Miracle-dz/UniFAR-FTUs huggingface dataset:
The translation elongation factor eEF1A1 couples transcription to translation during heat shock response

Translation elongation factor eEF1A has a well-defined role in protein synthesis. In this study, we demonstrate a new role for eEF1A: it participates in the entire process of the heat shock response (HSR) in mammalian cells from transcription through translation. Upon stress, isoform 1 of eEF1A rapidly activates transcription of HSP70 by recruiting the master regulator HSF1 to its promoter. eEF1A1 then associates with elongating RNA polymerase II and the 3′UTR of HSP70 mRNA, stabilizing it and facilitating its transport from the nucleus to active ribosomes. eEF1A1-depleted cells exhibit severely impaired HSR and compromised thermotolerance. In contrast, tissue-specific isoform 2 of eEF1A does not support HSR. By adjusting transcriptional yield to translational needs, eEF1A1 renders HSR rapid, robust, and highly selective; thus, representing an attractive therapeutic target for numerous conditions associated with disrupted protein homeostasis, ranging from neurodegeneration to cancer. DOI: http://dx.doi. org/10.7554/eLife.03164. 001
Genetic Basis for Saccharomyces cerevisiae Biofilm in Liquid Medium

Biofilm-forming microorganisms switch between two forms: free-living planktonic and sessile multicellular. Sessile communities of yeast biofilms in liquid medium provide a primitive example of multicellularity and are clinically important because biofilms tend to have other growth characteristics than free-living cells. We investigated the genetic basis for yeast, Saccharomyces cerevisiae, biofilm on solid surfaces in liquid medium by screening a comprehensive deletion mutant collection in the Σ1278b background and found 71 genes that were essential for biofilm development. Quantitative northern blots further revealed that AIM1, ASG1, AVT1, DRN1, ELP4, FLO8, FMP10, HMT1, KAR5, MIT1, MRPL32, MSS11, NCP1, NPR1, PEP5, PEX25, RIM8, RIM101, RGT1, SNF8, SPC2, STB6, STP22, TEC1, VID24, VPS20, VTC3, YBL029W, YBL029C-A, YFL054C, YGR161W-C, YIL014C-A, YIR024C, YKL151C, YNL200C, YOR034C-A, and YOR223W controlled biofilm through FLO11 induction. Almost all deletion mutants that were unable to form biofilms in liquid medium also lost the ability to form surface-spreading biofilm colonies (mats) on agar and 69% also lost the ability to grow invasively. The protein kinase A isoform Tpk3p functioned specifically in biofilm and mat formation. In a tpk3 mutant, transcription of FLO11 was induced three-fold compared with wild-type, but biofilm development and cell–cell adhesion was absent, suggesting that Tpk3p regulates FLO11 positive posttranscriptionally and negative transcriptionally. The study provides a resource of biofilm-influencing genes for additional research on biofilm development and suggests that the regulation of FLO11 is more complex than previously anticipated.
Neuroeconomics

REFERENCES Aragona, B. J., and Wang, Z. (2009). Dopamine regulation of social choice in a monogamous rodent species. Front. Behav. Neurosci. 3:15. doi: 10.3389/neuro.08. 015.2009 Carter, R. M. , MacInnes, J. J., Huettel, S. A. , and Adcock, R. A. (2009). Activation in the VTA and nucleus accumbens increases in anticipation of both gains and losses. Front. Behav. Neurosci. 3:21. doi: 10.3389/neuro.08. 021.2009 Chang, L. J., and Sanfey, A. G. (2009). Unforgettable ultimatums? Expectation violations promote enhanced social memory following economic bargaining. Front. Behav. Neurosci. 3:36. doi: 10.3389/neuro.08. 036.2009 Delgado, M. R. , Jou, R. L. , LeDoux, J. E. , and Phelps, E. A. (2009). Avoiding negative outcomes: tracking the mechanisms of avoidance learning in humans during fear conditioning. Front. Behav. Neurosci. 3:33. doi: 10.3389/neuro.08. 033.2009 Heldmann, M. ,Vogt, B. , Heinze, H. -J., and Münte, T. F. (2009). Different methods to define utility functions yield similar results but engage different neural processes. Front. Behav. Neurosci. 3:43. doi: 10.3389/neuro.08. 043.2009 Hwang, J., Kim, S. , and Lee, D. (2009). Temporal discounting and inter-temporal choice in rhesus monkeys. Front. Behav. Neurosci. 3:9. doi:10.3389/neuro.08. 009.2009. Kato, J., Ide, H. , Kabashima, I. , Kadota, H. , Takano, K. , and Kansaku, K. (2009). Neural correlates of attitude change following positive and negative advertisements. Front. Behav. Neurosci. 3:6. doi:10.3389/neuro.08. 006.2009 Luhmann, C. C. (2009). Temporal decision-making: insights from cognitive neuroscience. Front. Behav. Neurosci. 3:39. doi: 10.3389/neuro.08. 039.2009 Pearson, J., Roitman, J. D. , Brannon, E. M. , Platt, M. L. , and Raghavachari, S. (2010). A physiologically-inspired model of numerical classification based on graded stimulus coding. Front. Behav. Neurosci. 4:1. doi: 10.3389/neuro.08. 001.2010 Salamone, J. D. , Correa, M. , Farrar, A. M. , Nunes, E. J., and Pardo, M. (2009). Dopamine, behavioral economics, and effort. Front. Behav. Neurosci. 3:13. doi: 10.3389/ neuro.08. 013.2009 Seymour, B. , Yoshida, W. , and Dolan, R. (2009). Altruistic learning. Front. Behav. Neurosci. 3:23. doi: 10.3389/neuro.08. 023.2009 Thevarajah, D. , Webb, R. , Ferrall, C. , and Dorris, M. C. (2010). Modeling the value of strategic actions in the superior colliculus. Front. Behav. Neurosci. 3:57. doi: 10.3389/ neuro.08. 057.2009
A Bird’s Eye View of Human Language Evolution

Comparative studies of linguistic faculties in animals pose an evolutionary paradox: language involves certain perceptual and motor abilities, but it is not clear that this serves as more than an input–output channel for the externalization of language proper. Strikingly, the capability for auditory–vocal learning is not shared with our closest relatives, the apes, but is present in such remotely related groups as songbirds and marine mammals. There is increasing evidence for behavioral, neural, and genetic similarities between speech acquisition and birdsong learning. At the same time, researchers have applied formal linguistic analysis to the vocalizations of both primates and songbirds. What have all these studies taught us about the evolution of language? Is the comparative study of an apparently species-specific trait like language feasible? We argue that comparative analysis remains an important method for the evolutionary reconstruction and causal analysis of the mechanisms underlying language. On the one hand, common descent has been important in the evolution of the brain, such that avian and mammalian brains may be largely homologous, particularly in the case of brain regions involved in auditory perception, vocalization, and auditory memory. On the other hand, there has been convergent evolution of the capacity for auditory–vocal learning, and possibly for structuring of external vocalizations, such that apes lack the abilities that are shared between songbirds and humans. However, significant limitations to this comparative analysis remain. While all birdsong may be classified in terms of a particularly simple kind of concatenation system, the regular languages, there is no compelling evidence to date that birdsong matches the characteristic syntactic complexity of human language, arising from the composition of smaller forms like words and phrases into larger ones.
Influence of Vaginal Bacteria and d- and l-Lactic Acid Isomers on Vaginal Extracellular Matrix Metalloproteinase Inducer: Implications for Protection against Upper Genital Tract Infections

We evaluated levels of vaginal extracellular matrix metalloproteinase inducer (EMMPRIN) and matrix metalloprotei-nase (MMP-8) in vaginal secretions in relation to the composition of vaginal bacterial communities and D-and L-lactic acid levels. The composition of vaginal bacterial communities in 46 women was determined by pyrosequencing the V1 to V3 region of 16S rRNA genes. Of the lactobacillus-dominated communities, 51.5% were dominated by Lactobacillus crispatus, 36.4% by Lactobacillus iners, and 6.1% each by Lactobacillus gasseri and Lactobacillus jensenii. Concentrations of L-lactic acid were slightly higher in lactobacillus-dominated vaginal samples, but most differences were not statistically significant. D-Lactic acid levels were higher in samples containing L. crispatus than in those with L. iners (P < 0.0001) or Gardnerella (P ‫؍‬ 0.0002). The relative proportion of D-lactic acid in vaginal communities dominated by species of lactobacilli was in concordance with the proportions found in axenic cultures of the various species grown in vitro. Levels of L-lactic acid (P < 0.0001) and the ratio of L-lactic acid to D-lactic acid (P ‫؍‬ 0.0060), but not concentrations of D-lactic acid, were also correlated with EMMPRIN concentrations. Moreover, vaginal concentrations of EMMPRIN and MMP-8 levels were highly correlated (P < 0.0001). Taken together, the data suggest the relative proportion of L-to D-lactic acid isomers in the vagina may influence the extent of local EMMPRIN production and subsequent induction of MMP-8. The expression of these proteins may help determine the ability of bacteria to transverse the cervix and initiate upper genital tract infections. IMPORTANCE A large proportion of preterm births (>50%) result from infections caused by bacteria originating in the vagina, which requires that they traverse the cervix. Factors that influence susceptibility to these infections are not well understood; however, there is evidence that matrix metalloproteinase (MMP-8) is known to alter the integrity of the cervix. In this work, we show that concentrations of vaginal extracellular matrix metalloproteinase inducer (EMMPRIN) are influenced by members of the vaginal microbial community and concentrations of D-or L-lactic acid isomers in vaginal secretions. Elevated levels of D-lactic acid and the ratio of D-to L-lactic acid influence EMMPRIN concentrations as well as MMP-8 levels. Thus, isomers of lactic acid may function as signaling molecules that alter host gene expression and influence risk of infection-related preterm birth. Influence of vaginal bacteria and D-and L-lactic acid isomers on vaginal extracellular matrix metalloproteinase inducer: implications for protection against upper genital tract infections. mBio 4(4):e00460-13. T he …
Interação entre microrganismos do solo, feijoeiro e milho em monocultura ou consórcio

Differences in crop systems reflect in soil microorganisms and in this work some interactions among agronomically important microorganisms and common bean ( Phaseolus vulgaris ) and maize ( Zea mays ) grown in monoculture or intercropped were studied. Under controlled conditions, both bean and maize exudates stimulated rhizobial survival, growth, and nod gene inducing activity, bean nodulation and N accumulation in tissues, and Azospirillum lipoferum survival. After two years with bean and maize in monoculture or intercropped, Azospirillum spp. population was high and did not differ between treatments, while Rhizobium tropici , nitrite oxidizers and soil biomass were favored by bean plants. Rhizobium etli represented, on average, 15% of rhizobial population, except for soils with maize grown alone, where this species was absent, predominating Rhizobium spp. , which nodulate exclusively leucaena ( Leucaena leucocephala ). Soil extracts from the intercropped system showed higher content of nod gene inducing phenolic compounds. Mycorrhizal spore number was not affected by the treatments, although bean in monoculture favored species diversity.
Predictive Brain Signals of Linguistic Development

The ability to extract word forms from continuous speech is a prerequisite for constructing a vocabulary and emerges in the first year of life. Electrophysiological (ERP) studies of speech segmentation by 9- to 12-month-old listeners in several languages have found a left-localized negativity linked to word onset as a marker of word detection. We report an ERP study showing significant evidence of speech segmentation in Dutch-learning 7-month-olds. In contrast to the left-localized negative effect reported with older infants, the observed overall mean effect had a positive polarity. Inspection of individual results revealed two participant sub-groups: a majority showing a positive-going response, and a minority showing the left negativity observed in older age groups. We retested participants at age three, on vocabulary comprehension and word and sentence production. On every test, children who at 7 months had shown the negativity associated with segmentation of words from speech outperformed those who had produced positive-going brain responses to the same input. The earlier that infants show the left-localized brain responses typically indicating detection of words in speech, the better their early childhood language skills.
Current and emerging strategies for the treatment of acute pericarditis: a systematic review

Pericarditis is a common disorder that has multiple causes and presents in various primary-care and secondary-care settings. It is diagnosed in 0.1% of all hospital admissions and in 5% of emergency room visits for chest pain. Despite the advance of new diagnostic techniques, pericarditis is most commonly idiopathic, and radiation therapy, cardiac surgery, and percutaneous procedures have become important causes. Pericarditis is frequently benign and self-limiting. Nonsteroidal anti-inflammatory agents remain the first-line treatment for uncomplicated cases. Integrated use of new imaging methods facilitates accurate detection and management of complications such as pericardial effusion or constriction. In this article, we perform a systematic review on the etiology, clinical presentation, diagnostic evaluation, and management of acute pericarditis. We summarize current evidence on contemporary and emerging treatment strategies.
EasyClone: method for iterative chromosomal integration of multiple genes in Saccharomyces cerevisiae

Development of strains for efficient production of chemicals and pharmaceuticals requires multiple rounds of genetic engineering. In this study, we describe construction and characterization of EasyClone vector set for baker's yeast Saccharomyces cerevisiae, which enables simultaneous expression of multiple genes with an option of recycling selection markers. The vectors combine the advantage of efficient uracil excision reaction-based cloning and Cre-LoxP-mediated marker recycling system. The episomal and integrative vector sets were tested by inserting genes encoding cyan, yellow, and red fluorescent proteins into separate vectors and analyzing for co-expression of proteins by flow cytometry. Cells expressing genes encoding for the three fluorescent proteins from three integrations exhibited a much higher level of simultaneous expression than cells producing fluorescent proteins encoded on episomal plasmids, where correspondingly 95% and 6% of the cells were within a fluorescence interval of Log10 mean ± 15% for all three colors. We demonstrate that selective markers can be simultaneously removed using Cre-mediated recombination and all the integrated heterologous genes remain in the chromosome and show unchanged expression levels. Hence, this system is suitable for metabolic engineering in yeast where multiple rounds of gene introduction and marker recycling can be carried out.
Receptor-like kinase complexes in plant innate immunity

Receptor-like kinases (RLKs) are surface localized, transmembrane receptors comprising a large family of well-studied kinases. RLKs signal through their transmembrane and juxtamembrane domains with the aid of various interacting partners and downstream components. The N-terminal extracellular domain defines ligand specificity, and RLK families are sub-classed according to this domain. The most studied of these subfamilies include those with (1) leucine-rich repeat (LRR) domains, (2) LysM domains (LYM), and (3) the Catharanthus roseus RLK1-like (CrRLK1L) domain. These proteins recognize distinct ligands of microbial origin or ligands derived from intracellular protein/carbohydrate signals. For example, the pattern-recognition receptor (PRR) AtFLS2 recognizes flg22 from flagellin, and the PRR AtEFR recognizes elf18 from elongation factor (EF-Tu). Upon binding of their cognate ligands, the aforementioned RLKs activate generic immune responses termed pattern-triggered immunity (PTI). RLKs can form complexes with other family members and engage a variety of intracellular signaling components and regulatory pathways upon stimulation. This review focuses on interesting new data about how these receptors form protein complexes to exert their function.
A computational model to investigate assumptions in the headturn preference procedure

In this paper we use a computational model to investigate four assumptions that are tacitly present in interpreting the results of studies on infants' speech processing abilities using the Headturn Preference Procedure (HPP): (1) behavioral differences originate in different processing; (2) processing involves some form of recognition; (3) words are segmented from connected speech; and (4) differences between infants should not affect overall results. In addition, we investigate the impact of two potentially important aspects in the design and execution of the experiments: (a) the specific voices used in the two parts on HPP experiments (familiarization and test) and (b) the experimenter's criterion for what is a sufficient headturn angle. The model is designed to be maximize cognitive plausibility. It takes real speech as input, and it contains a module that converts the output of internal speech processing and recognition into headturns that can yield real-time listening preference measurements. Internal processing is based on distributed episodic representations in combination with a matching procedure based on the assumptions that complex episodes can be decomposed as positive weighted sums of simpler constituents. Model simulations show that the first assumptions hold under two different definitions of recognition. However, explicit segmentation is not necessary to simulate the behaviors observed in infant studies. Differences in attention span between infants can affect the outcomes of an experiment. The same holds for the experimenter's decision criterion. The speakers used in experiments affect outcomes in complex ways that require further investigation. The paper ends with recommendations for future studies using the HPP.
Application Of Intelligent Algorithms For Residential Building Energy Performance Rating Prediction

Energy Performance Certiﬁcates (EPC) provide an indication of buildings’ energy use. The creation of an EPC for individual building requires information surveys. Hence, these ratings are typically non-existent for entire building stock. This paper addresses these information gaps using machine-learning models. Developed models were evaluated with Irish EPC data that included approximately 650,000 residential buildings with 199 inputs variables. Results indicate that the deep learning algorithm produces results with highest accuracy level of 88% when only 82 input variables are available. This identiﬁed approach will allow stakeholders such as authorities, policymakers and urban-planners to determine the EPC rating for rest of the building stock using limited data.
Direct and indirect effects in the regulation of overlapping promoters

Optimal response to environmental stimuli often requires activation of certain genes and repression of others. Dual function regulatory proteins play a key role in the differential regulation of gene expression. While repression can be achieved by any DNA binding protein through steric occlusion of RNA polymerase in the promoter region, activation often requires a surface on the regulatory protein to contact RNAP and thus facilitate transcription initiation. RNAP itself is also a DNA binding protein, therefore it can function as a transcriptional repressor. Searching the Escherichia coli promoter database we found that ∼14% of the identified ‘forward’ promoters overlap with a promoter oriented in the opposite direction. In this article we combine a mathematical model with experimental analysis of synthetic regulatory regions to investigate interference of overlapping promoters. We find that promoter interference depends on the characteristics of overlapping promoters. The model predicts that promoter strength and interference can be regulated separately, which provides unique opportunities for regulation. Our experimental data suggest that in principle any DNA binding protein can be used for both activation and repression of promoter transcription, depending on the context. These findings can be exploited in the construction of synthetic networks.
Phospholipase A2 plays a key role in PMN transepithelial migration during S. pneumoniae infection (55.18)

Streptococcus pneumoniae lung infection is characterized by a massive alveolar infiltration of neutrophils (PMNs). Using an in vitro model of lung epithelium and human PMNs, we have shown that S. pneumoniae-induced PMN transepithelial migration is mediated by hepoxilin A3 (HXA3), an arachidonic acid (AA)-derived eicosanoid. Generation of AA is thought to be the rate-limiting step in generation of eicosanoids. Therefore, we studied the role of phospholipase A2 (PLA2), which generates AA from membrane phospholipids, on S. pneumoniae-elicited PMN transpeithelial migration. We found that pneumococcal infection of in vitro lung epithelium resulted in release of AA. This event was partially inhibited by pan-PLA2 inhibitors ONO-RS-082 and ACA, and also by diacylglycerol (DAG) lipase inhibitor RHC 80267. However, while the pan-PLA2 inhibitors significantly reduced S. pneumoniae-induced PMN transmigration, RHC 80267 had no effect on this event. We found that, cytosolic PLA2 (cPLA2) and calcium-independent PLA2 (iPLA2) are important for generation of free AA and inhibition of these enzymes lead to dramatic reduction in PMN transepithelial migration. On the other hand, secretory PLA2 (sPLA2) did not seem to pay a key role in this event. We observed that S. pneumoniae infection caused an increase in the phosphorylation of cPLA2, suggesting a mechanism whereby S. pneumoniae activates PLA2 to generate free AA that may ultimately be converted to the PMN chemoattractant HXA3.
The integration hypothesis of human language evolution and the nature of contemporary languages

How human language arose is a mystery in the evolution of Homo sapiens. Miyagawa et al. (2013) put forward a proposal, which we will call the Integration Hypothesis of human language evolution, that holds that human language is composed of two components, E for expressive, and L for lexical. Each component has an antecedent in nature: E as found, for example, in birdsong, and L in, for example, the alarm calls of monkeys. E and L integrated uniquely in humans to give rise to language. A challenge to the Integration Hypothesis is that while these non-human systems are finite-state in nature, human language is known to require characterization by a non-finite state grammar. Our claim is that E and L, taken separately, are in fact finite-state; when a grammatical process crosses the boundary between E and L, it gives rise to the non-finite state character of human language. We provide empirical evidence for the Integration Hypothesis by showing that certain processes found in contemporary languages that have been characterized as non-finite state in nature can in fact be shown to be finite-state. We also speculate on how human language actually arose in evolution through the lens of the Integration Hypothesis.