transfusion experiment was performed. A captive bolt gun injured the chest of anesthetized pigs that were mechanically ventilated with FiO2 = . 21, . 50, or . 50 plus indomethacin (5 mg/kg intravenous; 15 min before injury). Tube thoracostomy immediately followed. After 30 min, blood from these injured donors was transfused into three matched groups of naive recipients (n = 8, 6, and 4, respectively) for a 33% exchange transfusion. Two control groups received blood from uninjured donors with tube thoracostomies only (FiO2 = .21, n = 7; FiO2 = .50, n = 10). Within 15-30 min after transfusion, in recipients from injured donors versus controls, lung compliance was decreased 20%, stroke volume and cardiac output were decreased 50%, and pulmonary vascular resistance was increased >300% (all p < .05). These changes recovered to baseline within 60-90 min. The stable metabolite of thromboxane A2, thromboxane B2, increased >500% in plasma within 15 min and remained elevated for >120 min. All responses were similar at 21 % or 50% O2, which suggests that hypoxia per se is not a cause of mediator production. All responses were eliminated by indomethacin. By 24 h, histologic changes included atelectasis in 3/3 recipients from injured donors versus 0/3 recipients from uninjured donors. We conclude that 1) blunt chest trauma releases blood borne mediators, including prostanoids; 2) these mediators can cause secondary cardiopulmonary changes in naive recipients similar to those produced by chest trauma; 3) the progression to trauma-induced respiratory failure is multifactorial; 4) early pharmacologic intervention, rather than supportive care alone, may benefit some victims of severe chest trauma.
Curie: A method for protecting SVM Classifier from Poisoning Attack

Machine learning is used in a number of security related applications such as biometric user authentication, speaker identification etc. A type of causative integrity attack against machine learning called Poisoning attack works by injecting specially crafted data points in the training data so as to increase the false positive rate of the classifier. In the context of the biometric authentication, this means that more intruders will be classified as valid user, and in case of speaker identification system, user A will be classified user B. In this paper, we examine poisoning attack against SVM and introduce - Curie - a method to protect the SVM classifier from the poisoning attack. The basic idea of our method is to identify the poisoned data points injected by the adversary and filter them out. Our method is light weight and can be easily integrated into existing systems. Experimental results show that it works very well in filtering out the poisoned data.
Does transcranial electrical stimulation enhance corticospinal excitability of the motor cortex in healthy individuals? A systematic review and meta‐analysis

Numerous studies have explored the effects of transcranial electrical stimulation (tES) – including anodal transcranial direct current stimulation (a‐tDCS), cathodal transcranial direct current stimulation (c‐tDCS), transcranial alternative current stimulation (tACS), transcranial random noise stimulation (tRNS) and transcranial pulsed current stimulation (tPCS) – on corticospinal excitability (CSE) in healthy populations. However, the efficacy of these techniques and their optimal parameters for producing robust results has not been studied. Thus, the aim of this systematic review was to consolidate current knowledge about the effects of various parameters of a‐tDCS, c‐tDCS, tACS, tRNS and tPCS on the CSE of the primary motor cortex (M1) in healthy people. Leading electronic databases were searched for relevant studies published between January 1990 and February 2017; 126 articles were identified, and their results were extracted and analysed using RevMan software. The meta‐analysis showed that a‐tDCS application on the dominant side significantly increases CSE (P < 0.01) and that the efficacy of a‐tDCS is dependent on current density and duration of application. Similar results were obtained for stimulation of M1 on the non‐dominant side (P = 0.003). The effects of a‐tDCS reduce significantly after 24 h (P = 0.006). Meta‐analysis also revealed significant reduction in CSE following c‐tDCS (P < 0.001) and significant increases after tRNS (P = 0.03) and tPCS (P = 0.01). However, tACS effects on CSE were only significant when the stimulation frequency was ≥140 Hz. This review provides evidence that tES has substantial effects on CSE in healthy individuals for a range of stimulus parameters.
Mycobacterial Esx-3 Requires Multiple Components for Iron Acquisition

ABSTRACT The type VII secretion systems are conserved across mycobacterial species and in many Gram-positive bacteria. While the well-characterized Esx-1 pathway is required for the virulence of pathogenic mycobacteria and conjugation in the model organism Mycobacterium smegmatis, Esx-3 contributes to mycobactin-mediated iron acquisition in these bacteria. Here we show that several Esx-3 components are individually required for function under low-iron conditions but that at least one, the membrane-bound protease MycP3 of M. smegmatis, is partially expendable. All of the esx-3 mutants tested, including the ΔmycP3ms mutant, failed to export the native Esx-3 substrates EsxHms and EsxGms to quantifiable levels, as determined by targeted mass spectrometry. Although we were able to restore low-iron growth to the esx-3 mutants by genetic complementation, we found a wide range of complementation levels for protein export. Indeed, minute quantities of extracellular EsxHms and EsxGms were sufficient for iron acquisition under our experimental conditions. The apparent separation of Esx-3 function in iron acquisition from robust EsxGms and EsxHms secretion in the ΔmycP3ms mutant and in some of the complemented esx-3 mutants compels reexamination of the structure-function relationships for type VII secretion systems. IMPORTANCE Mycobacteria have several paralogous type VII secretion systems, Esx-1 through Esx-5. Whereas Esx-1 is required for pathogenic mycobacteria to grow within an infected host, Esx-3 is essential for growth in vitro. We and others have shown that Esx-3 is required for siderophore-mediated iron acquisition. In this work, we identify individual Esx-3 components that contribute to this process. As in the Esx-1 system, most mutations that abolish Esx-3 protein export also disrupt its function. Unexpectedly, however, ultrasensitive quantitation of Esx-3 secretion by multiple-reaction-monitoring mass spectrometry (MRM-MS) revealed that very low levels of export were sufficient for iron acquisition under similar conditions. Although protein export clearly contributes to type VII function, the relationship is not absolute. Mycobacteria have several paralogous type VII secretion systems, Esx-1 through Esx-5. Whereas Esx-1 is required for pathogenic mycobacteria to grow within an infected host, Esx-3 is essential for growth in vitro. We and others have shown that Esx-3 is required for siderophore-mediated iron acquisition. In this work, we identify individual Esx-3 components that contribute to this process. As in the Esx-1 system, most mutations that abolish Esx-3 protein export also disrupt its function. Unexpectedly, however, ultrasensitive quantitation of Esx-3 secretion by multiple-reaction-monitoring mass spectrometry (MRM-MS) revealed that very low levels of export were sufficient for iron acquisition under similar conditions. Although protein export clearly contributes to type VII function, the relationship is not absolute.
Eye tracking uncovered great apes' ability to anticipate that other individuals will act according to false beliefs

ABSTRACT Using a novel eye-tracking test, we recently showed that great apes anticipate that other individuals will act according to false beliefs. This finding suggests that, like humans, great apes understand others' false beliefs, at least in an implicit way. One key question raised by our study is why apes have passed our tests but not previous ones. In this article, we consider this question by detailing the development of our task. We considered 3 major differences in our task compared with the previous ones. First, we monitored apes' eye movements, and specifically their anticipatory looks, to measure their predictions about how agents will behave. Second, we adapted our design from an anticipatory-looking false belief test originally developed for human infants. Third, we developed novel test scenarios that were specifically designed to capture the attention of our ape participants. We then discuss how each difference may help explain differences in performance on our task and previous ones, and finally propose some directions for future studies.
Building a Responsibility Model Including Accountability, Capability and Commitment

This paper aims at building a responsibility model based on the concepts of Accountability, Capability and Commitment. The model's objectives are firstly to help organizations for verifying the organizational structure and detecting policy problems and inconsistency. Secondly, the paper brings up a conceptual framework to support organization for defining their corporate, security and access control policies. Our work provides a preliminary review of the researches performed in that field and proposes, based on the analyses, an UML responsibility model and a definition of all its concepts. Thereafter, to propose a formal representation of the model, we have selected the suitable language and logic system. The analyze highlights that an important variable is whether the responsibility is perceived at a user or at a company level.
Evidence that proteolysis of the surface is an initial step in the mechanism of formation of sperm cell surface domains

On terminally differentiated sperm cells, surface proteins are segregated into distinct surface domains that include the anterior and posterior head domains. We have analyzed the formation of the anterior and posterior head domains of guinea pig sperm in terms of both the timing of protein localization and the mechanism(s) responsible. On testicular sperm, the surface proteins PH-20, PH-30 and AH-50 were found to be present on the whole cell (PH-20) or whole head surface (PH- 30, AH-50). On sperm that have completed differentiation (cauda epididymal sperm), PH-20 and PH-30 proteins were restricted to the posterior head domain and AH-50 was restricted to the anterior head domain. Thus these proteins become restricted in their distribution late in sperm differentiation, after sperm leave the testis. We discovered that the differentiation process that localizes these proteins can be mimicked in vitro by treating testicular sperm with trypsin. After testicular sperm were treated with 20 micrograms/ml trypsin for 5 min at room temperature, PH-20, PH-30, and AH-50 were found localized to the same domains to which they are restricted during in vivo differentiation. The in vitro trypsin-induced localization of PH-20 to the posterior head mimicked the in vivo differentiation process quantitatively as well as qualitatively. The quantitative analysis showed the process of PH-20 localization involves the migration of surface PH-20 from other regions to the posterior head domain. Immunoprecipitation experiments confirmed that there is protease action in vivo on the sperm surface during the late stages of sperm differentiation. Both the PH-20 and PH-30 proteins were shown to be proteolytically cleaved late in sperm differentiation. These findings strongly implicate proteolysis of surface molecules as an initial step in the mechanism of formation of sperm head surface domains.
Effect of Thermal Treatment of Veneer on Formaldehyde Emission of Poplar Plywood

A large amount of poplar plywood is now being imported into Japan from China, and as a result, formaldehyde emitted from this plywood represents an undesirable chemical that must be controlled using a chemical catching agent. The aim of this study is to find an approach to reduce the formaldehyde emission of poplar plywood using thermal treatment without employing any chemicals. The experimental results obtained show that heating veneer sheets in the temperature range of 150 °C to 170 °C effectively reduced the formaldehyde emission of plywood, without diminishing the mechanical properties of the veneer. By applying Langmuir’s theory and Hailwood-Horrobin theory to the adsorption isotherm obtained in this study, the relationship between the formaldehyde emission of plywood and the adsorption properties of veneer as a material is discussed. When veneer sheets were heated in the temperature range of 150 °C to 170 °C, the amount of hydrated water (monomolecular layer) decreased slightly and that of dissolved water (polymolecular layer) did not change. It is hypothesized that the formaldehyde emission of plywood is related to the condition of the adsorption site of the wood.
Laparoscopic splenectomy by secondary pedicle division strategy: a highly cost-effective method.

BACKGROUND Laparoscopic splenectomy (LS) shows many advantages compared with open surgery except for the high cost. This study was aimed to recommend secondary pedicle division strategy as a method with high cost-effectiveness. METHODS From January 2003 to June 2005, 14 consecutive patients underwent laparoscopic splenectomy. The splenic pedicle was controlled by secondary pedicle division strategy in 8 cases and by Endo-GIA in the other 6 cases. A retrospective study was carried out to evaluate the operative time, blood loss, time to diet, operative morbidity, postoperative stay, and operative cost. RESULTS LS was performed successfully in a total of 14 cases. There was no significant difference between the two strategies in operative time, blood loss, time to diet, operative morbidity and postoperative stay. The operative cost of secondary pedicle division strategy group (RMB 8354.38 +/- 752.10) was significantly lower than that of Endo-GIA group (RMB 11053.33 +/- 602.27) (P < 0.01). CONCLUSIONS Laparoscopic splenectomy by secondary pedicle division strategy is a safe, effective and economical procedure with the value of popularization in developing countries.
Chemical Screens Identify Drugs that Enhance or Mitigate Cellular Responses to Antibody-Toxin Fusion Proteins

The intersection of small molecular weight drugs and antibody-based therapeutics is rarely studied in large scale. Both types of agents are currently part of the cancer armamentarium. However, very little is known about how to combine them in optimal ways. Immunotoxins are antibody-toxin gene fusion proteins engineered to target cancer cells via antibody binding to surface antigens. For fusion proteins derived from Pseudomonas exotoxin (PE), potency relies on the enzymatic domain of the toxin which catalyzes the ADP-ribosylation of EF2 causing inhibition of protein synthesis leading to cell death. Candidate immunotoxins have demonstrated clear value in clinical trials but generally have not been curative as single agents. Therefore we undertook three screens to discover effective combinations that could act synergistically. From the MIPE-3 library of compounds we identified various enhancers of immunotoxin action and at least one major class of inhibitor. Follow-up experiments confirmed the screening data and suggested that immunotoxins when administered with everolimus or nilotinib exhibit favorable combinatory activity and would be candidates for preclinical development. Mechanistic studies revealed that everolimus-immunotoxin combinations acted synergistically on elements of the protein synthetic machinery, including S61 kinase and 4E-BP1 of the mTORC1 pathway. Conversely, PARP inhibitors antagonized immunotoxins and also blocked the toxicity due to native ADP-ribosylating toxins. Thus, our goal of investigating a chemical library was justified based on the identification of several approved compounds that could be developed preclinically as ‘enhancers’ and at least one class of mitigator to be avoided.
The effectiveness of a mindfulness based stress reduction (MBSR) program in a mixed chronic pain population

Both qualitative and quantitative research approaches should be accompanied by a structured abstract of no more than 250 words. Commentaries and Essays may continue to use text based abstracts of no more than 150 words. All original articles should include the following headings in the abstract as appropriate:Background, Objective, Design, Setting, Methods, Participants, Results, and Conclusions. As an absolute minimum: Objectives, Methods, Results, and Conclusions must be provided for all original articles. Abstracts for reviews of the literature (in particular systematic reviews and meta-analysis) should include the following headings as appropriate: Objectives, Data Sources, Study Selection, Data Extraction, Data Synthesis, Conclusions. Abstracts for Case Studies should include the following headings as appropriate:Background, Objectives, Clinical Features, Intervention and Outcomes, Conclusions. Text The text of observational and experimental articles is usually, but not necessarily, divided into sections with the headings; introduction, methods, results, results and discussion. In longer articles, headings should be used only to enhance the readability. Three categories of headings should be used: • major headings should be typed in capital letter in the centre of the page and underlined (i.e.INTRODUCTION) • secondary ones should be typed in lower case (with an initial capital letter) in the left hand margin and underlined (i.e. Participants). • minor ones typed in lower case and italicised (i.e. questionnaire).
Trends in the Breeding Population of Adélie Penguins in the Ross Sea, 1981–2012: A Coincidence of Climate and Resource Extraction Effects

Measurements of the size of Adélie penguin (Pygoscelis adeliae) colonies of the southern Ross Sea are among the longest biologic time series in the Antarctic. We present an assessment of recent annual variation and trends in abundance and growth rates of these colonies, adding to the published record not updated for more than two decades. High angle oblique aerial photographic surveys of colonies were acquired and penguins counted for the breeding seasons 1981–2012. In the last four years the numbers of Adélie penguins in the Ross and Beaufort Island colonies (southern Ross Sea metapopulation) reached their highest levels since aerial counts began in 1981. Results indicated that 855,625 pairs of Adélie penguins established breeding territories in the western Ross Sea, with just over a quarter (28%) of those in the southern portion, constituting a semi-isolated metapopulation (three colonies on Ross Island, one on nearby Beaufort Island). The southern population had a negative per capita growth rate of −0.019 during 1981–2000, followed by a positive per capita growth rate of 0.067 for 2001–2012. Colony growth rates for this metapopulation showed striking synchrony through time, indicating that large-scale factors influenced their annual growth. In contrast to the increased colony sizes in the southern population, the patterns of change among colonies of the northern Ross Sea were difficult to characterize. Trends were similar to southern colonies until the mid-1990s, after which the signal was lost owing to significantly reduced frequency of surveys. Both climate factors and recovery of whale populations likely played roles in the trends among southern colonies until 2000, after which depletion of another trophic competitor, the Antarctic toothfish (Dissostichus mawsoni), may explain the sharp increasing trend evident since then.