Molecular architecture of the developing mouse brain

The mammalian brain develops through a complex interplay of spatial cues generated by diffusible morphogens, cell-cell interactions and intrinsic genetic programs that result in probably more than a thousand distinct cell types. A complete understanding of this process requires a systematic characterization of cell states over the entire spatiotemporal range of brain development. The ability of single-cell RNA sequencing and spatial transcriptomics to reveal the molecular heterogeneity of complex tissues has therefore been particularly powerful in the nervous system. Previous studies have explored development in specific brain regions^1-8, the whole adult brain⁹ and even entire embryos¹⁰. Here we report a comprehensive single-cell transcriptomic atlas of the embryonic mouse brain between gastrulation and birth. We identified almost eight hundred cellular states that describe a developmental program for the functional elements of the brain and its enclosing membranes, including the early neuroepithelium, region-specific secondary organizers, and both neurogenic and gliogenic progenitors. We also used in situ mRNA sequencing to map the spatial expression patterns of key developmental genes. Integrating the in situ data with our single-cell clusters revealed the precise spatial organization of neural progenitors during the patterning of the nervous system.

Human simulations of vocabulary learning

The work reported here experimentally investigates a striking generalization about vocabulary acquisition: Noun learning is superior to verb learning in the earliest moments of child language development. The dominant explanation of this phenomenon in the literature invokes differing conceptual requirements for items in these lexical categories: Verbs are cognitively more complex than nouns and so their acquisition must await certain mental developments in the infant. In the present work, we investigate an alternative hypothesis; namely, that it is the information requirements of verb learning, not the conceptual requirements, that crucially determine the acquisition order. Efficient verb learning requires access to structural features of the exposure language and thus cannot take place until a scaffolding of noun knowledge enables the acquisition of clause-level syntax. More generally, we experimentally investigate the hypothesis that vocabulary acquisition takes place via an incremental constraint-satisfaction procedure that bootstraps itself into successively more sophisticated linguistic representations which, in turn, enable new kinds of vocabulary learning. If the experimental subjects were young children, it would be difficult to distinguish between this information-centered hypothesis and the conceptual change hypothesis. Therefore the experimental "learners" are adults. The items to be "acquired" in the experiments were the 24 most frequent nouns and 24 most frequent verbs from a sample of maternal speech to 18-24-month-old infants. The various experiments ask about the kinds of information that will support identification of these words as they occur in mother-to-child discourse. Both the proportion correctly identified and the type of word that is identifiable changes significantly as a function of information type. We discuss these results as consistent with the incremental construction of a highly lexicalized grammar by cognitively and pragmatically sophisticated human infants, but inconsistent with a procedure in which lexical acquisition is independent of and antecedent to syntax acquisition.

Multiplexed precision genome editing with trackable genomic barcodes in yeast

Our understanding of how genotype controls phenotype is limited by the scale at which we can precisely alter the genome and assess the phenotypic consequences of each perturbation. Here we describe a CRISPR-Cas9-based method for multiplexed accurate genome editing with short, trackable, integrated cellular barcodes (MAGESTIC) in Saccharomyces cerevisiae. MAGESTIC uses array-synthesized guide-donor oligos for plasmid-based high-throughput editing and features genomic barcode integration to prevent plasmid barcode loss and to enable robust phenotyping. We demonstrate that editing efficiency can be increased more than fivefold by recruiting donor DNA to the site of breaks using the LexA-Fkh1p fusion protein. We performed saturation editing of the essential gene SEC14 and identified amino acids critical for chemical inhibition of lipid signaling. We also constructed thousands of natural genetic variants, characterized guide mismatch tolerance at the genome scale, and ascertained that cryptic Pol III termination elements substantially reduce guide efficacy. MAGESTIC will be broadly useful to uncover the genetic basis of phenotypes in yeast.

Sphingolipids control dermal fibroblast heterogeneity

Human cells produce thousands of lipids that change during cell differentiation and can vary across individual cells of the same type. However, we are only starting to characterize the function of these cell-to-cell differences in lipid composition. Here, we measured the lipidomes and transcriptomes of individual human dermal fibroblasts by coupling high-resolution mass spectrometry imaging with single-cell transcriptomics. We found that the cell-to-cell variations of specific lipid metabolic pathways contribute to the establishment of cell states involved in the organization of skin architecture. Sphingolipid composition is shown to define fibroblast subpopulations, with sphingolipid metabolic rewiring driving cell-state transitions. Therefore, cell-to-cell lipid heterogeneity affects the determination of cell states, adding a new regulatory component to the self-organization of multicellular systems.

Malignant ureteral obstruction: preliminary results of treatment with metallic self-expandable stents

Self-expandable metal stents 7 mm in diameter were percutaneously implanted into 13 ureters in 10 patients with malignant ureteral obstruction not amenable to double-J stent placement. In nine ureters, one stent was placed, and in four ureters, two overlapping stents were placed. Primary reconstitution of ureteral patency was achieved in all ureters. After 1-2 weeks, four ureters showed a urothelial reaction encroaching on the lumen of the ureter, and a double-J stent was placed coaxially. One ureter was occluded by urothelial hyperplasia 4 weeks after stent placement, and a double-J stent was therefore placed. One ureter was occluded 8 months after stent placement by distal tumor overgrowth. The other ureters showed no signs of obstruction during a follow-up of 3-14 (average, 5.8) months. Peristalsis was preserved at both ends of the stent in all ureters. The use of this stent alone or in combination with a double-J stent alleviated upper urinary tract obstruction and avoided external drainage in all patients.

Dehydropolymerisation of methylamine borane using a dinuclear 1,3-allenediyl bridged zirconocene complex

The dinuclear zirconocene chloride complex 1 is a highly active precatalyst for the dehydropolymerisation of methylamine borane. Comparison with mononuclear Zr chlorides and related dinuclear complexes suggests that the nature of the bridging motif is essential for the unique reactivity of 1.

Agenesis of the dorsal pancreas in a woman with diabetes mellitus and in both of her sons

Complete agenesis of the dorsal pancreas has rarely been described. Complete agenesis of the dorsal pancreas in a female who developed insulin-dependent diabetes mellitus at the age of 39 years is reported. The diagnosis of agenesis of the dorsal pancreas was suspected by abdominal ultrasound and confirmed by abdominal computed tomography (CT), magnetic resonance imaging, and endoscopic retrograde pancreatography. Her exocrine pancreatic function was essentially normal. Both of the patient's sons also had agenesis of the body and tail of the pancreas verified by abdominal CT but had no evidence of diabetes mellitus. This familial occurrence of agenesis of the dorsal pancreas suggests that hereditary mechanisms may play a role in the pathogenesis of this anomaly.

Chest sonography in the diagnosis of pulmonary embolism: a comparison with MRI angiography and ventilation perfusion scintigraphy

AIM

To compare the diagnostic performance of chest sonography, MRI angiography and ventilation/perfusion intigraphy in pulmonary embolism (PE).

METHOD

In a prospective clinical study, 55 patients (41 women, 14 men, age 23 - 91 years) with clinical signs of PE were investigated within 48 hours of the onset of symptoms. The final diagnosis was made by MRI angiography (reference method).

RESULTS

PE was diagnosed in a total of 36 patients. Chest sonography revealed rounded or wedge-shaped hypoechoic lesions in 30 patients. On ventilation/perfusion (V/P) scintigraphy, 41 patients had positive V/P scans, but only 23 were of high probability. Chest ultrasound had a positive predictive value of 97 % to diagnose PE. The sensitivity, specificity, the negative predictive value and accuracy were 81 %, 84 %, 84 % and 82 %, respectively. As 18 patients had inconclusive scans, the diagnostic performance of ventilation/perfusion scintigraphy was poor. The positive predictive value, sensitivity and specificity were 58 %, 42 % and 91 %, respectively. Patients in whom PE was excluded mainly suffered from congestive heart failure, bronchopulmonary infections or pulmonary hypertension.

CONCLUSION

A negative sonographic study cannot rule out PE with certainty. However, a chest sonography is of acceptable diagnostic value in patients with suspected PE and may be used as an adjunct or guide to more established methods.

Molecular profiling of stem cell-derived retinal pigment epithelial cell differentiation established for clinical translation

Human embryonic stem cell-derived retinal pigment epithelial cells (hESC-RPE) are a promising cell source to treat age-related macular degeneration (AMD). Despite several ongoing clinical studies, a detailed mapping of transient cellular states during in vitro differentiation has not been performed. Here, we conduct single-cell transcriptomic profiling of an hESC-RPE differentiation protocol that has been developed for clinical use. Differentiation progressed through a culture diversification recapitulating early embryonic development, whereby cells rapidly acquired a rostral embryo patterning signature before converging toward the RPE lineage. At intermediate steps, we identified and examined the potency of an NCAM1⁺ retinal progenitor population and showed the ability of the protocol to suppress non-RPE fates. We demonstrated that the method produces a pure RPE pool capable of maturing further after subretinal transplantation in a large-eyed animal model. Our evaluation of hESC-RPE differentiation supports the development of safe and efficient pluripotent stem cell-based therapies for AMD.

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Transcriptional analysis of hESC-RPE differentiation benchmarked to in vivo cells

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NCAM1 emerges as a cell-surface marker of multipotent neuroepithelial progenitors

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hESC-RPE cells are obtained through a divergence-convergence process


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hESC-RPE further mature in vivo upon subretinal injection into the rabbit eye

Transillumination and HDR Imaging for Proximal Caries Detection

The purpose of this study was to develop an in vitro model for the validation of near-infrared transillumination (NIRT) for proximal caries detection, to enhance NIRT with high-dynamic-range imaging (HDRI), and to compare both methods, using micro-computed tomography (µCT) as a reference standard. Both proximal surfaces of 53 healthy or decayed permanent human teeth were examined using the Diagnocam (DC) (KaVo) and NIRT with HDRI (NIRT-HDRI). NIRT was combined with HDRI to improve the diagnostic performance by reducing under- and overexposed image areas. For NIRT-HDRI, an exposure series was captured and merged into a single HDR image. A classification was applied according to lesion depth. All surfaces were assessed twice by 2 trained examiners, and additionally with µCT for validation. The Kappa statistic was used to calculate inter-rater reliability and agreement between DC and NIRT-HDRI. Inter-rater reliability (weighted Kappa, wκ) showed very good agreement for the DC (0.90) and NIRT-HDRI (0.96). The overall agreement (wκ) was almost perfect (0.85). In the individual categories (0 to 4), the agreement (simple Kappa) ranged from almost perfect (category 4) to moderate (1 and 2) to substantial (categories 0 and 3). Sensitivity and specificity of sound surfaces, enamel, and dentin caries ranged from 0.57 to 0.99 and were similar for both methods in the different categories. NIRT-HDRI had a higher sensitivity for sound surfaces and enamel caries, as well as a higher specificity for dentin caries. Regarding the obtained images, HDRI allowed for the detection of caries within a greater range of luminance levels, resulting in a more detailed visualization of structures without under- or overexposure. However, HDRI this did not improve the diagnostics significantly. Distinguishing between a processed demineralized enamel and dentin lesions appears to be a problem specific to NIRT and cannot be balanced using HDRI.

The Paf1 Complex Broadly Impacts the Transcriptome of Saccharomyces cerevisiae

The Polymerase Associated Factor 1 complex (Paf1C) is a multifunctional regulator of eukaryotic gene expression important for the coordination of transcription with chromatin modification and post-transcriptional processes. In this study, we investigated the extent to which the functions of Paf1C combine to regulate the Saccharomyces cerevisiae transcriptome. While previous studies focused on the roles of Paf1C in controlling mRNA levels, here, we took advantage of a genetic background that enriches for unstable transcripts, and demonstrate that deletion of PAF1 affects all classes of Pol II transcripts including multiple classes of noncoding RNAs (ncRNAs). By conducting a de novo differential expression analysis independent of gene annotations, we found that Paf1 positively and negatively regulates antisense transcription at multiple loci. Comparisons with nascent transcript data revealed that many, but not all, changes in RNA levels detected by our analysis are due to changes in transcription instead of post-transcriptional events. To investigate the mechanisms by which Paf1 regulates protein-coding genes, we focused on genes involved in iron and phosphate homeostasis, which were differentially affected by PAF1 deletion. Our results indicate that Paf1 stimulates phosphate gene expression through a mechanism that is independent of any individual Paf1C-dependent histone modification. In contrast, the inhibition of iron gene expression by Paf1 correlates with a defect in H3 K36 trimethylation. Finally, we showed that one iron regulon gene, FET4, is coordinately controlled by Paf1 and transcription of upstream noncoding DNA. Together, these data identify roles for Paf1C in controlling both coding and noncoding regions of the yeast genome.

Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations

Across biological systems, cells undergo coordinated changes in gene expression, resulting in transcriptome dynamics that unfold within a low-dimensional manifold. While low-dimensional dynamics can be extracted using RNA velocity, these algorithms can be fragile and rely on heuristics lacking statistical control. Moreover, the estimated vector field is not dynamically consistent with the traversed gene expression manifold. To address these challenges, we introduce a Bayesian model of RNA velocity that couples velocity field and manifold estimation in a reformulated, unified framework, identifying the parameters of an explicit dynamical system. Focusing on the cell cycle, we implement VeloCycle to study gene regulation dynamics on one-dimensional periodic manifolds and validate its ability to infer cell cycle periods using live imaging. We also apply VeloCycle to reveal speed differences in regionally defined progenitors and Perturb-seq gene knockdowns. Overall, VeloCycle expands the single-cell RNA sequencing analysis toolkit with a modular and statistically consistent RNA velocity inference framework.

Ex-Utero Intrapartum Treatment (EXIT) in a giant case of Congenital Cystic Adenomatoid Malformation (CCAM) of the lung

Congenital Cystic Adenomatoid Malformations (CCAM) of the lung are a relatively rare anomaly. The majority of cases do not require any antenatal or perinatal interventions. However, selected cases need special and intensified management. This article discusses a case of a CCAM of the left pulmonary lobe covering 2/3 to 3/4 of the thoracic volume, causing mediastinal shift and hydrops. The enormous size required the planning of an EXIT (Ex Utero-Intrapartum Treatment) procedure, which was performed when the trial of intraoperative ventilation of the lungs was unsuccessful. A thoracotomy and resection of the left upper lobe were performed with the fetus on feto-placental circulation. After resection and closure of the thoracotomy, improvement of lung ventilation allowed the delivery of the child. The child and mother were discharged in a healthy condition. We conclude that the EXIT procedure is a feasible and potentially life-saving method for select cases of prenatally detected CCAM.

Malignant fibrous histiocytoma of the mesentery--a rare cause of abdominal pain. Case report with a review of literature

Malignant fibrous histiocytoma (MFH) is a tumor most frequently occurring in lower and upper extremities and in retroperitoneum. This paper presents the extremely rare case of a 55-year-old male patient with a MFH of storiform pleomorphic subtype originating from the mesentery. Sonography, computed tomography as well as endoscopy and ERCP did not reveal the diagnosis. Finally the tumor was diagnosed by laparoscopy with biopsy and histological examination. Two months after diagnosis of the tumor the patient died of bronchopneumony and heart failure contracted during a generalisation of MFH.

[Feasibility of fetal echocardiography at 11-14 weeks scan]

PURPOSE

Sonographic diagnostics are increasingly brought forward into the first trimenon. Lately, more and more expert studies have been published on echocardiography in the context of the Nuchal Translucency (NT) screening (gestational age 11-14 weeks). The aim of this study has been to evaluate the feasibility of early echocardiography on the occasion of first trimenon screening in the context of routine operation.

MATERIALS AND METHODS

From February 2003 to March 2004, an echocardiography was prospectively sought in 130 assigned, unselected pregnant women during the first trimenon screening. Three doctors with different OGUM/DEGUM (Austrian and German societies for ultrasound in medicine) qualifications at our ward tried to represent the four-chamber view (4CV) and the outflow tracts (OFT), each via B-mode and color Doppler. The study conditions were "routine", in particular they were temporally limited. In case no sufficient visual representation was achievable with the transabdominal examination, transvaginal sonography was also used.

RESULTS

Via B-mode, 4CV was indicated as successful in 86/130, and OFTs in 37/130. Via color Doppler, on the other hand, it was possible to sufficiently represent 4CV in 75/130 and OFTs in 87/130.

CONCLUSION

In routine screening, early heart examination is a big challenge and in many cases even with good equipment no complete diagnostic echocardiography can be achieved. The utilisation of the color Doppler is helpful particularly for the representation of the outflow tracts.

[Extrinsic allergic alveolitis in CT and HR-CT]

The CT changes on conventional and high-resolution CT in 14 patients with exogenous allergic alveolitis (EAA) were analysed retrospectively. There were 8 patients with clinically subacute disease, 5 patients in a chronic stage and 1 patient with acute EAA. The appearances and their distribution were examined. Seven of the 8 patients in the subacute stage showed a ground glass pattern and multiple nodules of less than 2 mm. All patients in the chronic stage showed a combination of fine infiltrates, small nodules and irregular linear densities; distortion of the pulmonary pattern was present in 3 cases. The patient with acute EAA showed diffuse dense areas of consolidation in both lungs as well as multiple nodules and a ground glass pattern. The CT appearances of EAA correspond with the basic micropathology and, within the clinical context, permit diagnostic classification.