Miracle-dz/UniFAR-FTUs huggingface dataset:
F-type Pyocins are Diverse Non-Contractile Phage Tail-Like Weapons for Killing Pseudomonas aeruginosa

Most Pseudomonas aeruginosa strains produce bacteriocins derived from contractile or non-contractile phage tails known as R-type and F-type pyocins, respectively. These bacteriocins possess strain-specific bactericidal activity against P. aeruginosa and likely increase evolutionary fitness through intraspecies competition. R-type pyocins have been studied extensively and show promise as alternatives to antibiotics. Although they have similar therapeutic potential, experimental studies on F-type pyocins are limited. Here, we provide a bioinformatic and experimental investigation of F-type pyocins. We introduce a systematic naming scheme for genes found in R- and F-type pyocin operons and identify 15 genes invariably found in strains producing F-type pyocins. Five proteins encoded at the 3’-end of the F-type pyocin cluster are divergent in sequence, and likely determine bactericidal specificity. We use sequence similarities among these proteins to define 11 distinct F-type pyocin groups, five of which had not been previously described. The five genes encoding the variable proteins associate in two modules that have clearly re-assorted independently during the evolution of these operons. These proteins are considerably more diverse than the specificity-determining tail fibers of R-type pyocins, suggesting that F-type pyocins emerged earlier or have been subject to distinct evolutionary pressures. Experimental studies on six F-type pyocin groups show that each displays a distinct spectrum of bactericidal activity. This activity is strongly influenced by the lipopolysaccharide O-antigen type, but other factors also play a role. F-type pyocins appear to kill as efficiently as R-type pyocins. These studies set the stage for the development of F-type pyocins as anti-bacterial therapeutics. IMPORTANCE Pseudomonas aeruginosa is an opportunistic pathogen that causes a broad spectrum of antibiotic resistant infections with high mortality rates, particularly in immunocompromised individuals and cystic fibrosis patients. Due to the increasing frequency of multidrug-resistant P. aeruginosa infections, there is great interest in the development of alternative therapeutics. One alternative is protein-based antimicrobials called bacteriocins, which are produced by one strain of bacteria to kill other strains. In this study, we investigate F-type pyocins, bacteriocins naturally produced by P. aeruginosa that resemble non-contractile phage tails. We show that they are potent killers of P. aeruginosa, and distinct pyocin groups display different killing specificities. We have identified the probable specificity determinants of F-type pyocins, which opens up the potential to engineer them to precisely target strains of pathogenic bacteria. The resemblance of F-type pyocins to well characterized phage tails will greatly facilitate their development into effective antibacterials.
The Efficacy of Influenza Vaccination in Elderly Individuals: A Randomized Double-blind Placebo-Controlled Trial

Objective. —To determine the efficacy of influenza vaccination in elderly people. Design. —Randomized double-blind placebo-controlled trial. Setting. —Fifteen family practices in the Netherlands during influenza season 1991-1992. Participants. —A total of 1838 subjects aged 60 years or older, not known as belonging to those high-risk groups in which vaccination was previously given. Intervention. —Purified split-virion vaccine containing A/Singapore/6/86(H1N1), A/Beijing/353/89(H3N2), B/Beijing/1/87, and B/Panama/45/90 (n=927) or intramuscular placebo containing physiological saline solution (n=911). Main Outcome Measures. —Patients presenting with influenzalike illness up to 5 months after vaccination; self-reported influenza in postal questionnaires 10 weeks and 5 months after vaccination; serological influenza (fourfold increase of antibody titer between 3 weeks and 5 months after vaccination). Results. —The incidence of serological influenza was 4% in the vaccine group and 9% in the placebo group (relative risk [RR], 0.50; 95% confidence interval [CI], 0.35 to 0.61). The incidences of clinical influenza were 2% and 3%, respectively (RR, 0.53; 95% CI, 0.39 to 0.73). The effect was strongest for the combination of serological and clinical influenza (RR, 0.42; 95% CI, 0.23 to 0.74). The effect was less pronounced for self-reported influenza. Conclusion. —In the elderly, influenza vaccination may halve the incidence of serological and clinical influenza (in periods of antigenic drift). (JAMA. 1994;272:1661-1665)
Risk for Suicidal Ideation and Suicide Attempts Associated with Co-occurring Depression and Conduct Disorders in Early Adolescence

This study investigates the early manifestation of co-occurring depression and conduct disorders as a predictor of heightened risk for later suicidal ideation and behavior in a community sample of 521 adolescents. Self-reported symptoms of depression and conduct disorder were evaluated in early 6 th grade. Suicidal thoughts and behaviors were tracked through multiple assessments carried out over the middle school years. Compared to adolescents with depression symptoms only, conduct disorder symptoms only, or low psychopathology, those with co-occurring depression and conduct disorder symptoms had the highest risk for subsequent suicidal ideation, recurrent suicidal behaviors, and suicide attempts.
On representative and illustrative comparisons with real data in bioinformatics: response to the letter to the editor by Smith et al

Smith et al. (2013) recently published an interesting letter to the editors of Bioinformatics outlining the importance of validation of new proposed algorithms through a thorough comparison with existing approaches. We completely agree with the necessity of more comparison studies in general to help end users to make an informed choice based on objective criteria. We also agree that ‘The practical result [of the lack of comparison studies] is that practitioners stop short of exhaustively evaluating all the possible options and choose based on some other criteria (e.g. popularity, ease of use or familiarity)’, and that this may harm both algorithm developers and users—as also claimed in one of our previous publications on this topic (Boulesteix et al., 2013a). In a few words, we fully comply with the claim of the authors that everybody (users and algorithm makers) suffers from the trend observed in bioinformatics toward the publication of many new algorithms without proper comparison between these algorithms. We also agree with Smith et al. (2013) that articles suggesting new algorithms should always include a comparison with existing methods. Here we guess that the authors implicitly mean comparisons based on real datasets—as opposed to simulated data that are often investigated in other fields related to data analysis such as statistics. However, our opinion diverges when it comes to defining the goals of such comparison studies and their interpretation. Our major argument is that comparison studies conducted as a part of an article suggesting a new algorithm rarely reach the level of representativity and objectivity required to be used as guidance by other researchers when choosing their algorithm. The two underlying main ideas behind this claim are that (i) comparison studies comparing a new algorithm with existing algorithms are often severely biased for different reasons, as documented in our empirical study based on the example of supervised classification with high-dimensional data (Jelizarow et al., 2010); simply, when reading articles on new methods, most of us think ‘well, of course they say their method is better, but . ’; and (ii) as stressed by Smith et al. (2013), an extensive and fair comparison study requires a lot of work, care and attention in itself (Boulesteix et al., 2013a, b) and can hardly be conducted within a study focused on another problem—the development of a new algorithm. To specify our point of view, we suggest a taxonomy of comparison studies based on real datasets while referring to the ideas presented by Smith et al. (2013).
Using Mobile Positioning Data to Model Locations Meaningful to Users of Mobile Phones

The article introduces a model for the location of meaningful places for mobile telephone users, such as home and work anchor points, using passive mobile positioning data. Passive mobile positioning data is secondary data concerning the location of call activities or handovers in network cells that is automatically stored in the memory of service providers. This data source offers good potential for the monitoring of the geography and mobility of the population, since mobile phones are widespread, and similar standardized data can be used around the globe. We developed the model and tested it with 12 months' data collected by EMT, Estonia's largest mobile service provider, covering more than 0.5 million anonymous respondents. Modeling results were compared with population register data; this revealed that the developed model described the geography of the population relatively well, and can hence be used in geographical and urban studies. This approach also has potential for the development of location-based services such as targeting services or geographical infrastructure.
Impact of the invasive alien species, LANTANA CAMARA (L). on native vegetation in Northern Gonarezhou National Park, Zimbabwe

This study assessed the impact of Lantana camara invasion on native vegetation in Northern Gonarezhou National Park (GNP), Zimbabwe. Stratified random sampling was used with three categories; uninvaded, moderately invaded and heavily invaded. The distribution of L. camara in Northern Gonarezhou National Park was mapped using GIS. Soil properties and vegetation attributes were assessed in each category. L. camara was mainly distributed within the riparian vegetation and in the low-lying areas of Northern GNP. A total of 41 native woody species and 2AE’Â§ native herbaceous species were identified in the study area. Significant differences (ANOVA, P<0.05) in soil nitrogen, phosphorus, potassium and moisture among the three categories were noted. Soil nitrogen and phosphorus levels were highest in the heavily invaded category and lowest in the uninvaded category. Soil potassium and moisture levels were highest in the uninvaded category and lowest in the heavily invaded. For native vegetation attributes; basal area, canopy cover, herbaceous cover, woody plant density, species diversity (HÂiÂ¦) and species richness (S) varied significantly (ANOVA, P<0.05) among the categories of L. camara intensity. These variables were highest in the uninvaded category and lowest in the heavily invaded category. The uninvaded category was the most diverse (HÂiÂ¦=1.875) while the heavily invaded category was the least diverse (HÂiÂ¦=1.334). Edaphic factors influenced plant species structure and composition in northern GNP. The significant differences in soil and vegetation variables suggest that L. camara is altering soil properties and native vegetation structure and composition in GNP to the detriment of wildlife management. Active management of L. camara in Gonarezhou National Park is therefore urgently required for wildlife and biodiversity conservation in the area.
The eclogite engine: Chemical geodynamics as a Galileo thermometer

Migrating and incipient ridges and triple junctions sample the heterogeneous mantle created by plate tectonics and crustal stoping. The result is a yo-yo vertical convection mode that fertilizes, cools, and removes heat from the mantle. This mode of mantle convection is similar to the operation of a Galileo thermometer (GT). The GT mode of small-scale convection, as applied to the mantle, differs from the Rayleigh-Taylor (RT) instability of a homogeneous fluid in a thermal boundary layer. It involves stoping of over-thickened continental crust and the differences in density and melting behavior of eclogites and peridotites in the mantle. The fates of subducted and delaminated crust, underplated basalt, and peridotite differ because of differences in scale, age, temperature, melting temperature, chemistry, thermal properties, and density. Cold subducted oceanic crust—as eclogite—although denser than ambient mantle at shallow depths, may become less dense or neutrally buoyant somewhere in the upper mantle and transition zone, and may be gravitationally trapped to form mafic eclogite-rich blobs or layers. Detached lower continental crust starts out warmer; it thermally and gravitationally equilibrates at shallower depths than do slabs of cold mature lithosphere. The density jumps at the depths of 400 and 650 km act as barriers. Trapped eclogite is heated by conduction from the surrounding mantle and its own radioactivity. It is displaced, entrained, and melted as it warms up to ambient mantle temperature. Both the foundering and the re-emergence of mafic and ultramafic blobs create midplate magmatism and uplift. Mantle upwellings and partially molten blobs need not be hotter than ambient mantle or from a deep thermal boundary layer. The fertile blobs drift slowly in the opposite direction to plate motions—the counterflow model—thereby maintaining age progressions and small relative motions between hotspots. Large-scale midplate volcanism is due to mantle fertility anomalies, such as large chunks of delaminated crust or subducted seamount chains, or to the release of accumulated underplate when the plate experiences flexure or pre-breakup extension. Eclogite can have lower shear velocities than volatile-free peridotite and will show up in seismic tomograms as low-velocity, or red, regions, even when cold and dense. This model removes the paradoxes associated with deep thermal RT instabilities, propagating cracks and small-scale thermal convection. It explains such observations as relative fixity of melting spots, even though the fertile blobs are shallow.
Incorporating Novel Ecosystems into Management Frameworks

This chapter provides a framework that helps managers, whether scientists or stewards, navigate the decisions that lead to new management approaches in hybrid and novel ecosystems. It first presents a decision‐making flowchart that can be used as roadmap to navigate possible management actions. The chapter then explores the role of ecological and social barriers in creation and maintenance of hybrid and novel ecosystems. It argues that working to understand the historical structure and conditions in ecosystem is useful for planning current management strategy. Finally, the chapter highlights examples of challenging decision points which managers will likely face as they work to incorporate hybrid and novel ecosystems into strategies for restoration, conservation and management.
A comparison of 40 years of SBUV measurements of column ozone with data from the Dobson/Brewer network

Total column ozone data from the Nimbus‐4 Backscatter UltraViolet (BUV) instrument, Nimbus‐7 Solar Backscatter Ultraviolet (SBUV) instrument, as well as from seven NOAA SBUV/2 instruments have been newly reprocessed with the Version 8.6 ozone retrieval algorithm. This yields a coherent data set that, unlike the Total Ozone Mapping Spectrometer ozone record, has no data gaps or significant time periods with large uncertainties due to calibration issues from 1979 to the present. The column ozone data from the first 3 years of the BUV record (1970–1972) is of high quality and can be used to extend the satellite ozone record back over 40 years. With the new algorithm, an improved total column ozone value is calculated by summing up the profile information as opposed to a single direct column measurement, and the algorithm is optimized for the detection of long‐term trends. The results from this processing of these data have been systematically compared to total ozone data from Brewer and Dobson spectrophotometers for many individual ground stations as a function of time, satellite solar zenith angle, and latitude. The time series comparisons show an agreement within ± 1% over the past 40 years with the bias approaching zero over the last decade. The aerosols associated with the eruption of Mt Pinatubo in 1991 produced an underestimation of ozone for our retrievals at high slant columns while the near‐nadir values were relatively unaffected. There is very little systematic offset between the satellite and ground‐based measurements as a function of latitude with the Nimbus‐4 BUV data (1970–1976) showing the largest offsets. The comparisons as a function of satellite solar zenith angle show consistent behavior for all instruments. Comparisons with ozonesonde data show good agreement in the integrated column up to 25 hPa with differences of no more than 5%.
Single-cell Ca 2+ parameter inference reveals how transcriptional states inform dynamic cell fates

Inferring the parameters of dynamic models is a cornerstone of systems biology. Large single-cell transcriptomic datasets have opened up many possibilities for new analyses, but their potential to inform parameter inference of molecular or cellular dynamics has not yet been realized. Here, making use of coupled data: single-cell gene expression and dynamic molecular measurements, we develop new methods for parameter inference. We construct cell chains in which the posterior distribution of a cell is used to inform the prior of the subsequent cell in the chain. In application to the Ca 2+ signaling pathway, we show that cell predecessor-informed priors accelerate inference of the Ca 2+ model parameters in single cells. Though use of cell chains informed by single-cell gene expression does not improve sampling relative to random chain assignment, we show that the posteriors produced via gene expression-informed cell chains capture distinct properties of the dynamic Ca 2+ response. By clustering posterior parameters we can identify markers genes that correspond with variable Ca 2+ responses. Additionally, through analysis of the posterior distributions of hundreds of single cells, we discover that divergent co-variation of parameters within and between cells, highlighting the complex and competing sources of cell heterogeneity. Through the analysis of large populations of posterior distributions we are able to quantify the relationships between single-cell transcriptional states and dynamic cellular responses, paving the way for more detailed mappings between gene expression states and dynamic cell fates.
Genome-scale Analysis of Metazoan Replication Origins Reveals Their Organization in Specific but Flexible Sites Defined by Conserved Features

In metazoans, thousands of DNA replication origins (Oris) are activated to replicate DNA at each cell cycle. Although their timing of activation is better understood, their genomic organization and their genetic nature remain elusive. Here, we identified Oris by nascent strand (NS) purification and characterized their common features by performing a genome-wide analysis in both Drosophila and mouse cell lines. We show that in both species most CpG islands (CGI) contain Oris, although methylation is nearly absent in Drosophila, indicating that this epigenetic mark is not crucial for defining the initiation event. Initiation of DNA synthesis starts at the borders of CGIs, resulting in a striking bimodal distribution of NS, suggestive of a dual initiation event. We also found that Oris contain a unique nucleotide skew around NS peaks, characterized by G/T and C/A over-representation at the 5' and 3' of Ori sites, respectively. Repeated GC-rich elements were detected, which are good predictors of Oris, suggesting that common sequence features are part of metazoan Oris. In the heterochromatic chromosome 4 of Drosophila, Oris are strongly correlated with HP1 binding sites. At the chromosome level, regions rich in Oris are early replicating, whereas Ori-poor regions co-localize with late replicating domains during the cell cycle. The genome-wide analysis was coupled with a DNA combing analysis to unravel the organization of replication origins. The results indicate that Oris are present in a large excess, but their activation does not occur at random. They are organized in groups of site-specific but flexible origins that define replicons, where a single origin is activated in each replicon. This organization provides both site specificity and Ori firing flexibility in each replicon, allowing possible adaptation of DNA replication to environmental cues and cell fates. INTRODUCTION In metazoans, DNA replication is initiated at thousands of chromosomal sites during each S phase. These DNA replication origins (Oris) should be activated only once at each cell cycle to avoid any amplification and maintain genome integrity. This is an important task in human or mouse cells, where 30 000 replication Oris are activated at each cell division. In prokaryotes as well as in bacterial and animal viruses, Oris are sequence-specific. In Saccharomyces cerevisiae, Oris are identified by specific DNA elements, called Autonomous Replication Sequences (ARS), which have a common AT-rich 11 bp ARS Consensus Sequence (ACS). However, sequence-specificity identifies potential Oris, but does not determine their selection. Indeed, of the 12,000 ACS …
Trends in alcohol-related traffic risk behaviors among college students.

BACKGROUND Alcohol-impaired driving is a major public health problem. National studies indicate that about 25% of college students have driven while intoxicated in the past month and an even greater percentage drive after drinking any alcohol and/or ride with an intoxicated driver. The purpose of this investigation was to examine the change in these various alcohol-related traffic risk behaviors as students progressed through their college experience. METHODS A cohort of 1,253 first-time first-year students attending a large, mid-Atlantic university were interviewed annually for 4 years. Repeated measures analyses were performed using generalized estimating equations to evaluate age-related changes in prevalence and frequency of each behavior (i.e., ages 19 to 22). RESULTS At age 19, 17%(wt) of students drove while intoxicated, 42%(wt) drove after drinking any alcohol, and 38%(wt) rode with an intoxicated driver. For all 3 driving behaviors, prevalence and frequency increased significantly at age 21. Males were more likely to engage in these behaviors than females. To understand the possible relationship of these behaviors to changes in drinking patterns, a post hoc analysis was conducted and revealed that while drinking frequency increased every year, frequency of drunkenness was stable for females, but increased for males. CONCLUSIONS Alcohol-related traffic risk behaviors are quite common among college students and take a significant upturn when students reach the age of 21. Prevention strategies targeted to the college population are needed to prevent serious consequences of these alcohol-related traffic risk behaviors.