Miracle-dz/UniFAR-FTUs huggingface dataset:
The Intimin-Like Protein FdeC Is Regulated by H-NS and Temperature in Enterohemorrhagic Escherichia coli

ABSTRACT Enterohemorrhagic Escherichia coli (EHEC) is a Shiga-toxigenic pathogen capable of inducing severe forms of enteritis (e.g., hemorrhagic colitis) and extraintestinal sequelae (e.g., hemolytic-uremic syndrome). The molecular basis of colonization of human and animal hosts by EHEC is not yet completely understood, and an improved understanding of EHEC mucosal adherence may lead to the development of interventions that could disrupt host colonization. FdeC, also referred to by its IHE3034 locus tag ECOK1_0290, is an intimin-like protein that was recently shown to contribute to kidney colonization in a mouse urinary tract infection model. The expression of FdeC is tightly regulated in vitro, and FdeC shows promise as a vaccine candidate against extraintestinal E. coli strains. In this study, we characterized the prevalence, regulation, and function of fdeC in EHEC. We showed that the fdeC gene is conserved in both O157 and non-O157 EHEC and encodes a protein that is expressed at the cell surface and promotes biofilm formation under continuous-flow conditions in a recombinant E. coli strain background. We also identified culture conditions under which FdeC is expressed and showed that minor alterations of these conditions, such as changes in temperature, can significantly alter the level of FdeC expression. Additionally, we demonstrated that the transcription of the fdeC gene is repressed by the global regulator H-NS. Taken together, our data suggest a role for FdeC in EHEC when it grows at temperatures above 37°C, a condition relevant to its specialized niche at the rectoanal junctions of cattle.
Social media and mobilization to offline demonstrations: Transcending participatory divides?

This paper examines how the use of social media affects participation in offline demonstrations. Using individual web survey data from Norway, we ask whether social media usage serves to re-affirm or transcend socioeconomic divides in participation. In addition to data on demonstration participation in general, we also use the data on the Rose Marches that were organized after the 22/7 terror events as a critical case. Our results show that the type of participant mobilized via the social media is characterized by lower socioeconomic status and younger age than those mobilized via other channels. We also show that connections to information structures through social media exert a strong and independent effect on mobilization. Our findings thus appear to corroborate the mobilization thesis: social media represent an alternative structure alongside mainstream media and well-established political organizations and civil society that recruit in different ways and reach different segments of the population.
Follow the leader! Direct and indirect flows of political communication during the 2013 Italian general election campaign

This article evaluates the potential that Twitter affords politicians to communicate to citizens directly, through messages that they broadcast to users who follow them, and indirectly, to the extent that their followers autonomously re-circulate politicians’ messages to their own contacts. Analysis of more than 2 million accounts of followers of 10 national party leaders during the Italian 2013 general election campaign shows that most users are rather inactive and have very small followings. Moreover, the most followed politicians have on average the least active and followed users, and vice versa. Users’ activity and followings are also unevenly distributed, with very tiny minorities accounting for the vast majority of tweets and followers. The most followed followers of politicians are celebrities in realms other than politics, or people who are already highly visible in the politics-media ecosystem. Our findings suggest that most of the potential for indirect communication may lie in the “vital middle” of the Twitter population who are more active than average, but are not part of the restricted elite of high-impact outliers.
Treatment strategies in CNS metastases

Background: CNS metastases constitute the most common brain malignancy in adults and, therefore, represent a challenging issue in cancer treatment. Purpose: To review the role and indication of the various treatment options in the context of important prognostic factors that may guide the selection of patients who could benefit from each treatment modality. Methods: Therapeutic approaches in treating CNS metastases include surgery, radiotherapy and systemic chemotherapy, and are reviewed through a critical evaluation of published recent literature; however, in the majority of most common malignancies spreading to the CNS, treatment remains largely palliative and rarely curative, as is the case for other metastastic sites. Conclusions: It is anticipated that a multidisciplinary approach with rapid integration of new treatment strategies is required for the treatment of patients developing CNS metastases, ultimately aiming to prolong survival, preserve neurologic function and improve quality of life.
Control of Gene Expression in Leptospira spp. by Transcription Activator-Like Effectors Demonstrates a Potential Role for LigA and LigB in Leptospira interrogans Virulence

ABSTRACT Leptospirosis is a zoonotic disease that affects ∼1 million people annually, with a mortality rate of >10%. Currently, there is an absence of effective genetic manipulation tools for targeted mutagenesis in pathogenic leptospires. Transcription activator-like effectors (TALEs) are a recently described group of repressors that modify transcriptional activity in prokaryotic and eukaryotic cells by directly binding to a targeted sequence within the host genome. To determine the applicability of TALEs within Leptospira spp. , two TALE constructs were designed. First, a constitutively expressed TALE gene specific for the lacO-like region upstream of bgaL was trans inserted in the saprophyte Leptospira biflexa (the TALEβgal strain). Reverse transcriptase PCR (RT-PCR) analysis and enzymatic assays demonstrated that BgaL was not expressed in the TALEβgal strain. Second, to study the role of LigA and LigB in pathogenesis, a constitutively expressed TALE gene with specificity for the homologous promoter regions of ligA and ligB was cis inserted into the pathogen Leptospira interrogans (TALE lig ). LigA and LigB expression was studied by using three independent clones: TALE lig1 , TALE lig2 , and TALE lig3 . Immunoblot analysis of osmotically induced TALE lig clones demonstrated 2- to 9-fold reductions in the expression levels of LigA and LigB, with the highest reductions being noted for TALE lig1 and TALE lig2 , which were avirulent in vivo and nonrecoverable from animal tissues. This study reconfirms galactosidase activity in the saprophyte and suggests a role for LigA and LigB in pathogenesis. Collectively, this study demonstrates that TALEs are effective at reducing the expression of targeted genes within saprophytic and pathogenic strains of Leptospira spp. , providing an additional genetic manipulation tool for this genus.
Comparison of PCR Binary Typing (P-BIT), a New Approach to Epidemiological Subtyping of Campylobacter jejuni, with Serotyping, Pulsed-Field Gel Electrophoresis, and Multilocus Sequence Typing Methods

ABSTRACT To overcome some of the deficiencies with current molecular typing schema for Campylobacter spp. , we developed a prototype PCR binary typing (P-BIT) approach. We investigated the distribution of 68 gene targets in 58 Campylobacter jejuni strains, one Campylobacter lari strain, and two Campylobacter coli strains for this purpose. Gene targets were selected on the basis of distribution in multiple genomes or plasmids, and known or putative status as an epidemicity factor. Strains were examined with Penner serotyping, pulsed-field gel electrophoresis (PFGE; using SmaI and KpnI enzymes), and multilocus sequence typing (MLST) approaches for comparison. P-BIT provided 100% typeability for strains and gave a diversity index of 98.5%, compared with 97.0% for SmaI PFGE, 99.4% for KpnI PFGE, 96.1% for MLST, and 92.8% for serotyping. Numerical analysis of the P-BIT data clearly distinguished strains of the three Campylobacter species examined and correlated somewhat with MLST clonal complex assignations and with previous classifications of “high” and “low” risk. We identified 18 gene targets that conferred the same level of discrimination as the 68 initially examined. We conclude that P-BIT is a useful approach for subtyping, offering advantages of speed, cost, and potential for strain risk ranking unavailable from current molecular typing schema for Campylobacter spp.
Queer youth, Facebook and faith: Facebook methodologies and online identities

‘Making space for queer-identifying religious youth’ (2011–2013) is an Economic and Social Research Council (ESRC)-funded project, which seeks to shed light on youth cultures, queer community and religiosity. While non-heterosexuality is often associated with secularism, and some sources cast religion as automatically negative or harmful to the realisation of lesbian, gay, bisexual and transgender (LGBT) identity (or ‘coming out’), we explore how queer Christian youth negotiate sexual–religious identities. There is a dearth of studies on queer religious youth, yet an emerging and continuing interest in the role of digital technologies for the identities of young people. Based on interviews with 38 LGBT, ‘religious’ young people, this article examines Facebook, as well as wider social networking sites and the online environment and communities. Engaging with the key concept of ‘online embodiment’, this article takes a closer analysis of embodiment, emotion and temporality to approach the role of Facebook in the lives of queer religious youth. Furthermore, it explores the methodological dilemmas evoked by the presence of Facebook in qualitative research with specific groups of young people.
Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium

ABSTRACT Adaptive laboratory evolution (ALE) has emerged as an effective tool for scientific discovery and addressing biotechnological needs. Much of ALE's utility is derived from reproducibly obtained fitness increases. Identifying causal genetic changes and their combinatorial effects is challenging and time-consuming. Understanding how these genetic changes enable increased fitness can be difficult. A series of approaches that address these challenges was developed and demonstrated using Escherichia coli K-12 MG1655 on glucose minimal media at 37°C. By keeping E. coli in constant substrate excess and exponential growth, fitness increases up to 1.6-fold were obtained compared to the wild type. These increases are comparable to previously reported maximum growth rates in similar conditions but were obtained over a shorter time frame. Across the eight replicate ALE experiments performed, causal mutations were identified using three approaches: identifying mutations in the same gene/region across replicate experiments, sequencing strains before and after computationally determined fitness jumps, and allelic replacement coupled with targeted ALE of reconstructed strains. Three genetic regions were most often mutated: the global transcription gene rpoB, an 82-bp deletion between the metabolic pyrE gene and rph, and an IS element between the DNA structural gene hns and tdk. Model-derived classification of gene expression revealed a number of processes important for increased growth that were missed using a gene classification system alone. The methods described here represent a powerful combination of technologies to increase the speed and efficiency of ALE studies. The identified mutations can be examined as genetic parts for increasing growth rate in a desired strain and for understanding rapid growth phenotypes.
Cell phone disconnection disrupts access to healthcare and health resources: A technology maintenance perspective

Over 50% of people in poverty in the United States no longer have a landline telephone, and this same population is more likely to have a no-contract cell phone plan requiring the continuous purchase of minutes. As a result, the poor may increasingly experience short-term phonelessness, which may disrupt access to healthcare and other services. To explore this we conducted 37 client interviews and 7 staff interviews at two free health clinics. Cell phone disconnection was a regular occurrence that delayed access to care and threatened client privacy. Temporary disconnection also contributed to lost employment, lost welfare benefits, and strains on social support networks—all of which are critical for optimizing health. Results are interpreted through a lens of technology maintenance, which argues that the poor will struggle to maintain digital access after ownership and public availability are realized. The potential worsening of health inequalities and related policy implications are discussed.
With a little help from my friends: An analysis of the role of social support in digital inequalities

This article reports an empirical study on the composition and socio-economic background of social support networks and their moderating role in explaining digital inequalities. It conceptually draws upon and empirically reaffirms Van Dijk’s multiple access model, acknowledging motivational, material, skill and usage divides, while focussing on the under-researched issue of social support as indispensible source of social learning. Besides a small group of self-reliants, the results indicate a pattern of relatively socially disadvantaged domestic support receivers, characterized by lower digital resources. A second social support pattern points to a relatively socially advantaged non-domestic support receivers (i.e. friends/colleagues), high in digital resources. Drawing upon the concept of homophily in social networks, the results indicate a link between offline and online exclusion, perpetuating digital inequalities.
Hacktivism and the male-only stereotype

This research explores hacktivism as a new form of online political activism. It uses qualitative interviews with a gender-equal sample of 10 self-defined hacktivists to address issues of gender and the discursive strategies used by males and females to handle the hacktivist community’s male-only stereotype. The semi-structured interviews are analysed using Foucauldian discourse analysis (FDA). The analysis indicates that male hacktivists relate to this dominant male-only representation through discursive techniques such as the suppression of gender (Male Oblivious Discourse) or mechanisms of vindication (Male Justification Discourse). Female hacktivists use the accentuation of gender and sexism to counteract male-dominant discourses and establish Female Discourses of Resistance (Emphasis Discourse; Negation Discourse). These gender-related argumentative positions and rhetorical mechanisms demonstrate how the male-only stereotype is created and maintained and how it affects not only hacktivists’ talk and sense-making but also their identity and the hacktivist actions they perform.
“It Gets Better”: Internet memes and the construction of collective identity

In September 2010, a video titled “It Gets Better” was uploaded to YouTube, responding to suicides of gay teens who had suffered from homophobic bullying. Before long, thousands of Internet users added their own versions of the clip, creating a mass appeal to young people while simultaneously negotiating the norms of lesbian, gay, bisexual, transgender and queer (LGBTQ) collective identity. Conceptualizing this body of videos as an Internet meme, we examine the extent to which participants imitate or alter textual components presented in previous videos. A combined quantitative and qualitative analysis of 200 clips shows that in an arena ostensibly free of formal gatekeepers, participants tend to police themselves, toeing the line with conformist norms. We also identify domains of potential subversion, related not only to the content of the videos but mainly to the forms facilitated by digital media.
Identification of the Monooxygenase Gene Clusters Responsible for the Regioselective Oxidation of Phenol to Hydroquinone in Mycobacteria

ABSTRACT Mycobacterium goodii strain 12523 is an actinomycete that is able to oxidize phenol regioselectively at the para position to produce hydroquinone. In this study, we investigated the genes responsible for this unique regioselective oxidation. On the basis of the fact that the oxidation activity of M. goodii strain 12523 toward phenol is induced in the presence of acetone, we first identified acetone-induced proteins in this microorganism by two-dimensional electrophoretic analysis. The N-terminal amino acid sequence of one of these acetone-induced proteins shares 100% identity with that of the protein encoded by the open reading frame Msmeg_1971 in Mycobacterium smegmatis strain mc2155, whose genome sequence has been determined. Since Msmeg_1971, Msmeg_1972, Msmeg_1973, and Msmeg_1974 constitute a putative binuclear iron monooxygenase gene cluster, we cloned this gene cluster of M. smegmatis strain mc2155 and its homologous gene cluster found in M. goodii strain 12523. Sequence analysis of these binuclear iron monooxygenase gene clusters revealed the presence of four genes designated mimABCD, which encode an oxygenase large subunit, a reductase, an oxygenase small subunit, and a coupling protein, respectively. When the mimA gene (Msmeg_1971) of M. smegmatis strain mc2155, which was also found to be able to oxidize phenol to hydroquinone, was deleted, this mutant lost the oxidation ability. This ability was restored by introduction of the mimA gene of M. smegmatis strain mc2155 or of M. goodii strain 12523 into this mutant. Interestingly, we found that these gene clusters also play essential roles in propane and acetone metabolism in these mycobacteria.
On receiver structures for channels having memory

This paper is concerned with m -ary communication channels (m \geq 2) having intersymbol interference between L time periods (L \geq 2) . Receiver structures are developed for making jointly optimum (minimum probability of error) decisions about L consecutive symbols on the basis of the complete message received. The decision statistics are computed by a sequential procedure, and the number of computations increases only linearly with the message length. The method can be applied to the general problem of making decisions about the states of a discrete-state Markov information source which is observable only through a channel with additive Gaussian or non-Gaussian noise.
Antimicrobial resistance among lower respiratory tract isolates of Streptococcus pneumoniae: results of a 1992–93 Western Europe and USA collaborative surveillance study

: One thousand, eight hundred and fifty-six Streptococcus pneumoniae strains, collected in 1992 and 1993 from 15 centres in Western Europe and USA were tested for susceptibility to 16 antibiotics. The overall resistance to penicillin was 23% (range 6-54%), with the highest prevalences in Madrid, Barcelona, Toulouse and Cleveland. Seven centres reported low-level penicillin resistance only. Amoxycillin was more active than ceftriaxone against strains with intermediate resistance to penicillin, and at least four-fold more active than cefuroxime; cefaclor and cefixime had poor activity. Against penicillin-resistant strains, ceftriaxone was slightly more active than amoxycillin, cefuroxime exhibited borderline activity and cefixime and cefaclor were inactive. Ten strains fully susceptible to penicillin had MICs of ceftriaxone > or = 0.1 mg/L; this may represent a first step towards the development of cephalosporin resistance. With the exception of fluoroquinolones, resistance to non-beta-lactam antibiotics (chloramphenicol, doxycycline, co-trimoxazole, erythromycin, clarithromycin and azithromycin) was considerably higher in penicillin-resistant strains compared with penicillin-susceptible isolates. Erythromycin-resistant isolates were also resistant to the other macrolides tested.
Autoinduction Specificities of the Lantibiotics Subtilin and Nisin

ABSTRACT The biosynthesis of the lantibiotics subtilin and nisin is regulated by autoinduction via two-component systems. Although subtilin is structurally closely related to nisin and contains the same lanthionine ring structure, both lantibiotics specifically autoinduce their biosynthesis. Subtilin and also the subtilin-like lantibiotics entianin and ericin autoinduce the two-component system SpaRK of Bacillus subtilis, whereas the biosynthesis of nisin is autoinduced via the two-component system NisRK of Lactococcus lactis. Autoinduction is highly specific for the respective lantibiotic and therefore of major importance for the functional expression of genetically engineered subtilin-like lantibiotics. To identify the structural features required for subtilin autoinduction, subtilin-nisin hybrids and specific point mutations of amino acid position 1 were generated. For subtilin autoinduction, the N-terminal tryptophan is the most important for full SpaK activation. The failure of subtilin to autoinduce the histidine kinase NisK mainly depends on the N-terminal tryptophan, as its single exchange to the aliphatic amino acid residues isoleucine, leucine, and valine provided NisK autoinduction. In addition, the production of subtilin variants which did not autoinduce their own biosynthesis could be rescued upon heterologous coexpression in B. subtilis DSM15029 by the autoinducing subtilin-like lantibiotic entianin.