CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting

BACKGROUND: All known genomes code for a large number of transcription factors. It is important to develop methods that will reveal how these transcription factors act on a genome wide level, that is, through what target genes they exert their function. RESULTS: We describe here a program pipeline aimed at identifying transcription factor target genes in whole genomes. Starting from a consensus binding site, represented as a weight matrix, potential sites in a pre-filtered genome are identified and then further filtered by assessing conservation of the putative site in the genome of a related species, a process called phylogenetic footprinting. CisOrtho has been successfully used to identify targets for two homeodomain transcription factors in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. CONCLUSIONS: CisOrtho will identify targets of other nematode transcription factors whose DNA binding specificity is known and can be easily adapted to search other genomes for transcription factor targets

Lawson criterion for ignition exceeded in an inertial fusion experiment

For more than half a century, researchers around the world have been engaged in attempts to achieve fusion ignition as a proof of principle of various fusion concepts. Following the Lawson criterion, an ignited plasma is one where the fusion heating power is high enough to overcome all the physical processes that cool the fusion plasma, creating a positive thermodynamic feedback loop with rapidly increasing temperature. In inertially confined fusion, ignition is a state where the fusion plasma can begin "burn propagation" into surrounding cold fuel, enabling the possibility of high energy gain. While "scientific breakeven" (i.e., unity target gain) has not yet been achieved (here target gain is 0.72, 1.37 MJ of fusion for 1.92 MJ of laser energy), this Letter reports the first controlled fusion experiment, using laser indirect drive, on the National Ignition Facility to produce capsule gain (here 5.8) and reach ignition by nine different formulations of the Lawson criterion

Outcomes from elective colorectal cancer surgery during the SARS-CoV-2 pandemic

This study aimed to describe the change in surgical practice and the impact of SARS-CoV-2 on mortality after surgical resection of colorectal cancer during the initial phases of the SARS-CoV-2 pandemic

Predicting transmembrane beta-barrels in proteomes

Very few methods address the problem of predicting beta-barrel membrane proteins directly from sequence. One reason is that only very few high-resolution structures for transmembrane beta-barrel (TMB) proteins have been determined thus far. Here we introduced the design, statistics and results of a novel profile-based hidden Markov model for the prediction and discrimination of TMBs. The method carefully attempts to avoid over-fitting the sparse experimental data. While our model training and scoring procedures were very similar to a recently published work, the architecture and structure-based labelling were significantly different. In particular, we introduced a new definition of beta- hairpin motifs, explicit state modelling of transmembrane strands, and a log-odds whole-protein discrimination score. The resulting method reached an overall four-state (up-, down-strand, periplasmic-, outer-loop) accuracy as high as 86%. Furthermore, accurately discriminated TMB from non-TMB proteins (45% coverage at 100% accuracy). This high precision enabled the application to 72 entirely sequenced Gram-negative bacteria. We found over 164 previously uncharacterized TMB proteins at high confidence. Database searches did not implicate any of these proteins with membranes. We challenge that the vast majority of our 164 predictions will eventually be verified experimentally. All proteome predictions and the PROFtmb prediction method are available at http://www.rostlab.org/services/PROFtmb/

Handlingsrommet - hvilket rom er det? Et studie av mellomlederes handlingsrom i NAV

Organisasjoner tar i bruk styring og ledelse for å koordinere organisert atferd. Forholdet mellom styring og ledelse vil variere og ut i fra teorien vil de enten kunne erstatte hverandre, konkurrere eller betinge hverandre. Forholdet mellom styring og ledelse forventes å påvirke handlingsrommet. Handlingsrommet er mulighet for å gjøre valg i rommet mellom begrensninger (lover, avtaleverk, økonomi o.l.) og krav (forventninger fra omgivelsene og en selv, standarder, mål, tidsfrister o.l.). Studiet er gjennomført som et casestudie ved bruk av kvalitativ analyse. Undersøkelsen har vært gjennomført gjennom dybdeintervjuer av mellomledere, syv NAV-ledere i Sør-Troms. Funnene fra studiet viser at mellomlederne forstår styring og ledelse, og forskjellen på disse likt. Forståelse av og opplevd handlingsrom defineres imidlertid svært ulikt. Det eksisterer ikke en felles definisjon av hva handlingsrommet er i NAV. Funnene dokumenterer ikke at det har blitt mindre styring og mer ledelse i NAV. En forklaring på dette kan være at styring og ledelse betinger (er gjensidig avhengig av) hverandre i NAV. Nye styringssystemer, gjennom resultatkrav kan kreve mer ledelse samtidig som summen av styring oppleves uforandret. Informantene formidler også at deres handlingsrom er uforandret. Teorien opererer med et formelt og subjektivt handlingsrom, hvor det subjektive gir mellomledere mulighet til fortolkning av sin rolle og de krav som stilles til dem. Funnene viser at de av mellomlederne som opplever å ha et stort handlingsrom er de som aktivt bruker det subjektive handlingsrommet