Petabyte-scale innovations at the European Nucleotide Archive

Dramatic increases in the throughput of nucleotide sequencing machines, and the promise of ever greater performance, have thrust bioinformatics into the era of petabyte-scale data sets. Sequence repositories, which provide the feed for these data sets into the worldwide computational infrastructure, are challenged by the impact of these data volumes. The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/embl), comprising the EMBL Nucleotide Sequence Database and the Ensembl Trace Archive, has identified challenges in the storage, movement, analysis, interpretation and visualization of petabyte-scale data sets. We present here our new repository for next generation sequence data, a brief summary of contents of the ENA and provide details of major developments to submission pipelines, high-throughput rule-based validation infrastructure and data integration approaches

Stężenia chemeryny w surowicy i ślinie u pacjentów z rakiem jelita grubego i towarzyszącą otyłością

INTRODUCTION: Chemerin is an adipokine, whose pro-inflammatory and carcinogenesis-related properties have recently been emphasized. The aim of this study was to examine the concentrations of chemerin in the serum and saliva of healthy subjects and patients with colorectal cancer (CRC) in II and III stage of TNM (tumor, node, metastasis) classification as well as to assess the relationship between the results and the clinical and pathological parameters. MATERIAL AND METHODS: 52 persons were qualified to the study, divided into two equal groups – control and study with cancer in stage II N0 and in stage III N+ according to TNM classification. Inside the groups, subgroups of persons with normal body weight 18.5 ≤ BMI < 25 and obese and overweight persons with a BMI ≥ 25 were distinguished. Serum and saliva chemerin concentrations were determined by immunoenzymatic methods. RESULTS: The median concentrations of chemerin were significantly higher in the study group as compared to the control group both in serum (384.36 ng/ml vs. 170.53 ng/ml) and saliva (15.45 ng/ml vs. 4.57 ng/ml; p < 0.0001). In the subgroups with a BMI above and below 25, we found no significant differences in the concentrations of chemerin either group. There were no significant differences in the levels of chemerin in the serum or saliva between stage II and III stage of TNM (p = 0.82 and p = 0.52). CONCLUSIONS: The assessment of serum and saliva chemerin concentrations in patients with CRC suggests that chemerin may be a valuable biomarker for early diagnosis of CRC. The influence of BMI on the results seems to be insignificant in patients with CRC. It seems that in some cases an easily accepted saliva test can replace a serum one.WSTĘP: Chemeryna jest hormonem wydzielanym przez adipocyty. W ostatnim czasie zwraca się uwagę na jej właściwości prozapalne i związane z karcynogenezą. Celem pracy było zbadanie stężeń chemeryny w surowicy i ślinie osób zdrowych oraz chorych z rakiem jelita grubego (RJG) w II i III stopniu zawansowania według klasyfikacji TNM (tumor, node, metastasis), a także ocena związku uzyskanych wartości z otyłością oraz wybranymi parametrami kliniczno-patologicznymi. MATERIAŁ I METODY: Do badania zakwalifikowano 52 osoby, które podzielono na dwie równe grupy – kontrolną i badaną z nowotworem w II stopniu zaawansowania z cechą N0 oraz w III stopniu z cechą N+ według klasyfikacji TNM. Wewnątrz grup wyróżniono podgrupy osób o prawidłowej masie ciała (18,5 ≤ BMI < 25) oraz osoby otyłe i z nadwagą (BMI ≥ 25). Stężenia chemeryny w surowicy i ślinie oznaczano metodami immunoenzymatycznymi. WYNIKI: Mediany stężeń chemeryny były istotnie wyższe w grupie badanej w porównaniu z grupą kontrolną, zarówno w surowicy (384,36 ng/ml wobec 170,53 ng/ml), jak i ślinie (15,45 ng/ml wobec 4,57 ng/ml; p < 0,0001). W żadnej grupie w podgrupach z BMI powyżej i poniżej 25 nie znaleziono istotnych różnic w stężeniach badanej adipokininy. Nie odnotowano również istotnych różnic stężeń chemeryny w surowicy i ślinie między nowotworami w II i III stopniu zaawansowania TNM (p = 0,82 i p = 0,52). WNIOSKI: Ocena stężeń chemeryny w surowicy i ślinie u pacjentów z RJG sugeruje, że badana adipokina może być cennym biomarkerem wczesnej diagnostyki tego nowotworu. Wpływ BMI na uzyskane wyniki stężeń w surowicy i ślinie wydaje się nieistotny u chorych z RJG. Wydaje się, że w pewnych przypadkach łatwo akceptowane przez chorych badanie śliny może zastąpić badanie surowicy

Associations between Patient Report of Pain and Intervertebral Foramina Changes Visible on Axial-Loaded Lumbar Magnetic Resonance Imaging

The intervertebral foramen may influence spinal nerve roots and, therefore, be related to the corresponding dermatomal pain. In vivo evaluation of the intervertebral foramen–dermatome relationship is essential for understanding low back pain (LBP) pathophysiology. The study aimed to correlate the lumbar MRI unloaded-loaded foraminal area changes with dermatomal pain in the patient’s pain drawings. Dynamic changes of the dermatomal pain distribution related to the intervertebral foramen area changes between quantitative conventional supine MRI (unloaded MRI) and axial-loading MRI (alMRI) were analyzed. The MRI axial-loading intervertebral foramen area changes were observed, and the most significant effect of reducing the foraminal area (−6.9%) was reported at levels of L2–L3. The incidence of pain in the dermatomes increases linearly with the spine level, from 15.6% at L1 to 63.3% at L5 on the right and from 18.9% at L1 to 76.7% at L5 on the left. No statistically significant effect of changes in the intervertebral foramen area on the odds of pain along the respective dermatomes was confirmed. Changes in the foraminal area were observed between the unloaded and loaded phases, but differences in area changes between foramen assigned to painful dermatomes and foramen assigned to non-painful dermatomes were not significant

Calcifying Fibrous Tumor of the Small Bowel Mesentery in a 27-Year Old Male Patient - Case Report

Calcifying fibrous tumor is a rare disease entity, usually concerning the soft tissues of the limbs, neck, trunk, or scrotum. Cases of the above-mentioned pathology have also been reported considering the pleural and peritoneal cavity, and small bowel mesentery. The essence of the disease, whose etiology and pathogenesis remains unclear, is the fibrous tissue infiltration and diffuse inflammation with focal calcifications. The study presented a case of a 27-year old male patient subjected to surgical intervention, due to an abdominal cavity tumor. The tumor was radically removed, and its character and definitive diagnosis were established postoperatively. After a seven-year follow-up period, recurrence was not observed

Primary Duodenal Carcinoma - Case Report

Duodenal carcinoma is a rare tumor of the gastrointestinal tract of an insidious and secretive course, often diagnosed during the advanced stage of the disease. The study presented a case of a female patient diagnosed with duodenal carcinoma, subjected to two-staged surgery. The initial surgical intervention consisted in the implementation of a gastrointestinal anastomosis, followed by radical surgery by means of Whipple's method performed after three years

Study on Speciation of As, Cr, and Sb in Bottled Flavored Drinking Water Samples Using Advanced Analytical Techniques IEC/SEC-HPLC/ICP-DRC-MS and ESI-MS/MS

The main aim of the research was to develop a complementary analytical approach consisting of bespoke speciation analysis and non-targeted speciation analysis of As, Sb, and Cr in flavored bottled drinking water samples using HPLC/ICP-DRC-MS and ESI-MS/MS. The scope of two previously developed analytical procedures, (1) multielemental speciation procedure for AsIII, AsV, CrVI, SbIII, and SbV analysis and (2) arsenic speciation procedure for AsB, AsIII, DMA, MMA, and AsV quantification, was extended to the analysis of a new sample type in terms of bespoke speciation analysis. As for the non-targeted speciation, analysis size exclusion chromatography was used with ICP-MS and a complementary technique, ESI-MS/MS, was used for the organic species of As, Sb, and Cr screening. Full validation of procedures 1 and 2 was conducted. Procedure 1 and 2 were characterized with precision values in the range from 2.5% to 5.5% and from 3.6% to 7.2%, respectively. Obtained recoveries ranged from 97% to 106% and from 99% to 106% for procedures 1 and 2, respectively. Expanded uncertainties calculated for procedures 1 and 2 ranged from 6.1% to 9.4% and from 7.4% to 9.9%, respectively. The applicability of the proposed procedures was tested on bottled drinking water samples. Results for the real samples in procedure 1 were in the range from 0.286 &#177; 0.027 [&#956;g L&#8722;1] to 0.414 &#177; 0.039 [&#956;g L&#8722;1] for AsIII, from 0.900 &#177; 0.083 [&#956;g L&#8722;1] to 3.26 &#177; 0.30 [&#956;g L&#8722;1] for AsV, and from 0.201 &#177; 0.012 [&#956;g L&#8722;1] to 0.524 &#177; 0.032 [&#956;g L&#8722;1] for SbV. CrVI and SbIII were not detected in any sample. As for procedure 2, results were in the range from 0.0541 &#177; 0.0053 [&#956;g L&#8722;1] to 0.554 &#177; 0.054 [&#956;g L&#8722;1] for AsB. Results for AsIII and AsV obtained with procedure 2 were in good accordance with results obtained with procedure 1. DMA and MMA were not detected in any sample

Research stand-up for testing medium frequency transformers and chokes

W artykule przedstawiono system energoelektroniczny pozwalający na badania transformatorów i dławików średniej częstotliwości przeznaczonych do systemów przetwarzania energii z wykorzystaniem przekształtników energoelektronicznych. Przedmiotem badań mają być właściwości i parametry transformatorów oraz dławików, których rdzeń został zbudowany w oparciu o nowoczesne materiały magnetyczne, w tym nanokrystaliczne. Stanowisko umożliwia regulację wartości skutecznej i częstotliwości napięcia wyjściowego w zakresie do 20 kHz i amplitudzie prądu wyjściowego do 200 A.The article presents an electronic power system that allows testing of medium frequency transformers and chokes designed for energy conversion systems using power electronic converters. The object of research is to be the properties and parameters of transformers and chokes whose core has been built based on modern magnetic materials, including nanocrystalline ones. The stand allows adjustment of the effective value and frequency of the output voltage in the range up to 20 kHz and the amplitude of the output current up to 200 A

Salivary Concentrations of Chemerin, &alpha;-Defensin 1, and TNF-&alpha; as Potential Biomarkers in the Early Diagnosis of Colorectal Cancer

Colorectal cancer is one of the most prevalent cancers worldwide. There is a great interest and need to find simple, inexpensive, and minimally invasive diagnostic tests. The aim of the study was to analyze the salivary concentrations of chemerin, &alpha;-defensin 1, and TNF-&alpha; in colorectal cancer (CRC) patients and in a healthy control group. The concentration of these proteins was simultaneously determined in the serum of subjects. We also aimed to assess the correlation of these results and selected clinicopathological features. This prospective study was comprised of 39 CRC patients and 40 control group patients. Salivary and serum concentrations were determined by enzyme immunoassays. The salivary and serum concentrations of chemerin, &alpha;-defensin 1, and TNF-&alpha; were significantly higher in cancer patients compared to the control group. No correlation was found between concentrations of the proteins and the clinical stage of cancer and tumor location. The ROC curve analysis showed that although salivary concentrations of all proteins showed 100% sensitivity and 100% specificity, serum concentrations of the analyzed proteins were characterized by 100% sensitivity and over 90% specificity. The assessment of chemerin, &alpha;-defensin 1, and TNF-&alpha; concentrations in saliva seem to have great potential as quick and useful biomarkers in the early diagnosis of CRC