scROSHI: robust supervised hierarchical identification of single cells.

Identifying cell types based on expression profiles is a pillar of single cell analysis. Existing machine-learning methods identify predictive features from annotated training data, which are often not available in early-stage studies. This can lead to overfitting and inferior performance when applied to new data. To address these challenges we present scROSHI, which utilizes previously obtained cell type-specific gene lists and does not require training or the existence of annotated data. By respecting the hierarchical nature of cell type relationships and assigning cells consecutively to more specialized identities, excellent prediction performance is achieved. In a benchmark based on publicly available PBMC data sets, scROSHI outperforms competing methods when training data are limited or the diversity between experiments is large.

Advanced Diffusion-Weighted Imaging Sequences for Breast MRI: Comprehensive Comparison of Improved Sequences and Ultra-High B-Values to Identify the Optimal Combination.

This study investigated the image quality and choice of ultra-high b-value of two DWI breast-MRI research applications. The study cohort comprised 40 patients (20 malignant lesions). In addition to s-DWI with two m-b-values (b50 and b800) and three e-b-values (e-b1500, e-b2000, and e-b2500), z-DWI and IR m-b1500 DWI were applied. z-DWI was acquired with the same measured b-values and e-b-values as the standard sequence. For IR m-b1500 DWI, b50 and b1500 were measured, and e-b2000 and e-b2500 were mathematically extrapolated. Three readers used Likert scales to independently analyze all ultra-high b-values (b1500-b2500) for each DWI with regards to scan preference and image quality. ADC values were measured in all 20 lesions. z-DWI was the most preferred (54%), followed by IR m-b1500 DWI (46%). b1500 was significantly preferred over b2000 for z-DWI and IR m-b1500 DWI (p = 0.001 and p = 0.002, respectively). Lesion detection was not significantly different among sequences or b-values (p = 0.174). There were no significant differences in measured ADC values within lesions between s-DWI (ADC: 0.97 [±0.09] × 10-3 mm2/s) and z-DWI (ADC: 0.99 [±0.11] × 10-3 mm2/s; p = 1.000). However, there was a trend toward lower values in IR m-b1500 DWI (ADC: 0.80 [±0.06] × 10-3 mm2/s) than in s-DWI (p = 0.090) and z-DWI (p = 0.110). Overall, image quality was superior and there were fewer image artifacts when using the advanced sequences (z-DWI + IR m-b1500 DWI) compared with s-DWI. Considering scan preferences, we found that the optimal combination was z-DWI with a calculated b1500, especially regarding examination time.

Quantitative Assessment of Iteratively Denoised 3D SPACE with Inner-Volume Excitation and Simultaneous Multi-Slice BLADE for Optimizing Female Pelvis Magnetic Resonance Imaging at 1.5 T.

RATIONALE AND OBJECTIVES: High-resolution T2-weighted magnetic resonance imaging (MRI) of the pelvis is the main technique used for diagnosing benign and malignant uterine diseases. However, the procedure may be time-consuming and requires training and experience. Therefore, this study was performed to compare the image quality of standard clinical BLADE (stBLADE) with a prototypical accelerated simultaneous multi-slice (SMS) BLADE procedure with either improved temporal resolution (tr) at the same slice thickness (SL) or improved spatial resolution (sr) with the same examination time and a prototypical isotropic 3D SPACE procedure with inner-volume excitation and iterative denoising. MATERIALS AND METHODS: Patients who underwent clinically indicated MRI of the uterus were included in this prospective study and underwent stBLADE (acquisition time, 2 min 59 s; SL, 4 mm) and SMS BLADE (tr) with the same SL (4 mm) but reduced examination time (1 min 20 s) as well as SMS BLADE (sr) with thinner slices (3 mm) and comparable examination time (3 min 16 s). In addition, 3D SPACE was acquired in a sagittal orientation (5 min 36 s). The short axis of the cervix and the long axis of the corpus uteri were reconstructed in 1-mm and 3-mm SLs, retrospectively. Subjective overall image impression, delineation of anatomy/organs, lesion demarcation, and motion artifacts were assessed using a 5-point Likert scale and compared among the different techniques. The preferred sequence was then selected by three independent assessors. RESULTS: The analysis was based on 38 women (mean age, 44 ± 15 years). The overall image impression was similar for stBLADE, SMS BLADE (sr), and SMS BLADE (tr) but was significantly lower for 3D SPACE than stBLADE (p = 0.01). SMS BLADE (sr) was considered the preferred sequence because of slightly better performance in terms of overall image impression, organ delineation, and lesion demarcation, but without statistical significance. Both SMS BLADE (tr) and (sr) produced significantly fewer motion artifacts than stBLADE (p < 0.01 and p = 0.01), with no significant difference between SMS BLADE (tr) and (sr), while 3D SPACE had a significantly lower rating than stBLADE (p < 0.01). Image quality was rated as the least diagnostic criterion in all sequences and all cases. CONCLUSION: SMS BLADE (sr) was the preferred sequence for MRI of the female pelvis, with higher sr than stBLADE. SMS BLADE (tr) may also be used to reduce the acquisition time without compromising image quality. Despite its lower image quality, 3D SPACE can also reduce the examination time and improve the workflow because of the possibility of retrospective multiplanar reconstructions.

Can Dynamic Contrast-enhanced MRI Contribute to Improved Assessment of Rectosigmoid Involvement in Deep Infiltrating Endometriosis?

BACKGROUND/AIM: To determine whether a prototypical compressed-sensing volume-interpolated breath-hold (csVIBE) provides diagnostic value in detecting rectosigmoid infiltration in deep infiltrating endometriosis (DIE). PATIENTS AND METHODS: csVIBE was employed in 151 women undergoing pelvic magnetic resonance imaging, of whom 43 had undergone surgery for suspected endometriosis. The accuracy of T2-weighted BLADE and BLADE/csVIBE, additional diagnostic value of csVIBE, and diagnostic confidence were rated by two readers. Additionally, the presence of the "mushroom cap sign" was assessed on BLADE and csVIBE. RESULTS: The diagnostic accuracy, sensitivity, and specificity of BLADE and BLADE/csVIBE were not significantly different between Readers A and B. For both readers, the confidence in the diagnosis increased with csVIBE, but this increase in the odds ratio was not significant for both readers. Both readers preferred csVIBE over BLADE with regard to detection of the "mushroom cap sign." CONCLUSION: csVIBE may provide a diagnostic benefit for surgical strategy selection through better delineation of the "mushroom cap sign."

Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice.

Isobiotic mice, with an identical stable microbiota composition, potentially allow models of host-microbial mutualism to be studied over time and between different laboratories. To understand microbiota evolution in these models, we carried out a 6-year experiment in mice colonized with 12 representative taxa. Increased non-synonymous to synonymous mutation rates indicate positive selection in multiple taxa, particularly for genes annotated for nutrient acquisition or replication. Microbial sub-strains that evolved within a single taxon can stably coexist, consistent with niche partitioning of ecotypes in the complex intestinal environment. Dietary shifts trigger rapid transcriptional adaptation to macronutrient and micronutrient changes in individual taxa and alterations in taxa biomass. The proportions of different sub-strains are also rapidly altered after dietary shift. This indicates that microbial taxa within a mouse colony adapt to changes in the intestinal environment by long-term genomic positive selection and short-term effects of transcriptional reprogramming and adjustments in sub-strain proportions.

Dissection of the mutation accumulation process during bacterial range expansions.

BACKGROUND: Recent experimental work has shown that the evolutionary dynamics of bacteria expanding across space can differ dramatically from what we expect under well-mixed conditions. During spatial expansion, deleterious mutations can accumulate due to inefficient selection on the expansion front, potentially interfering with and modifying adaptive evolutionary processes. RESULTS: We used whole genome sequencing to follow the genomic evolution of 10 mutator Escherichia coli lines during 39 days ( ~ 1650 generations) of a spatial expansion, which allowed us to gain a temporal perspective on the interaction of adaptive and non-adaptive evolutionary processes during range expansions. We used elastic net regression to infer the positive or negative effects of mutations on colony growth. The colony size, measured after three day of growth, decreased at the end of the experiment in all 10 lines, and mutations accumulated at a nearly constant rate over the whole experiment. We find evidence that beneficial mutations accumulate primarily at an early stage of the experiment, leading to a non-linear change of colony size over time. Indeed, the rate of colony size expansion remains almost constant at the beginning of the experiment and then decreases after ~ 12 days of evolution. We also find that beneficial mutations are enriched in genes encoding transport proteins, and genes coding for the membrane structure, whereas deleterious mutations show no enrichment for any biological process. CONCLUSIONS: Our experiment shows that beneficial mutations target specific biological functions mostly involved in inter or extra membrane processes, whereas deleterious mutations are randomly distributed over the whole genome. It thus appears that the interaction between genetic drift and the availability or depletion of beneficial mutations determines the change in fitness of bacterial populations during range expansion.

Mutational and Selective Processes Involved in Evolution during Bacterial Range Expansions.

Bacterial populations have been shown to accumulate deleterious mutations during spatial expansions that overall decrease their fitness and ability to grow. However, it is unclear if and how they can respond to selection in face of this mutation load. We examine here if artificial selection can counteract the negative effects of range expansions. We examined the molecular evolution of 20 mutator lines selected for fast expansions (SEL) and compared them to 20 other mutator lines freely expanding without artificial selection (CONTROL). We find that the colony size of all 20 SEL lines have increased relative to the ancestral lines, unlike CONTROL lines, showing that enough beneficial mutations are produced during spatial expansions to counteract the negative effect of expansion load. Importantly, SEL and CONTROL lines have similar numbers of mutations indicating that they evolved for the same number of generations and that increased fitness is not due to a purging of deleterious mutations. We find that loss of function mutations better explain the increased colony size of SEL lines than nonsynonymous mutations or a combination of the two. Interestingly, most loss of function mutations are found in simple sequence repeats (SSRs) located in genes involved in gene regulation and gene expression. We postulate that such potentially reversible mutations could play a major role in the rapid adaptation of bacteria to changing environmental conditions by shutting down expensive genes and adjusting gene expression.

Relaxed Selection During a Recent Human Expansion.

Humans have colonized the planet through a series of range expansions, which deeply impacted genetic diversity in newly settled areas and potentially increased the frequency of deleterious mutations on expanding wave fronts. To test this prediction, we studied the genomic diversity of French Canadians who colonized Quebec in the 17th century. We used historical information and records from ∼4000 ascending genealogies to select individuals whose ancestors lived mostly on the colonizing wave front and individuals whose ancestors remained in the core of the settlement. Comparison of exomic diversity reveals that: (i) both new and low-frequency variants are significantly more deleterious in front than in core individuals, (ii) equally deleterious mutations are at higher frequencies in front individuals, and (iii) front individuals are two times more likely to be homozygous for rare very deleterious mutations present in Europeans. These differences have emerged in the past six to nine generations and cannot be explained by differential inbreeding, but are consistent with relaxed selection mainly due to higher rates of genetic drift on the wave front. Demographic inference and modeling of the evolution of rare variants suggest lower effective size on the front, and lead to an estimation of selection coefficients that increase with conservation scores. Even though range expansions have had a relatively limited impact on the overall fitness of French Canadians, they could explain the higher prevalence of recessive genetic diseases in recently settled regions of Quebec.

Accumulation of Deleterious Mutations During Bacterial Range Expansions.

Recent theory predicts that the fitness of pioneer populations can decline when species expand their range, due to high rates of genetic drift on wave fronts making selection less efficient at purging deleterious variants. To test these predictions, we studied the fate of mutator bacteria expanding their range for 1650 generations on agar plates. In agreement with theory, we find that growth abilities of strains with a high mutation rate (HMR lines) decreased significantly over time, unlike strains with a lower mutation rate (LMR lines) that present three to four times fewer mutations. Estimation of the distribution of fitness effect under a spatially explicit model reveals a mean negative effect for new mutations (-0.38%), but it suggests that both advantageous and deleterious mutations have accumulated during the experiment. Furthermore, the fitness of HMR lines measured in different environments has decreased relative to the ancestor strain, whereas that of LMR lines remained unchanged. Contrastingly, strains with a HMR evolving in a well-mixed environment accumulated less mutations than agar-evolved strains and showed an increased fitness relative to the ancestor. Our results suggest that spatially expanding species are affected by deleterious mutations, leading to a drastic impairment of their evolutionary potential.

Genetic surfing in human populations: from genes to genomes.

Genetic surfing describes the spatial spread and increase in frequency of variants that are not lost by genetic drift and serial migrant sampling during a range expansion. Genetic surfing does not modify the total number of derived alleles in a population or in an individual genome, but it leads to a loss of heterozygosity along the expansion axis, implying that derived alleles are more often in homozygous state. Genetic surfing also affects selected variants on the wave front, making them behave almost like neutral variants during the expansion. In agreement with theoretical predictions, human genomic data reveals an increase in recessive mutation load with distance from Africa, an expansion load likely to have developed during the expansions of human populations out of Africa.

Protection of Erwinia amylovora bacteriophage Y2 from UV-induced damage by natural compounds.

Bacteriophages have regained much attention as biocontrol agents against bacterial pathogens. However, with respect to stability, phages are biomolecules and are therefore sensitive to a number of environmental influences. UV-irradiation can readily inactivate phage infectivity, which impedes their potential application in the plant phyllosphere. Therefore, phages for control of Erwinia amylovora, the causative agent of fire blight, need to be protected from UV-damage by adequate measures. We investigated the protective effect of different light-absorbing substances on phage particles exposed to UV-light. For this, natural extracts from carrot, red pepper, and beetroot, casein and soy peptone in solution, and purified substances such as astaxanthin, aromatic amino acids, and Tween 80 were prepared and tested as natural sunscreens for phage. All compounds were found to significantly increase half-life of UV-irradiated phage particles and they did not negatively affect phage viability or infectivity. Altogether, a range of readily available, natural substances are suitable as UV-protectants to prevent phage particles from UV-light damage.