Molekularna identifikacija netuberkuloznih mikobakterija primjenom genotype Mycobacterium CM/AS testa

The study aims to determine the frequency and diversity of clinical isolates of nontuberculous mycobacteria (NTM). Of the 306 samples, the presence of NTM was confirmed in 65 (21.20%). The most frequently isolated species were M. fortuitum (30.3%), M. gordonae (24.2%), M. chelonae (15.2%), M. xenopi (7.6%), M. kansasii (4.5%), M. avium ssp. (3%), M. celatum (3%), M. mucogenicum (1.5%), M. peregrinum (1.5%), M. goodii (1.5%) and Mycobacterium sp. (7.6%). The determination of the local spectrum NTM is important because of the significant geographical variation. Although molecular testing is relatively expensive, they provide a rapid and accurate identification of different types of NTM.Istraživanje ima za cilj utvrditi učestalost i raznolikost kliničkih izolata netuberkuloznih mikobakterija (NTM). Od 306 uzoraka primjenom molekularnog testa prisustvo NTM je potvrđeno kod 65 (21,20%). Najčešće izolovane vrste su M. fortuitum (30,3%), M. gordonae (24,2%), M. chelonae (15,2%), M. xenopi (7,6%), M. kansasii (4,5%), M. avium ssp. (3%), M. celatum (3%), M. mucogenicum (1,5%), M. peregrinum (1,5%), M. goodii (1,5%) i Mycobacterium sp. (7,6%). Utvrđivanje lokalnog spektra NTM važno je zbog značajnih geografskih varijacija izolovanih vrsta. Iako su molekularna ispitivanja relativno skupa, ona imaju prednost što osiguravaju brzu i tačnu identifikaciju različitih vrsta NTM

Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children's Oncology Group.

BackgroundNew prognostic markers are needed to identify patients with Ewing sarcoma (EWS) and osteosarcoma unlikely to benefit from standard therapy. We describe the incidence and association with outcome of circulating tumour DNA (ctDNA) using next-generation sequencing (NGS) assays.MethodsA NGS hybrid capture assay and an ultra-low-pass whole-genome sequencing assay were used to detect ctDNA in banked plasma from patients with EWS and osteosarcoma, respectively. Patients were coded as positive or negative for ctDNA and tested for association with clinical features and outcome.ResultsThe analytic cohort included 94 patients with EWS (82% from initial diagnosis) and 72 patients with primary localised osteosarcoma (100% from initial diagnosis). ctDNA was detectable in 53% and 57% of newly diagnosed patients with EWS and osteosarcoma, respectively. Among patients with newly diagnosed localised EWS, detectable ctDNA was associated with inferior 3-year event-free survival (48.6% vs. 82.1%; p = 0.006) and overall survival (79.8% vs. 92.6%; p = 0.01). In both EWS and osteosarcoma, risk of event and death increased with ctDNA levels.ConclusionsNGS assays agnostic of primary tumour sequencing results detect ctDNA in half of the plasma samples from patients with newly diagnosed EWS and osteosarcoma. Detectable ctDNA is associated with inferior outcomes

LEAN concept – possibilities of implementation and improvement of business processes in public healthcare organizations

Uvod: Osnovni je postulat lean koncepta da se veća efikasnost procesa rada može postići kroz proces kontinuiranog poboljšanja. To znači eliminiranje otpada i maksimiziranje aktivnosti koje dodaju vrijednost. Zdravstveni sustavi u Nizozemskoj, Velikoj Britaniji, Italiji i Sjedinjenim Američkim Državama implementirali su lean koncept. Cilj rada: Ispitati mišljenje zdravstvenih radnika javne bolnice na području Sarajeva o mogućnostima unaprjeđenja poslovnih procesa implementacijom lean koncepta. Metoda: Istraživanje je provedeno kao presječna studija u javnoj bolnici na području Sarajeva. Upitnik je poslane-poštom zdravstvenim radnicima. Obuhvaćen je 91 ispitanik oba spola (doktori medicine, specijalizanti, diplomirane medicinske sestre, medicinske sestre i administrativno osoblje). Rezultati: Utvrđena je pozitivna korelacija stavova o efektivnosti i efikasnosti poslovnih procesa. Prema mišljenju ispitanika, veća efektivnost poslovnih procesa pridonosi većoj efikasnosti (r = 0,846; p < 0,05). Spearmanov koeficijent rs = 0,81 pokazuje jaku povezanost efektivnosti i efikasnosti poslovnih procesa. Zaključak: Istraživanje je pokazalo da postoji pozitivan stav o utjecaju lean koncepta na poboljšanje učinkovitosti poslovnih procesa. Očekivani pozitivni učinciimplementacije lean koncepta manifestiraju se kroz: brže pružanje usluge pacijentima, smanjivanje vremena čekanja usluge i generalno poboljšanje poslovnih procesa.Introduction: The basic postulate of the lean concept is that greater efficiency of the work process can be achieved through a process of continuous improvement, which aims to eliminate waste and maximize activities that add value.The Netherlands, Great Britain, Italy and the United States were examples of healthcare systems that implemented the lean concept. Aim: To examine the opinion of health workers of a public hospitals in the Sarajevo area about the possibilities of improving business processes by implementing the lean concept. Method: The cross-sectional study was conducted using a questionnaire. The questionnaire was sent to the e-mail addresses of health workers of public health organizations. 91 respondents of both sexes (doctors of medicine, residents, registered nurses, nurses and administrative staff) were included. Results: A positive correlation was establishedin the attitude toward the effectiveness and efficiency of business processes. According to the participant’s opinion, the greater effectiveness of business processes contributes to greater efficiency (r=0.846; p<0,05). Spearman’s coefficient rs=0.81 shows a strong connection between the effectiveness and efficiency of business processes. Conclusion: The study showed that there is a positive attitude towards the impact of the lean concept on improving the efficiency of business processes. The reducexpected positive effects of the implementation of the lean concept are manifested through faster provision of services to patients, reduction of service waiting times and general improvement of business processes

Försäljningseffekter av exponeringar i butik : ett experiment i två dagligvarubutiker

Med hjälp av denna studie ska det klargöras vilka effekter butiksaktivteter kan ha på försäljningen i butiker inom livsmedelsbranscher. Vi har utformat två olika exponeringar i två ICA nära butiker. Exponeringarna har baserats på AIDAS-modellen i stor utsträckning samtidigt som vi studerade relevant teori om marknadsföring i butik har vi utformat våra exponeringar. Vi har tittat närmre på hur sinnesmarknadsföring kan påverka vid dessa aktiviteter. Butiksaktiviteterna har varit en tyst och en högljud exponering av maträtten "Korv Stroganoff". Med hjälp av försäljningsrapporter har vi dragit slutsatser om vilken som gav mest ökning på just dessa varor som ingår i denna maträtt. I vår slutsats har vi kommit fram till att butiksaktiviteter höjer försäljningen procentuellt mer än vi hade förväntat oss. Det som också kan ha påverkat att försäljningen ökade mer vid provsmakningen var att vi uppmärksammades mer än vid den tysta exponeringen. Genom att man stod mitt i kundvarvet bredvid mjölkavdelningen var det inte många kunder som missade oss. På så sätt fångade vi kundens intresse som sedan ledde till en önskan hos kunden att äta "Korv Stroganoff" till middag. Procentuellt sett ökade försäljningen mer medans man bjöd på mat än vid den tysta exponeringen. Frågan som vi då ställer oss nu är "Vilken aktivitet ska man arbeta mer med?" och "Vilken kostnad kan vara rimlig att spendera på en sådan här aktivitet?". Vi stod i butikerna fem timmar vardera utan någon kostnad. Hur mycket pengar vill man som butikschef spendera för olika aktiviteter? Kan man ha någon som står och bjuder kunderna på provsmakning varje dag, en gång i veckan, en gång i månaden eller någon gång per år? Dessa frågor är viktiga att ställa sig innan man utformar sina aktiviteter som butikschef. Det är också viktigt att man utformar olika mål för aktiviteterna så man vet i förhand vad som förväntas kunna inbringas i pengar under dessa aktiviteter. Detta för att i förhand kunna räkna ut om aktiviteten man tänkt ha är lönsam eller inte

Complete Genome Sequence of Algoriphagus sp. PR1, Bacterial Prey of a Colony-Forming Choanoflagellate ▿

Bacteria are the primary food source of choanoflagellates, the closest known relatives of animals. Studying signaling interactions between the Gram-negative Bacteroidetes bacterium Algoriphagus sp. PR1 and its predator, the choanoflagellate Salpingoeca rosetta, provides a promising avenue for testing hypotheses regarding the involvement of bacteria in animal evolution. Here we announce the complete genome sequence of Algoriphagus sp. PR1 and initial findings from its annotation

Genome update of the dimorphic human pathogenic fungi causing Paracoccidioidomycosis

Paracoccidiodomycosis (PCM) is a clinically important fungal disease that can acquire serious systemic forms and is caused by the thermodimorphic fungal Paracoccidioides spp. PCM is a tropical disease that is endemic in Latin America, where up to ten million people are infected; 80% of reported cases occur in Brazil, followed by Colombia and Venezuela. To enable genomic studies and to better characterize the pathogenesis of this dimorphic fungus, two reference strains of P. brasiliensis (Pb03, Pb18) and one strain of P. lutzii (Pb01) were sequenced [1]. While the initial draft assemblies were accurate in large scale structure and had high overall base quality, the sequences had frequent small scale defects such as poor quality stretches, unknown bases (N's), and artifactual deletions or nucleotide duplications, all of which caused larger scale errors in predicted gene structures. Since assembly consensus errors can now be addressed using next generation sequencing (NGS) in combination with recent methods allowing systematic assembly improvement, we re-sequenced the three reference strains of Paracoccidioides spp. using Illumina technology. We utilized the high sequencing depth to re-evaluate and improve the original assemblies generated from Sanger sequence reads, and obtained more complete and accurate reference assemblies. The new assemblies led to improved transcript predictions for the vast majority of genes of these reference strains, and often substantially corrected gene structures. These include several genes that are central to virulence or expressed during the pathogenic yeast stage in Paracoccidioides and other fungi, such as HSP90, RYP1-3, BAD1, catalase B, alpha-1,3-glucan synthase and the beta glucan synthase target gene FKS1. The improvement and validation of these reference sequences will now allow more accurate genome-based analyses. To our knowledge, this is one of the first reports of a fully automated and quality-assessed upgrade of a genome assembly and annotation for a non-model fungus. © 2014 Muñoz et al

Genome update of the dimorphic human pathogenic fungi causing Paracoccidioidomycosis

Paracoccidiodomycosis (PCM) is a clinically important fungal disease that can acquire serious systemic forms and is caused by the thermodimorphic fungal Paracoccidioides spp. PCM is a tropical disease that is endemic in Latin America, where up to ten million people are infected; 80% of reported cases occur in Brazil, followed by Colombia and Venezuela. To enable genomic studies and to better characterize the pathogenesis of this dimorphic fungus, two reference strains of P. brasiliensis (Pb03, Pb18) and one strain of P. lutzii (Pb01) were sequenced [1]. While the initial draft assemblies were accurate in large scale structure and had high overall base quality, the sequences had frequent small scale defects such as poor quality stretches, unknown bases (N's), and artifactual deletions or nucleotide duplications, all of which caused larger scale errors in predicted gene structures. Since assembly consensus errors can now be addressed using next generation sequencing (NGS) in combination with recent methods allowing systematic assembly improvement, we re-sequenced the three reference strains of Paracoccidioides spp. using Illumina technology. We utilized the high sequencing depth to re-evaluate and improve the original assemblies generated from Sanger sequence reads, and obtained more complete and accurate reference assemblies. The new assemblies led to improved transcript predictions for the vast majority of genes of these reference strains, and often substantially corrected gene structures. These include several genes that are central to virulence or expressed during the pathogenic yeast stage in Paracoccidioides and other fungi, such as HSP90, RYP1-3, BAD1, catalase B, alpha-1,3-glucan synthase and the beta glucan synthase target gene FKS1. The improvement and validation of these reference sequences will now allow more accurate genome-based analyses. To our knowledge, this is one of the first reports of a fully automated and quality-assessed upgrade of a genome assembly and annotation for a non-model fungus. © 2014 Muñoz et al

A comparative assessment of clinical whole exome and transcriptome profiling across sequencing centers: implications for precision cancer medicine

Advances in next generation sequencing technologies provide approaches to comprehensively determine genomic alterations within a tumor that occur as a cause or consequence of neoplastic growth. Though providers offering various cancer genomics assays have multiplied, the level of reproducibility in terms of the technical sensitivity and the conclusions resulting from the data analyses have not been assessed. We sought to determine the reproducibility of ascertaining tumor genome aberrations using whole exome sequencing (WES) and RNAseq. Samples of the same metastatic tumors were independently processed and subjected to WES of tumor and constitutional DNA, and RNAseq of RNA, at two sequencing centers. Overall, the sequencing results were highly comparable. Concordant mutation calls ranged from 88% to 93% of all variants including 100% agreement across 154 cancer-associated genes. Regions of copy losses and gains were uniformly identified and called by each sequencing center and chromosomal plots showed nearly identical patterns. Transcript abundance levels also exhibited a high degree of concordance (r2 ≥ 0.78;Pearson). Biologically-relevant gene fusion events were concordantly called. Exome sequencing of germline DNA samples provided a minimum of 30X coverage depth across 56 genes where incidental findings are recommended to be reported. One possible pathogenic variant in the APC gene was identified by both sequencing centers. The findings from this study demonstrate that results of somatic and germline sequencing are highly concordant across sequencing centers that have substantial experience in the technological requirements for preparing, sequencing and annotating DNA and RNA from human biospecimens

Genome Update of the Dimorphic Human Pathogenic Fungi Causing Paracoccidioidomycosis

<div><p>Paracoccidiodomycosis (PCM) is a clinically important fungal disease that can acquire serious systemic forms and is caused by the thermodimorphic fungal <i>Paracoccidioides</i> spp. PCM is a tropical disease that is endemic in Latin America, where up to ten million people are infected; 80% of reported cases occur in Brazil, followed by Colombia and Venezuela. To enable genomic studies and to better characterize the pathogenesis of this dimorphic fungus, two reference strains of <i>P. brasiliensis</i> (Pb03, Pb18) and one strain of <i>P. lutzii</i> (Pb01) were sequenced <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003348#pntd.0003348-Desjardins1" target="_blank">[1]</a>. While the initial draft assemblies were accurate in large scale structure and had high overall base quality, the sequences had frequent small scale defects such as poor quality stretches, unknown bases (N's), and artifactual deletions or nucleotide duplications, all of which caused larger scale errors in predicted gene structures. Since assembly consensus errors can now be addressed using next generation sequencing (NGS) in combination with recent methods allowing systematic assembly improvement, we re-sequenced the three reference strains of <i>Paracoccidioides</i> spp. using Illumina technology. We utilized the high sequencing depth to re-evaluate and improve the original assemblies generated from Sanger sequence reads, and obtained more complete and accurate reference assemblies. The new assemblies led to improved transcript predictions for the vast majority of genes of these reference strains, and often substantially corrected gene structures. These include several genes that are central to virulence or expressed during the pathogenic yeast stage in <i>Paracoccidioides</i> and other fungi, such as <i>HSP90</i>, <i>RYP1-3</i>, <i>BAD1</i>, catalase B, alpha-1,3-glucan synthase and the beta glucan synthase target gene <i>FKS1</i>. The improvement and validation of these reference sequences will now allow more accurate genome-based analyses. To our knowledge, this is one of the first reports of a fully automated and quality-assessed upgrade of a genome assembly and annotation for a non-model fungus.</p></div

Circulating Tumor DNA Is Prognostic in Intermediate-Risk Rhabdomyosarcoma: A Report From the Children's Oncology Group

International audiencePURPOSE Novel biomarkers are needed to differentiate outcomes in intermediate-risk rhabdomyosarcoma (IR RMS). We sought to evaluate strategies for identifying circulating tumor DNA (ctDNA) in IR RMS and to determine whether ctDNA detection before therapy is associated with outcome. PATIENTS AND METHODS Pretreatment serum and tumor samples were available from 124 patients with newly diagnosed IR RMS from the Children's Oncology Group biorepository, including 75 patients with fusion-negative rhabdomyosarcoma (FN-RMS) and 49 with fusion-positive rhabdomyosarcoma (FP-RMS) disease. We used ultralow passage whole-genome sequencing to detect copy number alterations and a new custom sequencing assay, Rhabdo-Seq, to detect rearrangements and single-nucleotide variants. RESULTS We found that ultralow passage whole-genome sequencing was a method applicable to ctDNA detection in all patients with FN-RMS and that ctDNA was detectable in 13 of 75 serum samples (17%). However, the use of Rhabdo-Seq in FN-RMS samples also identified single-nucleotide variants, such as MYOD1 L122R , previously associated with prognosis. Identification of pathognomonic translocations between PAX3 or PAX7 and FOXO1 by Rhabdo-Seq was the best method for measuring ctDNA in FP-RMS and detected ctDNA in 27 of 49 cases (55%). Patients with FN-RMS with detectable ctDNA at diagnosis had significantly worse outcomes than patients without detectable ctDNA (event-free survival, 33.3% v 68.9%; P = .0028; overall survival, 33.3% v 83.2%; P < .0001) as did patients with FP-RMS (event-free survival, 37% v 70%; P = .045; overall survival, 39.2% v 75%; P = .023). In multivariable analysis, ctDNA was independently associated with worse prognosis in FN-RMS but not in the smaller FP-RMS cohort. CONCLUSION Our study demonstrates that baseline ctDNA detection is feasible and is prognostic in IR RMS