A microfluidic flow-cell for the study of the ultrafast dynamics of biological systems

The study of biochemical dynamics by ultrafast spectroscopic methods is often restricted by the limited amount of liquid sample available, while the high repetition rate of light sources can induce photodamage. In order to overcome these limitations, we designed a high flux, sub-ml, capillary flow-cell. While the 0.1 mm thin window of the 0.5 mm cross-section capillary ensures an optimal temporal resolution and a steady beam deviation, the cell-pump generates flows up to ∼0.35 ml/s that are suitable to pump laser repetition rates up to ∼14 kHz, assuming a focal spot-diameter of 100 μm. In addition, a decantation chamber efficiently removes bubbles and allows, via septum, for the addition of chemicals while preserving the closed atmosphere. The minimal useable amount of sample is ∼250 μl

Multilevel use of image repository in the field of veterinary imaging and dissemination of training tools

[Extract] Until now the veterinary teaching environment is limited to static two dimensional materials. In order to improve the teaching experience we decided to adapt our educational PACS to build 2D and 3D viewing veterinary datasets. As entry level of education we setup a knowledge base consisting out of normal anatomy [1, 2]. The second step is the construction of an imaging atlas compared with the normal anatomy of every animal. The third step is the construction of a database containing a wide variety of radiopathology cases. The final level is the integration in an e-learning platform namely WikiVet [3] which is a collaborative initiative involving UK veterinary schools. The project is creating a comprehensive online knowledge base and will provide a reliable reference source to supersede Wikipedia for veterinary students, paramedics and graduates anywhere in the world, improving diagnostic skills using diagnostic imaging

Quantification of biological nitrogen fixation in primary forest and secondary vegetation in NE Amazonia.

Publicado também em: SHIFT-WORKSHOP, 3., 1998, Manaus. Program, abstracts of presentation and posters. [S.l.]: SHIFT, 1998. A6

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis

<p>Abstract</p> <p>Background</p> <p>Inferring viral tropism from genotype is a fast and inexpensive alternative to phenotypic testing. While being highly predictive when performed on clonal samples, sensitivity of predicting CXCR4-using (X4) variants drops substantially in clinical isolates. This is mainly attributed to minor variants not detected by standard bulk-sequencing. Massively parallel sequencing (MPS) detects single clones thereby being much more sensitive. Using this technology we wanted to improve genotypic prediction of coreceptor usage.</p> <p>Methods</p> <p>Plasma samples from 55 antiretroviral-treated patients tested for coreceptor usage with the Monogram Trofile Assay were sequenced with standard population-based approaches. Fourteen of these samples were selected for further analysis with MPS. Tropism was predicted from each sequence with geno2pheno_[coreceptor].</p> <p>Results</p> <p>Prediction based on bulk-sequencing yielded 59.1% sensitivity and 90.9% specificity compared to the trofile assay. With MPS, 7600 reads were generated on average per isolate. Minorities of sequences with high confidence in CXCR4-usage were found in all samples, irrespective of phenotype. When using the default false-positive-rate of geno2pheno_[coreceptor](10%), and defining a minority cutoff of 5%, the results were concordant in all but one isolate.</p> <p>Conclusions</p> <p>The combination of MPS and coreceptor usage prediction results in a fast and accurate alternative to phenotypic assays. The detection of X4-viruses in all isolates suggests that coreceptor usage as well as fitness of minorities is important for therapy outcome. The high sensitivity of this technology in combination with a quantitative description of the viral population may allow implementing meaningful cutoffs for predicting response to CCR5-antagonists in the presence of X4-minorities.</p

Septic Thrombophlebitis of the Right Ovarian Vein

Background: A 26-year-old woman presented at the emergency department with a painful abdomen and fever up to 39°C, despite antibiotics. She had given prematurely birth by caesarian section to a twin 8 days earlier. On clinical examination she had a diffuse painful and tender abdomen, especially on the right side and suprapubic region. Laboratory findings showed an increased c-reactive protein of 24 mg/dL (normal < 0,3) and increased white blood cell count of 13 Å~ 10E9/L (normal 4,3-10 Å~ 10E9/L). There was also a decreased hemoglobin level of 8,4 g/dL (normal 12-15 g/dL). An ultrasonography was performed by the gynecologist and revealed a large heterogeneous fluid collection anteriorly of the uterus

Fertility and gonadal function in female survivors after treatment of early unfavorable Hodgkin lymphoma (HL) within the German Hodgkin Study Group HD14 trial

Background In the HD14 trial, 2× BEACOPPescalated+2× ABVD (2+2) has improved the primary outcome. Compared with 4× ABVD, this benefit might be compromised by more infertility in women. Therefore, we analyzed gonadal function and fertility. Patients and methods Women ≤45 years in ongoing remission at least 1 year after therapy were included. Hormone parameters, menopausal symptoms, measures to preserve fertility, menstrual cycle, pregnancies, and offspring were evaluated. Results Three hundred and thirty one of 579 women addressed participated (57.2%) and 263 per-protocol treated patients qualified (A=ABVD: 137, B=2+2: 126, mean time after therapy 42 and 43 months, respectively). Regular menstrual cycle after treatment (A: 87%, B: 83%) and time to recovery (≤12 months) were not different. Follicle-stimulating hormone and anti-Muellerian hormone were significantly better in arm A. However, pregnancies after therapy favored arm B (A: 15%, B: 26%, P=0.043) and motherhood rates were equivalent to the German normal population. Multivariate analysis revealed prophylactic use of gonadotropin-releasing hormone (GnRH) analogues as highly significant prognostic factor for preservation of fertility (odds ratio=12.87, P=0.001). Severe menopausal symptoms were frequent in women ≥30 years (A: 21%, B: 25%). Conclusions Hormonal levels after 2+2 indicate a reduced ovarian reserve. However, 2+2 in combination with GnRH analogues does not compromise fertility within the evaluated observation tim

How do I know if my forecasts are better? Using benchmarks in Hydrological ensemble prediction

The skill of a forecast can be assessed by comparing the relative proximity of both the forecast and a benchmark to the observations. Example benchmarks include climatology or a naïve forecast. Hydrological ensemble prediction systems (HEPS) are currently transforming the hydrological forecasting environment but in this new field there is little information to guide researchers and operational forecasters on how benchmarks can be best used to evaluate their probabilistic forecasts. In this study, it is identified that the forecast skill calculated can vary depending on the benchmark selected and that the selection of a benchmark for determining forecasting system skill is sensitive to a number of hydrological and system factors. A benchmark intercomparison experiment is then undertaken using the continuous ranked probability score (CRPS), a reference forecasting system and a suite of 23 different methods to derive benchmarks. The benchmarks are assessed within the operational set-up of the European Flood Awareness System (EFAS) to determine those that are ‘toughest to beat’ and so give the most robust discrimination of forecast skill, particularly for the spatial average fields that EFAS relies upon. Evaluating against an observed discharge proxy the benchmark that has most utility for EFAS and avoids the most naïve skill across different hydrological situations is found to be meteorological persistency. This benchmark uses the latest meteorological observations of precipitation and temperature to drive the hydrological model. Hydrological long term average benchmarks, which are currently used in EFAS, are very easily beaten by the forecasting system and the use of these produces much naïve skill. When decomposed into seasons, the advanced meteorological benchmarks, which make use of meteorological observations from the past 20 years at the same calendar date, have the most skill discrimination. They are also good at discriminating skill in low flows and for all catchment sizes. Simpler meteorological benchmarks are particularly useful for high flows. Recommendations for EFAS are to move to routine use of meteorological persistency, an advanced meteorological benchmark and a simple meteorological benchmark in order to provide a robust evaluation of forecast skill. This work provides the first comprehensive evidence on how benchmarks can be used in evaluation of skill in probabilistic hydrological forecasts and which benchmarks are most useful for skill discrimination and avoidance of naïve skill in a large scale HEPS. It is recommended that all HEPS use the evidence and methodology provided here to evaluate which benchmarks to employ; so forecasters can have trust in their skill evaluation and will have confidence that their forecasts are indeed better

A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing

Background: Ultra deep sequencing is of increasing use not only in research but also in diagnostics. For implementation of ultra deep sequencing assays in clinical laboratories for routine diagnostics, intra- and inter-laboratory testing are of the utmost importance. Methods: A multicenter study was conducted to validate an updated assay design for 454 Life Sciences’ GS FLX Titanium system targeting protease/reverse transcriptase (RTP) and env (V3) regions to identify HIV-1 drug-resistance mutations and determine co-receptor use with high sensitivity. The study included 30 HIV-1 subtype B and 6 subtype non-B samples with viral titers (VT) of 3,940–447,400 copies/mL, two dilution series (52,129–1,340 and 25,130–734 copies/mL), and triplicate samples. Amplicons spanning PR codons 10–99, RT codons 1–251 and the entire V3 region were generated using barcoded primers. Analysis was performed using the GS Amplicon Variant Analyzer and geno2pheno for tropism. For comparison, population sequencing was performed using the ViroSeq HIV-1 genotyping system. Results: The median sequencing depth across the 11 sites was 1,829 reads per position for RTP (IQR 592–3,488) and 2,410 for V3 (IQR 786–3,695). 10 preselected drug resistant variants were measured across sites and showed high inter-laboratory correlation across all sites with data (P20% were missed, variants 2–10% were detected at most sites (even at low VT), and variants 1–2% were detected by some sites. All mutations detected by population sequencing were also detected by UDS. Conclusions: This assay design results in an accurate and reproducible approach to analyze HIV-1 mutant spectra, even at variant frequencies well below those routinely detectable by population sequencing