Finite temperature phase diagram of a polarized Fermi gas in an optical lattice

We present phase diagrams for a polarized Fermi gas in an optical lattice as a function of temperature, polarization, and lattice filling factor. We consider the Fulde-Ferrel-Larkin-Ovchinnikov (FFLO), Sarma or breached pair (BP), and BCS phases, and the normal state and phase separation. We show that the FFLO phase appears in a considerable portion of the phase diagram. The diagrams have two critical points of different nature. We show how various phases leave clear signatures to momentum distributions of the atoms which can be observed after time of flight expansion.Comment: Journal versio

Noise correlations of the ultra-cold Fermi gas in an optical lattice

In this paper we study the density noise correlations of the two component Fermi gas in optical lattices. Three different type of phases, the BCS-state (Bardeen, Cooper, and Schieffer), the FFLO-state (Fulde, Ferrel, Larkin, and Ovchinnikov), and BP (breach pair) state, are considered. We show how these states differ in their noise correlations. The noise correlations are calculated not only at zero temperature, but also at non-zero temperatures paying particular attention to how much the finite temperature effects might complicate the detection of different phases. Since one-dimensional systems have been shown to be very promising candidates to observe FFLO states, we apply our results also to the computation of correlation signals in a one-dimensional lattice. We find that the density noise correlations reveal important information about the structure of the underlying order parameter as well as about the quasiparticle dispersions.Comment: 25 pages, 11 figures. Some figures are updated and text has been modifie

3D reflection seismic investigation for mine planning and exploration in the Kevitsa Ni-Cu-PGE deposit, Northern Finland

A 3D reflection seismic survey was conducted over an area of about 9 km2 at the Kevitsa Ni-Cu-PGE (platinum group elements) deposit, Northern Finland. The principal objective of the survey was to image major fault and fracture zones at depth. Understanding the geometry of these zones is important for designing a steep open-pit for mining. Initial processing results suggest that the 3D seismic survey has been successful in imaging both gently dipping and steeply dipping reflections as shallow as 50 ms (or about 150 m), many of which correlate with fault systems and lithological contacts observed at the surface. Several new target areas can be identified in the seismic data that require further investigations for their mineralization potential

Universal platform for quantitative analysis of DNA transposition

<p>Abstract</p> <p>Background</p> <p>Completed genome projects have revealed an astonishing diversity of transposable genetic elements, implying the existence of novel element families yet to be discovered from diverse life forms. Concurrently, several better understood transposon systems have been exploited as efficient tools in molecular biology and genomics applications. Characterization of new mobile elements and improvement of the existing transposition technology platforms warrant easy-to-use assays for the quantitative analysis of DNA transposition.</p> <p>Results</p> <p>Here we developed a universal <it>in vivo </it>platform for the analysis of transposition frequency with class II mobile elements, i.e., DNA transposons. For each particular transposon system, cloning of the transposon ends and the cognate transposase gene, in three consecutive steps, generates a multifunctional plasmid, which drives inducible expression of the transposase gene and includes a mobilisable <it>lacZ</it>-containing reporter transposon. The assay scores transposition events as blue microcolonies, papillae, growing within otherwise whitish <it>Escherichia coli </it>colonies on indicator plates. We developed the assay using phage Mu transposition as a test model and validated the platform using various MuA transposase mutants. For further validation and to illustrate universality, we introduced IS<it>903 </it>transposition system components into the assay. The developed assay is adjustable to a desired level of initial transposition via the control of a plasmid-borne <it>E. coli </it>arabinose promoter. In practice, the transposition frequency is modulated by varying the concentration of arabinose or glucose in the growth medium. We show that variable levels of transpositional activity can be analysed, thus enabling straightforward screens for hyper- or hypoactive transposase mutants, regardless of the original wild-type activity level.</p> <p>Conclusions</p> <p>The established universal papillation assay platform should be widely applicable to a variety of mobile elements. It can be used for mechanistic studies to dissect transposition and provides a means to screen or scrutinise transposase mutants and genes encoding host factors. In succession, improved versions of transposition systems should yield better tools for molecular biology and offer versatile genome modification vehicles for many types of studies, including gene therapy and stem cell research.</p

TAFFEL: Independent Enrichment Analysis of gene sets

<p>Abstract</p> <p>Background</p> <p>A major challenge in genomic research is identifying significant biological processes and generating new hypotheses from large gene sets. Gene sets often consist of multiple separate biological pathways, controlled by distinct regulatory mechanisms. Many of these pathways and the associated regulatory mechanisms might be obscured by a large number of other significant processes and thus not identified as significant by standard gene set enrichment analysis tools.</p> <p>Results</p> <p>We present a novel method called Independent Enrichment Analysis (IEA) and software TAFFEL that eases the task by clustering genes to subgroups using Gene Ontology categories and transcription regulators. IEA indicates transcriptional regulators putatively controlling biological functions in studied condition.</p> <p>Conclusions</p> <p>We demonstrate that the developed method and TAFFEL tool give new insight to the analysis of differentially expressed genes and can generate novel hypotheses. Our comparison to other popular methods showed that the IEA method implemented in TAFFEL can find important biological phenomena, which are not reported by other methods.</p

Kelan järjestämä kuntoutus vuonna 1987 syntyneille

Tutkimuksessa tarkasteltiin vuonna 1987 Suomessa syntyneiden henkilöiden Kelan järjestämän kuntoutuksen käyttöä. Aineistona oli Kelan kuntoutusratkaisu- ja kuntoutuskustannustiedot Kansallinen syntymäkohortti 1987 -rekisteriaineistoon kuuluville henkilöille vuosilta 1987–2012. Kaikkiaan 6,2 % kohortin henkilöistä oli 25 ikävuoteen mennessä saanut myönteisen ratkaisun jollekin Kelan myöntämälle kuntoutustoimenpiteelle. Eri lakiperustein myönnettyjä kuntoutusratkaisuja tutkittiin omina kokonaisuuksinaan kuntoutustoimenpiteiden, pääsairausdiagnoosien ja kuntoutuksen kustannusten osalta. Myönteisen ratkaisun vaikeavammaisen lääkinnälliselle kuntoutukselle saaneiden henkilöiden määrät olivat pieniä (1,3 % syntymäkohortista) mutta kuntoutustoimenpiteitä eri terapiamuodoissa oli näillä henkilöillä runsaasti, ja myös kuntoutuksen henkilöä kohden lasketut kustannukset olivat korkeimmat. Yleisimmät diagnoosiryhmät olivat älyllinen kehitysvammaisuus ja CP-oireyhtymä. Ammatillista kuntoutusta oli myönnetty 2,3 %:lle kohortista, ja merkittävimmät kuntoutusmuodot henkilömäärittäin olivat ammattikoulutus ja kuntoutustutkimus. Ammatillisen kuntoutuksen kustannuksissa havaittiin selkeää nousua vuoden 2007 jälkeen. Merkittävimmät pääsairausdiagnoosit olivat masennustila ja lievä älyllinen kehitysvammaisuus. Myönteisen kuntoutuspäätöksen oli harkinnanvaraisen kuntoutuksen lakiperusteella saanut 3,2 % kohortista, ja näistä kuntoutustoimenpiteistä yli puolet oli ennen vuoden 2011 alkua myönnettyä kuntoutuspsykoterapiaa. Tämän lisäksi kuntoutus- ja sopeutumisvalmennuskurssit olivat myös merkittävä kuntoutustoimenpide. Masennustila sekä ahdistuneisuushäiriöt olivat merkittävimmät diagnoosiryhmät – myös niillä, joilla kuntoutusmuoto oli jokin muu kuin psykoterapia. Kuntoutuspsykoterapiaa omalla lakiperusteellaan oli saanut 1,3 % henkilöistä, ja psykoterapia olikin fysioterapian jälkeen määrällisesti merkittävin terapiamuoto. Alustavassa alueellisessa tarkastelussa havaittiin huomattavia eroja kuntoutustoimenpiteiden käytössä eri alueilla

Remission of hypertension after treatment of giant simple renal cyst: a case report

Renal cysts are common in old patients, and usually remain untreated. Giant renal cysts measuring more than 15 cm in greatest diameter are uncommon and the association with hypertension is very rare. We present a case of a 25-year-old woman with a giant right renal cyst associated with hypertension that was treated by laparoscopic excision, followed by resolution hypertension

FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data

<p>Abstract</p> <p>Background</p> <p>Genomics research produces vast amounts of experimental data that needs to be integrated in order to understand, model, and interpret the underlying biological phenomena. Interpreting these large and complex data sets is challenging and different visualization methods are needed to help produce knowledge from the data.</p> <p>Results</p> <p>To help researchers to visualize and interpret integrated genomics data, we present a novel visualization method and bioinformatics software tool called FORG3D that is based on real-time three-dimensional force-directed graphs. FORG3D can be used to visualize integrated networks of genome scale data such as interactions between genes or gene products, signaling transduction, metabolic pathways, functional interactions and evolutionary relationships. Furthermore, we demonstrate its utility by exploring gene network relationships using integrated data sets from a <it>Caenorhabditis elegans </it>Parkinson's disease model.</p> <p>Conclusion</p> <p>We have created an open source software tool called FORG3D that can be used for visualizing and exploring integrated genome scale data.</p

Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues

Our knowledge on tissue- and disease-specific functions of human genes is rather limited and highly context-specific. Here, we have developed a method for the comparison of mRNA expression levels of most human genes across 9,783 Affymetrix gene expression array experiments representing 43 normal human tissue types, 68 cancer types, and 64 other diseases. This database of gene expression patterns in normal human tissues and pathological conditions covers 113 million datapoints and is available from the GeneSapiens website

GRINL1A Complex Transcription Unit Containing GCOM1, MYZAP, and POLR2M Genes Associates with Fully Penetrant Recessive Dilated Cardiomyopathy

Background: Familial dilated cardiomyopathy (DCM) is a monogenic disorder typically inherited in an autosomal dominant pattern. We have identified two Finnish families with familial cardiomyopathy that is not explained by a variant in any previously known cardiomyopathy gene. We describe the cardiac phenotype related to homozygous truncating GCOM1 variants.Methods and Results: This study included two probands and their relatives. All the participants are of Finnish ethnicity. Whole-exome sequencing was used to test the probands; bi-directional Sanger sequencing was used to identify the GCOM1 variants in probands' family members. Clinical evaluation was performed, medical records and death certificates were obtained. Immunohistochemical analysis of myocardial samples was conducted. A homozygous GCOM1 variant was identified altogether in six individuals, all considered to be affected. None of the nine heterozygous family members fulfilled any cardiomyopathy criteria. Heart failure was the leading clinical feature, and the patients may have had a tendency for atrial arrhythmias.Conclusions: This study demonstrates the significance of GCOM1 variants as a cause of human cardiomyopathy and highlights the importance of searching for new candidate genes when targeted gene panels do not yield a positive outcome.Peer reviewe