Miracle-dz/UniFAR-FTUs huggingface dataset:
Biochemical Characteristics of Vibrio sputorum and Relationship to Vibrio bubulus and Vibrio fetus

Loesche, Walter J. (Forsyth Dental Center and Harvard School of Dental Medicine, Boston, Mass.), Ronald J. Gibbons, and Sigmund S. Socransky. Biochemical characteristics of Vibrio sputorum and relationship to Vibrio bubulus and Vibrio fetus. J. Bacteriol. 89:1109–1116. 1965. —Twenty-seven strains of Vibrio sputorum were isolated from human gingival debris. All strains reduced nitrate beyond nitrite, and all produced H2S. None produced catalase, indole, or acetylmethylcarbinol. Carbohydrates were not fermented, and acid end products or volatile neutral products could not be detected. Motility was observed infrequently, although 14-hr cultures usually had a few cells which displayed darting motility. Shadowed electron microscopic preparations demonstrated that most cells in a given culture were nonflagellated, although some cells with a single terminal or subterminal flagellum were always observed. V. sputorum was demonstrated not to be a strict anaerobe as previously described, but rather a microaerophile. Addition of nitrate to culture media markedly enhanced growth. V. sputorum was found to be closely related to the animal microaerophilic vibrios, V. bubulus and V. fetus. V. sputorum differed from V. fetus by being capable of anaerobic growth, producing H2S, and failing to produce catalase or to grow in 10% O2. Antigens of V. sputorum cross-reacted in low titer with antisera to V. fetus serotypes I, II, III, and V. V. sputorum differed from V. bubulus by being inhibited by 3.5% NaCl and by qualitative differences in growth in the presence of 1% glycine and 10% O2. These differences do not appear sufficient to recognize two distinct species, and it is proposed that both species be recognized as V. sputorum, which has priority. Strains unable to grow in 3.5% NaCl would be considered V. sputorum var. sputorum, whereas strains capable of growth in 3.5% NaCl would be V. sputorum var. bubulum.
Characterization of an Apparently Novel β-Cell Line-enriched 80–88 kDa Transcriptional Activator of the MafA and Pdx1 Genes*

Background: There is limited knowledge of transcription factors controlling pancreatic β-cell MafA and Pdx1 expression. Results: An 80–88 kilodalton activator with unique DNA binding specificity regulates conserved MafA and Pdx1 control elements. Conclusion: MafA and Pdx1 are regulated by a novel trans-activator. Significance: Identifying transcriptional networks governing key β-cell genes may lead to improved cell-based diabetes therapies. MafA and Pdx1 represent critical transcriptional regulators required for the maintenance of pancreatic islet β-cell function. The in vivo β-cell-enriched expression pattern of these genes is principally directed by islet transcription factors binding within conserved Region 3 (base pairs (bp) −8118/−7750) of MafA and Area II (bp −2153/−1923) of the Pdx1 gene. Comprehensive mutational analysis of conserved MafA Region 3 revealed two new β-cell line-specific cis-activation elements, termed Site 4 (bp −7997 to −7988) and Site 12 (bp −7835 to −7826). Gel mobility and antibody super-shift analysis identified Pdx1 as the Site 4 binding factor, while an 80–88 kilodalton (kDa) β-cell line-enriched protein complex bound Site 12 and similar aligned nucleotides within Pdx1 Area II. The 80–88 kDa activator was also found in adult mouse islet extract. Strikingly, the molecular weight, DNA binding, and antibody recognition properties of this activator were unique when compared with all other key islet transcription factors tested, including Prox1 (83 kDa), Hnf1α (67 kDa), FoxA2 (48 kDa), MafA (46 kDa), Isl1 (44 kDa), Pdx1 (42 kDa), and Nkx2.2 (30 kDa). Collectively, these data define an apparently novel MafA Region 3 and Pdx1 Area II activator contributing to expression in β-cells.
Conditional use of word lattices, confusion networks and 1-best string hypotheses in a sequential interpretation strategy

Within the context of a deployed spoken dialog service, this study presents a new interpretation strategy based on the sequential use of different ASR output representations: 1-best strings, word lattices and confusion networks. The goal is to reject as early as possible in the decoding process the nonrelevant messages containing non-speech or out-of-domain content. This is done through the 1-pass of the ASR decoding process thanks to specific acoustic and language models. A confusion network (CN) is then calculated for the remaining messages and another rejection process is applied with the confidence measures obtained in the CN. The messages kept at this stage are considered relevant; therefore the search for the best interpretation is applied to a richer search space than just the 1-best word string: either the whole CN or the whole word lattice. An improved, SLU oriented, CN generation algorithm is also proposed that significantly reduces the size of the CN obtained while improving the recognition performance. This strategy is evaluated on a large corpus of real users’ messages obtained from a deployed service. 1
A model of neocortex

Prompted by considerations about (i) the compositionality of cognitive functions, (ii) the physiology of individual cortical neurons, (iii) the role of accurately timed spike patterns in cortex, and (iv) the regulation of global cortical activity, we suggest that the dynamics of cortex on the 1-ms time scale may be described as the activation of circuits of the synfire-chain type (Abeles 1982, 1991). We suggest that the fundamental computational unit in cortex may be a wave-like spatio-temporal pattern of synfire type, and that the binding mechanism underlying compositionality in cognition may be the accurate synchronization of synfire waves that propagate simultaneously on distinct, weakly coupled, synfire chains. We propose that Hebbian synaptic plasticity may result in a superposition of synfire chains in cortical connectivity, whereby a given neuron participates in many distinct chains. We investigate the behaviour of a much-simplified model of cortical dynamics devised along these principles. Calcula.
Well-Being After Stroke in Canadian Seniors: Findings From the Canadian Study of Health and Aging

Background and Purpose— After a stroke many people continue to live with their residual impairments and disabilities in the community, which can pose a significant problem for survivors’ well-being. The purpose of this research was to investigate patterns of well-being in community-dwelling stroke survivors to identify those factors that restrict and enhance well-being. Methods— A secondary analysis was conducted on data from the second wave of the Canadian Study of Health and Aging (CSHA-2). A national sample of 5395 community-dwelling Canadian seniors (aged ≥65 years) was interviewed for CSHA-2, including 339 stroke survivors (6.3%). Information was collected on health, social and demographic characteristics, and well-being. Comparisons were made between the health and functional status of stroke survivors and community-dwelling seniors who have not experienced a stroke. Multiple regression was used to examine the factors associated with well-being in stroke survivors. Results— Compared with community-dwelling seniors who have not experienced a stroke, stroke survivors report a lower sense of well-being. Stroke survivors are also more likely to be restricted in their physical and cognitive function, to report worse mental health, and to be living with a greater number of comorbid health conditions. Mental health and physical and cognitive disabilities are associated with a reduced sense of well-being in stroke survivors, but social supports and educational resources moderate the impact of functional status on well-being. Conclusions— Community-dwelling seniors who have had a stroke experience a reduced sense of well-being. However, social resources can help to alleviate the subjective burden of this common neurological condition.
The Movement Model of Pilots ’ Visual Attention

This paper describes the application of an important tool which can capture shifting information from pilots’ visual attention data. In order to investigate the shifting information, the shifting state space is defined by visual tracking, visual interference and visual dormancy. Using this analysis, the movement of pilots’ visual attention can be completely measured. The results that the forecast of the probability shifting model is coincident with the fact suggest the use of the model as a powerful technique for measuring the movement of pilots’ visual attention. Furthermore, the link between visual attention and driving experience or sexual distinction are also discussed in the probability shifting model. Copyright © 2013 IFSA
Predictive discomfort of non-neutral head–neck postures in fore–aft whole-body vibration

It seems obvious that human head–neck posture in whole-body vibration (WBV) contributes to discomfort and injury risk. While current mechanical measures such as transmissibility have shown good correlation with the subjective-reported discomfort, they showed difficulties in predicting discomfort for non-neutral postures. A new biomechanically based methodology is introduced in this work to predict discomfort due to non-neutral head–neck postures. Altogether, 10 seated subjects with four head–neck postures—neutral, head-up, head-down and head-to-side—were subjected to WBV in the fore–aft direction using discrete sinusoidal frequencies of 2, 3, 4, 5, 6, 7 and 8 Hz and their subjective responses were recorded using the Borg CR-10 scale. All vibrations were run at constant acceleration of 0.8 m/s2 and 1.15 m/s2. The results have shown that the subjective-reported discomfort increases with head-down and decreases with head-up and head-to-side postures. The proposed predictive discomfort has closely followed the reported discomfort measures for all postures and rides under investigation. Statement of Relevance: Many occupational studies have shown strong relevance between non-neutral postures, discomfort and injury risk in WBV. With advances in computer human modelling, the proposed predictive discomfort may provide efficient ways for developing reliable biodynamic models. It may also be used to assess discomfort and modify designs inside moving vehicles.
I E S ADVANTAGE OF THE CLASSICAL CORPORATION TAX OVER THE IMPUTATION SYSTEM AS A MEANS OF TAX HARMONIZATION

The classical corporation tax entails double taxation of corporate income. The current EU practise is to grant a credit from or impute the corporation tax to the domestic recipients of dividends. In case of a company with international owners the feature converts the imputation system back to a classical corporation tax. When the exemption method is applied to the taxation of repatriated dividends, their onward distribution to the international owners of the parent requires complex rules for exempting them from the minimum corporation tax, which equals the tax credit on dividends, in order to avoid the cumulation of the corporation tax internationally. In contrast, the classical corporation tax, combined with the tax exemption of foreign and domestic dividends within the corporate sector, maintains its simplicity and can be designed neutral with respect to the financing and dividend decisions of multinationals, by adopting double taxation of interest income. Broad tax bases and low statutory tax rates are advocated as general policy. JEL classification: H25, G32, G35
Avaliação do funcionamento do eixo HPA em deprimidos por meio de medidas basais: revisão sistemática da literatura e análise das metodologias utilizadas

Objective We performed a systematic literature review in order to assess the hypothalamic-pituitary-adrenal (HPA) axis activity in depressed considering the baseline measurements of the hormones of this axis and perform a critical analysis of the methodologies used. Methods We performed search for articles in the databases PubMed and SciELO. In the first database, was introduced the keywords: “depressive disorder”, “HPA axis” and in the second used the terms “depression” or “depressao” and “HPA” or “HPA axis”. We limit to research in adult humans, in English and Portuguese, from the year 2000 until 2011. Results Of the 27 selected articles, obtained HPA axis hyperactivity, unregulated activity, hypoactivity or remains unchanged. These results depend on the variables and hormones studied, collected fluid: plasma, urine, saliva, cerebrospinal fluid; the time of collection, the number of collections, the subtype of the depressive disease, among others. Conclusion The results do not have consensus on HPA activity. Considering the variables studied, the HPA axis, in most cases, it appears dysfunctional in the presence of depression.
Monocyte-derived inhibitor of interleukin 1 induced by human cytomegalovirus

It has previously been shown that human cytomegalovirus (HCMV) can exert immunosuppressive effects, and it has been suggested that these may be mediated by monocytes, although the mechanism is unclear. We showed that infection of human monocytes with the AD169 strain of HCMV abrogates their production of interleukin 1 (IL-1) activity. This was associated with the release from infected monocytes of an inhibitor of IL-1 activity which was also released after HCMV infection of the U937 macrophage-like cell line. The inhibitor of IL-1 activity is a protein with an apparent molecular weight of ca. 95,000. This action of HCMV strain AD169 was virus specific and required infectious virus but occurred without virus replication or detectable expression of viral proteins. This effect may account, at least in part, for the previously observed immunosuppressive properties of HCMV.
Cytokine Regulation of the Synthesis of Plasminogen Activator Inhibitor-2 by Human Vascular Endothelial Cells

Summary Plasminogen activators are inhibited by plasminogen activator inhibitors-1 (PAI-1) and -2 (PAI-2). We describe the synthesis of PAI-2 by human vascular endothelial cells (EC) cultured from umbilical vein, saphenous vein and foreskin microvasculature in response to interleukin-1α (IL־1α) and tumour necrosis factor α (TNFα) and compare it with that of PAI-1. Both PAI-2 and PAI-1 were quantitated by ELIS As. PAI-2 was cell-associated while PAI-1 was secreted by EC. IL-lα and TNFα increased the synthesis of PAI-2 and PAI-1 by EC in a dose-dependent manner. IL-1α was a stronger stimulus for PAI-2 synthesis than TNFα, while both cytokines were equally effective for PAI-1. Northern blot analysis revealed similar changes in mRNA levels to those in antigen levels. PAI-2 synthesis by cytokine-stimulated EC may be important in thrombus formation and inflammation.
Mitochondrial-Derived Reactive Oxygen Species Play a Vital Role in the Salicylic Acid Signaling Pathway in Arabidopsis thaliana

Plant mitochondria constitute a major source of ROS and are proposed to act as signaling organelles in the orchestration of defense response. At present, the signals generated and then integrated by mitochondria are still limited. Here, fluorescence techniques were used to monitor the events of mitochondria in vivo, as well as the induction of mitochondrial signaling by a natural defensive signal chemical salicylic acid (SA). An inhibition of respiration was observed in isolated mitochondria subjected to SA. The cytochrome reductase activity analysis in isolated mitochondria demonstrated that SA might act directly on the complex III in the respiration chain by inhibiting the activity. With this alteration, a quick burst of mitochondrial ROS (mtROS) was stimulated. SA-induced mtROS caused mitochondrial morphology transition in leaf tissue or protoplasts expressing mitochondria-GFP (43C5) and depolarization of membrane potential. However, the application of AsA, an H2O2 scavenger, significantly prevented both events, indicating that both of them are attributable to ROS accumulation. In parallel, SA-induced mtROS up-regulated AOX1a transcript abundance and this induction was correlated with the disease resistance, whereas AsA-pretreatment interdicted this effect. It is concluded that mitochondria play an essential role in the signaling pathway of SA-induced ROS generation, which possibly provided new insight into the SA-mediated biological processes, including plant defense response.
Characterization of N‐linked oligosaccharides attached to recombinant human antithrombin expressed in the yeast Pichia pastoris

We studied the structures of four N‐linked oligosaccharide chains of the recombinant human antithrombin (rAT) expressed in the yeast Pichia pastoris. rAT was fully glycosylated at Asn 96 and Asn 155, whereas the glycosylation on Asn 135 and Asn 192 was partial. The glycosylation level on Asn 135 was only 12% and this reduction is assumed to be one of the reasons for a higher heparin‐binding affinity of rAT than plasma‐derived human antithrombin (pAT). In order to determine the sizes and electrostatic charges of the N‐linked oligosaccharides, rAT was treated with PNGase F, and the reduced ends were labelled by pyridylamination followed by analysis using anion exchange and amide adsorption columns. The N‐linked oligosaccharides were 78% neutral and 22% phosphomannosylated. The neutral oligosaccharides were thought to be Man9–12GlcNAc2 as their major components. The phosphomannosylated oligosaccharides were then subjected to mild acid hydrolysis and/or digestion with alkaline phosphatase, and their charge shifts were analysed by the affinity to an anion exchange column. Among phosphomannosylated oligosaccharides, monophosphate diester type was predominant, whereas negatively charged diphosphate diester and monophosphate monoester types were minor components. The mannose residues at the non‐reducing end(s) of Man9–12GlcNAc2 were phosphomannosylated or phosphorylated and these are the major components. Because rAT is less negatively charged than pAT, which has disialyl biantennary N‐glycans, it might be less repulsive to pentasaccharide‐bearing anticoagulantly active heparan sulphate proteoglycan molecules exposed on the surface of the damaged vascular vessels. Copyright © 2002 John Wiley & Sons, Ltd.
Climate change hastens population extinctions

Climate change is expected to alter the distribution and abundance of many species. Predictions of climate-induced population extinctions are supported by geographic range shifts that correspond to climatic warming, but few extinctions have been linked mechanistically to climate change. Here we show that extinctions of two populations of a checkerspot butterfly were hastened by increasing variability in precipitation, a phenomenon predicted by global climate models. We model checkerspot populations to show that changes in precipitation amplified population fluctuations, leading to rapid extinctions. As populations of checkerspots and other species become further isolated by habitat loss, climate change is likely to cause more extinctions, threatening both species diversity and critical ecosystem services.
Transcultural Effects of Product Placement in Movies

Abstract. Product placement represents an alternative strategy of advertisers to overcome restrictions of traditional commercial communication. The paper describes different types of placement and resumes the small body of research in the field, both serving as a starting point for empirical research. As a matter of fact, placements which have become part of top movies will be distributed in cinemas and on screens all over the world. A quasi-experimental study carried out in Germany and the USA was designed in order to detect awareness and attitude effects of the respective placements as well as general evaluations. The results indicate small but noteworthy differences between the American and the German audience: To a certain degree, product placement was more effective on the awareness dimension in Germany, and more effective on the evaluative dimension in the USA (a result that may be traced back to the perceived function of creating a realistic impression). High placement awareness led to smaller atti.
Critical Issues in Researching Domestic Violence Among People of Color with Disabilities

While there are a number of programs emerging providing services to people of color with disabilities who experience domestic violence, there is little research on the needs of this population. Using data collected from two national focus groups of 19 expert informants, this article outlines key areas of research needed for providing better services to people of color who are Deaf or have disabilities and appropriate research methods for collecting data about this population. Respondents indicated that a research agenda should include investigating the scope of the problem, in-depth needs of domestic violence survivors, cost-effectiveness of culturally and disability-specific programs, and development of best practices through in-depth evaluations of existing programs.
KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans

Histone posttranslational modifications (HPTMs) are involved in chromatin-based regulation of fungal secondary metabolite biosynthesis (SMB) in which the corresponding genes—usually physically linked in co-regulated clusters—are silenced under optimal physiological conditions (nutrient-rich) but are activated when nutrients are limiting. The exact molecular mechanisms by which HPTMs influence silencing and activation, however, are still to be better understood. Here we show by a combined approach of quantitative mass spectrometry (LC-MS/MS), genome-wide chromatin immunoprecipitation (ChIP-seq) and transcriptional network analysis (RNA-seq) that the core regions of silent A. nidulans SM clusters generally carry low levels of all tested chromatin modifications and that heterochromatic marks flank most of these SM clusters. During secondary metabolism, histone marks typically associated with transcriptional activity such as H3 trimethylated at lysine-4 (H3K4me3) are established in some, but not all gene clusters even upon full activation. KdmB, a Jarid1-family histone H3 lysine demethylase predicted to comprise a BRIGHT domain, a zinc-finger and two PHD domains in addition to the catalytic Jumonji domain, targets and demethylates H3K4me3 in vivo and mediates transcriptional downregulation. Deletion of kdmB leads to increased transcription of about ~1750 genes across nutrient-rich (primary metabolism) and nutrient-limiting (secondary metabolism) conditions. Unexpectedly, an equally high number of genes exhibited reduced expression in the kdmB deletion strain and notably, this group was significantly enriched for genes with known or predicted functions in secondary metabolite biosynthesis. Taken together, this study extends our general knowledge about multi-domain KDM5 histone demethylases and provides new details on the chromatin-level regulation of fungal secondary metabolite production.
A random walk on the red carpet: rating movies with user reviews and pagerank

Although PageRank has been designed to estimate the popularity of Web pages, it is a general algorithm that can be applied to the analysis of other graphs other than one of hypertext documents. In this paper, we explore its application to sentiment analysis and opinion mining: i.e. the ranking of items based on user textual reviews. We first propose various techniques using collocation and pivot words to extract a weighted graph of terms from user reviews and to account for positive and negative opinions. We refer to this graph as the sentiment graph. Using PageRank and a very small set of adjectives (such as 'good', 'excellent', etc.) we rank the different items. We illustrate and evaluate our approach using reviews of box office movies by users of a popular movie review site. The results show that our approach is very effective and that the ranking it computes is comparable to the ranking obtained from the box office figures. The results also show that our approach is able to compute context-dependent ratings.