U-Net based vessel segmentation for murine brains with small micro-magnetic resonance imaging reference datasets.

Identification and quantitative segmentation of individual blood vessels in mice visualized with preclinical imaging techniques is a tedious, manual or semiautomated task that can require weeks of reviewing hundreds of levels of individual data sets. Preclinical imaging, such as micro-magnetic resonance imaging (µMRI) can produce tomographic datasets of murine vasculature across length scales and organs, which is of outmost importance to study tumor progression, angiogenesis, or vascular risk factors for diseases such as Alzheimer's. Training a neural network capable of accurate segmentation results requires a sufficiently large amount of labelled data, which takes a long time to compile. Recently, several reasonably automated approaches have emerged in the preclinical context but still require significant manual input and are less accurate than the deep learning approach presented in this paper-quantified by the Dice score. In this work, the implementation of a shallow, three-dimensional U-Net architecture for the segmentation of vessels in murine brains is presented, which is (1) open-source, (2) can be achieved with a small dataset (in this work only 8 µMRI imaging stacks of mouse brains were available), and (3) requires only a small subset of labelled training data. The presented model is evaluated together with two post-processing methodologies using a cross-validation, which results in an average Dice score of 61.34% in its best setup. The results show, that the methodology is able to detect blood vessels faster and more reliably compared to state-of-the-art vesselness filters with an average Dice score of 43.88% for the used dataset.

Lossy Image Compression in a Preclinical Multimodal Imaging Study.

The growing use of multimodal high-resolution volumetric data in pre-clinical studies leads to challenges related to the management and handling of the large amount of these datasets. Contrarily to the clinical context, currently there are no standard guidelines to regulate the use of image compression in pre-clinical contexts as a potential alleviation of this problem. In this work, the authors study the application of lossy image coding to compress high-resolution volumetric biomedical data. The impact of compression on the metrics and interpretation of volumetric data was quantified for a correlated multimodal imaging study to characterize murine tumor vasculature, using volumetric high-resolution episcopic microscopy (HREM), micro-computed tomography (µCT), and micro-magnetic resonance imaging (µMRI). The effects of compression were assessed by measuring task-specific performances of several biomedical experts who interpreted and labeled multiple data volumes compressed at different degrees. We defined trade-offs between data volume reduction and preservation of visual information, which ensured the preservation of relevant vasculature morphology at maximum compression efficiency across scales. Using the Jaccard Index (JI) and the average Hausdorff Distance (HD) after vasculature segmentation, we could demonstrate that, in this study, compression that yields to a 256-fold reduction of the data size allowed to keep the error induced by compression below the inter-observer variability, with minimal impact on the assessment of the tumor vasculature across scales.

Cross-Modality Imaging of Murine Tumor Vasculature-a Feasibility Study.

Tumor vasculature and angiogenesis play a crucial role in tumor progression. Their visualization is therefore of utmost importance to the community. In this proof-of-principle study, we have established a novel cross-modality imaging (CMI) pipeline to characterize exactly the same murine tumors across scales and penetration depths, using orthotopic models of melanoma cancer. This allowed the acquisition of a comprehensive set of vascular parameters for a single tumor. The workflow visualizes capillaries at different length scales, puts them into the context of the overall tumor vessel network and allows quantification and comparison of vessel densities and morphologies by different modalities. The workflow adds information about hypoxia and blood flow rates. The CMI approach includes well-established technologies such as magnetic resonance imaging (MRI), positron emission tomography (PET), computed tomography (CT), and ultrasound (US), and modalities that are recent entrants into preclinical discovery such as optical coherence tomography (OCT) and high-resolution episcopic microscopy (HREM). This novel CMI platform establishes the feasibility of combining these technologies using an extensive image processing pipeline. Despite the challenges pertaining to the integration of microscopic and macroscopic data across spatial resolutions, we also established an open-source pipeline for the semi-automated co-registration of the diverse multiscale datasets, which enables truly correlative vascular imaging. Although focused on tumor vasculature, our CMI platform can be used to tackle a multitude of research questions in cancer biology.

Impact of Processed Food (Canteen and Oil Wastes) on the Development of Black Soldier Fly (Hermetia illucens) Larvae and Their Gut Microbiome Functions.

Canteens represent an essential food supply hub for educational institutions, companies, and business parks. Many people in these locations rely on a guaranteed service with consistent quality. It is an ongoing challenge to satisfy the demand for sufficient serving numbers, portion sizes, and menu variations to cover food intolerances and different palates of customers. However, overestimating this demand or fluctuating quality of dishes leads to an inevitable loss of unconsumed food due to leftovers. In this study, the food waste fraction of canteen leftovers was identified as an optimal diet for black soldier fly (Hermetia illucens) larvae based on 50% higher consumption and 15% higher waste reduction indices compared with control chicken feed diet. Although the digestibility of food waste was nearly twice as high, the conversion efficiency of ingested and digested chicken feed remains unparalleled (17.9 ± 0.6 and 37.5 ± 0.9 in CFD and 7.9 ± 0.9 and 9.6 ± 1.0 in FWD, respectively). The oil separator waste fraction, however, inhibited biomass gain by at least 85% and ultimately led to a larval mortality of up to 96%. In addition to monitoring larval development, we characterized physicochemical properties of pre- and post-process food waste substrates. High-throughput amplicon sequencing identified Firmicutes, Proteobacteria, and Bacteroidota as the most abundant phyla, and Morganella, Acinetobacter, and certain Lactobacillales species were identified as indicator species. By using metagenome imputation, we additionally gained insights into the functional spectrum of gut microbial communities. We anticipate that the results will contribute to the development of decentralized waste-management sites that make use of larvae to process food waste as it has become common practice for biogas plants.

Methane yields and methanogenic community changes during co-fermentation of cattle slurry with empty fruit bunches of oil palm.

The biomethane potential and structural changes of the methanogenic community in a solid-state anaerobic digestion process co-digesting cattle slurry and empty fruit bunches were investigated under mesophilic (37°C) and thermophilic (55°C) conditions. Phylogenetic microarrays revealed the presence of two hydrogenotrophic genera (Methanoculleus and Methanobrevibacter) and one acetoclastic genus (Methanosarcina). Methanosarcina numbers were found to increase in both mesophilic and thermophilic treatments of empty fruit bunches. Methanobrevibacter, which dominated in the cattle slurry, remained constant during anaerobic digestion (AD) at 37°C and decreased in numbers during digestion at 55°C. Numbers of Methanoculleus remained constant at 37°C and increased during the thermophilic digestion. Physicochemical data revealed non-critical concentrations for important monitoring parameters such as total ammonia nitrogen, free ammonia nitrogen and volatile fatty acids in all treatments after AD. The biomethane potential of empty fruit bunches was higher under thermophilic conditions than under mesophilic conditions.

Crowded chromatin is not sufficient for heterochromatin formation and not required for its maintenance.

In contrast to cytoplasmic organelles, which are usually separated from the rest of the cell by phospholipid membranes, nuclear compartments are readily accessible to diffusing proteins and must rely on different mechanisms to maintain their integrity. Specific interactions between scaffolding proteins are known to have important roles for the formation and maintenance of nuclear structures. General physical mechanisms such as molecular crowding, phase separation or colloidal behavior have also been suggested, but their physiological significance remains uncertain. For macromolecular crowding, a role in the maintenance of nucleoli and promyelocytic leukemia (PML) nuclear bodies has been shown. Here, we tested whether a modulation of the compaction state of chromatin, which directly influences the local crowding state, has an impact on the formation and maintenance of densely packed heterochromatin. By osmotic perturbations, we could modify the packing state of chromatin in a controlled manner and show that chromatin compaction, which is associated with increased crowding conditions, is not, per se, sufficient to initiate the formation of new bona fide heterochromatin structures nor is it necessary to maintain already established heterochromatin domains. In consequence, if an increase in crowding induced by chromatin compaction maybe an early step in heterochromatin formation, specific protein-protein interactions are nevertheless required to make heterochromatin long lasting and independent of the crowding state.

Gyrate atrophy: clinical and genetic findings in a female without arginine-restricted diet during her first 39 years of life and report of a new OAT gene mutation.

We report the clinical and genetic data obtained at a 17-year follow-up examination of a patient with gyrate atrophy, without an arginine-restricted diet. Patient examinations included visual acuity (VA), perimetry, biomicroscopy, funduscopy, fundus photography, fundus autofluorescence (FAF), spectral-domain optical coherence tomography (OCT), and standard full-field electroretinography (ERG). Blood samples were taken for measurement of serum ornithine level and molecular genetic analysis of the OAT gene. The female was 22 years of age when gyrate atrophy was diagnosed based on peripheral chorioretinal atrophy and an increased ornithine level. Reexamination after 17 years revealed a reduced VA (0.25 OU), dense cataract, extensive peripheral chorioretinal atrophy, a further increased ornithine level, but only slow progression of visual field constriction, and still detectable ERG amplitudes. FAF was absent in the atrophic periphery and almost homogeneous at the posterior pole except parafoveally. OCT showed interruption of the foveal inner/outer segment junction and parafoveal microcystoid spaces. After cataract surgery, VA increased to the same values as those found at the age of 22 years (0.5 OD, 0.6 OS). Molecular analysis revealed a new deletion c.532_536delTGGGG (p.Trp178X) and a known mutation c.897C>G (p.Tyr299X) in the OAT gene. Although the patient had refused to diet during her first 39 years of life, the gyrate atrophy showed a very slow progression. FAF allows evaluating the integrity of the retinal pigment epithelium and may help to delimit gyrate atrophy from choroideremia. Interruption of foveal inner/outer segment junction and cystoid macula edema appears in gyrate atrophy.

Interobserver variability for retreatment indications after Ranibizumab loading doses in neovascular age-related macular degeneration.

PURPOSE: To assess the interobserver variability (IOV) in indicating retreatment for neovascular Age-related macular degeneration 4 weeks after three Ranibizumab loading doses using spectral domain OCT (SD-OCT) as the primary objective diagnostic tool. MATERIAL AND METHODS: Four observers decided for or against 4th Ranibizumab injection in 108 patients by six different rating rounds (RR) based on the SD-OCT findings after the loading doses. Postoperative OCT images were supplemented consecutively with information from a chart review as the 'patients subjective estimation of vision (SE)', the course of best-corrected visual acuity (BCVA) and the preoperative OCT as well as all information collectively. Agreement rates (AR) and Kappa statistics were calculated. RESULTS: Based on post-treatment OCT findings only (RR1), mean reinjection rate of all observers was 37.5%. Adding supplementary information, mean reinjection rate decreased to 20% when all information was available reflecting the 'real' situation (RR 6). Interobserver agreement rates varied from 66.7% to 90.7% depending on rating rounds and interobserver pairs. Mean AR and Kappa values (KV) were as following: AR 81.6%, KV 0.61 (RR1: 'only post-OP OCT'); AR 76.7%, KV 0.33 (RR2: post-OP OCT + SE); AR 80.3%, KV 0.45 (RR3: post-OP OCT + BCVA); AR 80.7%, KV 0.46 (RR4: pre- and post-OP OCT); AR 82.2%, KV 0.49 (RR5: post-OP OCT + SE + BCVA); and finally AR 83.6%, KV 0.47 (RR6: pre- and post-OP OCT + SE + BCVA). The overall mean agreement rate was 80.9% with a Kappa of 0.47. CONCLUSION: IOV for indicating retreatment after three Ranibizumab loading doses reveals only moderate agreement in Kappa statistics, which seems to be too low considering the high costs for retreatments. More concise guidelines based on the post-treatment OCT scans as the presumably most sensitive and noninvasive objective tool to follow choroidal neovascularization activity by judging the course of sub- and intraretinal fluid are necessary.

[Sampling studies in ambulatory quality assurance -- using the example of colonoscopy]. / Stichproben in der ambulanten Qualitätssicherung am Beispiel der Koloskopie.

BACKGROUND: Sampling inspections are an approved instrument for assuring and promoting the quality of healthcare. Individual documentations of medical services are requested from physicians and randomly selected for quality rating by experienced peer reviewers. For example, sampling inspections are stipulated by law for certain ambulatory services (e.g., colonoscopies) delivered by SHI-authorised physicians in order to maintain professional performance standards of colonoscopists. OBJECTIVES: On behalf of the regional Association of Statutory Health Insurance Physicians (ASHIP) experienced colonoscopists regularly rate selected visual documentations (videotapes, photographs) of colonoscopies performed by SHI-authorised physicians in the ambulatory care sector. For anatomical reasons, however, a certain proportion of colonoscopies of inadequate quality will generally be tolerated. Whenever this value is exceeded, ASHIP may impose sanctions against the physician. The question is how sampling inspections have to be performed and dimensioned in order to ensure that the tests be sufficiently meaningful in terms of sensitivity and specificity. METHODS: Relevant sampling test parameters such as the false-positive rate (physicians are wrongly accused of inadequate quality) and the false-negative rate (existing deficiencies are not identified) are calculated. The calculations are performed analytically or, in the case of complex sampling test scenarios, numerically by means of computer simulations. RESULTS: The calculations show that single-stage sampling tests usually do not result in acceptable values for the false-positive and the false-negative rates. For example, a sampling test which requires the documentation of 20 colonoscopies will -- assuming some reasonable tolerance of inadequately performed colonoscopies -- result in a false-positive rate of 6% and a false-negative rate of 47%. The false-positive-rate, which is particularly relevant from a legal point of view, can be reduced by providing a two-stage sampling test. A significant reduction of the false-negative-rate may be achieved by (multiple) repetition of the single-stage sampling test and consideration of cumulative probabilities. CONCLUSIONS: In principle, sampling inspections permit statements in terms of probabilities only. In sampling inspections of healthcare quality false-negative rates are usually considered, i.e., the probability that the test is unable to identify existing quality deficiencies. However, false-positive rates also need to be considered in cases where sanctions may be imposed against the physician on the basis of a positive sampling test. Numerical calculations of false-positive and false-negative rates for simple and complex sampling test scenarios should be performed in order to choose the optimum procedure and dimension of a sampling test.

Comparison of threshold irradiances and online dosimetry for selective retina treatment (SRT) in patients treated with 200 nanoseconds and 1.7 microseconds laser pulses.

BACKGROUND: Selective retina therapy (SRT) solely affecting the RPE while sparing of the photoreceptors is usually performed with a train of repetitive laser pulses of 1.7 microseconds in duration. It was our purpose to evaluate the principle feasibility of SRT with shorter 200 nanoseconds laser pulses in patients. METHODS: Nineteen patients with macular disorders [diabetic maculopathy (DMP), geographic atrophy (GA), drusen maculopathy and central serous chorioretinopathy (CSR)] were treated with a prototype of a SRT laser (Nd:YLF laser; 527 nm; 1.7 microseconds and 200 nanoseconds pulse duration; 30 pulses at 100 Hz; spot size: 200 microm). Test lesions (n = 175) with increasing energy were applied at the lower arcade to determine the individual angiographic and ophthalmoscopic threshold radiant exposures (therapeutic window) before applying the central treatment lesions within these ranges additionally guided by online optoacoustic measurements. Postoperatively RPE damage was visualized and confirmed by fluorescein angiographic leakage and correlated with optoacoustic results. Additionally ED(50) damage thresholds were calculated by probit analysis. RESULTS: None of the short repetitive 200 nanoseconds laser pulses led to retinal hemorrhages or retinal ruptures. Nearly all of the test- and treatment lesions could be visualized by angiography indicating desired RPE damage but were ophthalmoscopically invisible suggesting intact neurosensory retinal structures. ED(50) cell damage threshold energies were significantly lower using 200 nanoseconds (99.6 microJ; n = 122) instead of 1.7 microseconds (196.3 microJ; n = 53) laser pulses. Optoacoustic and angiographic visibility correlated in 83.7% (200 nanoseconds) and 87.5% (1.7 microseconds). CONCLUSIONS: Selective RPE effects can safely be achieved using shorter 200 nanoseconds laser pulses in patients without adverse effects to the neurosensory retina. The required pulse energy compared to the standard 1.7 microseconds regime was reduced by about a factor of 2 suggesting a reduced heat generation and flow into adjacent tissues during the shorter laser impact and thus possibly enhancing selectivity. Optoacoustics also seem to be a viable alternative in 200 nanoseconds treatment for a non-invasive online dosimetry control system.

Chemoembolization combined with pravastatin improves survival in patients with hepatocellular carcinoma.

BACKGROUND/AIMS: Pravastatin, a 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitor, has been shown to inhibit growth and to induce apoptosis in human hepatocellular carcinoma (HCC) cells. However, the potential benefit of pravastatin in HCC patients has still not been characterized, which prompted us to test the efficacy of pravastatin in patients with advanced HCC. METHODS: We investigated prospectively a cohort of 183 HCC patients who had been selected for palliative treatment by transarterial chemoembolization (TACE). Fifty-two patients received TACE combined with pravastatin (20-40 mg/day) and 131 patients received chemoembolization alone. Six independent predictors of survival according to the Vienna survival model for HCC were equally distributed in both groups. RESULTS: During the observation period of up to 5 years, 31 (23.7%) out of 131 patients treated by TACE alone and 19 (36.5%) out of 52 patients treated by TACE and pravastatin survived. Median survival was significantly longer in HCC patients treated by TACE and pravastatin (20.9 months, 95% CI 15.5-26.3, p = 0.003) than in HCC patients treated by TACE alone (12.0 months, 95% CI 10.3-13.7). CONCLUSION: Combined treatment of chemoembolization and pravastatin improves survival of patients with advanced HCC in comparison to patients receiving chemoembolization alone.

Bevacizumab in the treatment of idiopathic macular telangiectasia.

BACKGROUND: To describe functional and morphological long-term follow-up results in patients with idiopathic macular telangiectasia (IMT) treated with intravitreal bevacizumab. METHODS: Retrospective case series of three consecutive male patients with IMT who were treated with intravitreal bevacizumab injections. Best corrected visual acuity (BCVA) as well as fluorescein angiography (FA) and optical coherence tomography (OCT) were monitored over the period of up to 12 months. RESULTS: Single intravitreal bevacizumab injection resulted in a marked increase in BCVA from 20/50 to 20/20 in the patient with type 1 (aneurysmal) IMT during the first 4 weeks. Late-phase leakage on FA and cystoid macular oedema on OCT decreased significantly. This was sustained over the whole follow-up period of 12 months. In contrast, in the two patients with type 2 (perifoveal) IMT, leakage on FA decreased likewise, but this was not accompanied by an increase in BCVA despite triple injections. Small cystic changes seen on OCT remained unchanged. CONCLUSION: Patients with type 1 IMT with pronounced macular oedema on OCT may benefit from intravitreal bevacizumab injections, showing functional as well as morphological improvement, while patients with type 2 IMT with minimal cystic changes on OCT do not show functional improvement despite repeated injections.

Fundus autofluorescence before and after photodynamic therapy for choroidal neovascularization secondary to age-related macular degeneration.

BACKGROUND AND OBJECTIVE: To describe fundus autofluorescence patterns in choroidal neovascularization secondary to age-related macular degeneration before and after photodynamic therapy (PDT). PATIENTS AND METHODS: Sixty-eight consecutive eyes were indicated for PDT after standard fluorescein angiography, which showed completely classic choroidal neovascularization (CNV) (n=52), occult with no classic CNV (n=7), and predominantly classic CNV (n=9). Standardized PDT was performed and patients were examined 2 to 3 months later. Angiography and autofluorescence measurements were performed again and compared with preoperative values. RESULTS: At baseline, autofluorescence was mainly decreased in areas of completely classic CNV (79%), but showed a regular or mottled pattern in occult CNV. A slightly increased (50%) or normal (50%) autofluorescence was seen at the rim of the classic lesions within the junctional zone. Membrane demarcation was improved (90%) in classic membranes 2 to 3 months after PDT. After PDT for occult membranes, a transformation into classic membranes with residual leakage and need for further PDT was observed (6 of 7 eyes), showing the described autofluorescence patterns. For the mixed type of CNV, both described patterns of autofluorescence distribution were found. CONCLUSION: Especially classic CNVs reveal distinct characteristics of significantly decreased autofluorescence, presumably due to their localization above the retinal pigment epithelium level, leading to blockage of autofluorescence. Autofluorescence patterns after PDT included enhanced demarcation of the membrane, suggesting reactive retinal pigment epithelial changes. Autofluorescence might be an interesting tool to distinguish noninvasively between classic and occult CNV in age-related macular degeneration and to monitor changes after PDT.

Measurement of interleukin 8 in combination with C-reactive protein reduced unnecessary antibiotic therapy in newborn infants: a multicenter, randomized, controlled trial.

OBJECTIVE: Neonatal bacterial infections carry a high mortality when diagnosed late. Early diagnosis is difficult because initial clinical signs are nonspecific. Consequently, physicians frequently prescribe antibiotic treatment to newborn infants for fear of missing a life-threatening infection. This study was designed to test the hypotheses that a diagnostic algorithm that includes measurements of interleukin 8 (IL-8) and C-reactive protein (CRP) 1) reduces antibiotic therapy and 2) does not result in more initially missed infections compared with standard management that does not include an IL-8 measurement. METHODS: Term and preterm infants who were <72 hours of age and had clinical signs or obstetric risk factors suggesting neonatal bacterial infection but stable enough to wait for results of diagnostic tests were enrolled into the study. A total of 1291 infants were randomly assigned to receive antibiotic therapy according to the guidelines of each center (standard group) or to receive antibiotic therapy when IL-8 was >70 pg/mL and/or CRP was >10 mg/L (IL-8 group). The primary outcome variables were 1) the number of infants treated with antibiotics and 2) the number of infants with infections missed at the initial evaluation. RESULTS: In the IL-8 group, fewer infants received antibiotic therapy than in the standard group (36.1% [237 of 656] vs 49.6% [315 of 635]). In the IL-8 group, 24 (14.5%) of 165 infants with infection were not detected at the initial evaluation, compared with 28 (17.3%) of 162 in the standard group. CONCLUSIONS: The number of newborn infants who received postnatal antibiotic therapy can be reduced with a diagnostic algorithm that includes measurements of IL-8 and CRP. This diagnostic strategy seemed to be safe.