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Proteins are key molecular players in a cell, and their abundance is extensively regulated not just at the level of gene expression but also post-transcriptionally. Here, we describe a genetic screen in yeast that enables systematic characterization of how protein abundance regulation is encoded in the genome. The screen combines a CRISPR/Cas9 base editor to introduce point mutations with fluorescent tagging of endogenous proteins to facilitate a flow-cytometric readout. We first benchmarked base editor performance in yeast with individual gRNAs as well as in positive and negative selection screens. We then examined the effects of 16,452 genetic perturbations on the abundance of eleven proteins representing a variety of cellular functions. We uncovered hundreds of regulatory relationships, including a novel link between the GAPDH isoenzymes Tdh1/2/3 and the Ras/PKA pathway. Many of the identified regulators are specific to one of the eleven proteins, but we also found genes that, upon perturbation, affected the abundance of most of the tested proteins. While the more specific regulators usually act transcriptionally, broad regulators often have roles in protein translation. Overall, our novel screening approach provides unprecedented insights into the components, scale and connectedness of the protein regulatory network., eLife, 11, ISSN:2050-084X

Background The imbalance of cardiac autonomic nervous system function plays an important role in heart failure associated mortality. ARNI has demonstrated a paramount effect in reducing risk of death and hospitalization for worsening of heart failure. However, its exact mechanism of action remains only partly understood. We sought to prospectively compare heart rate variability as a noninvasive measure of cardiac autonomic nervous system function. Methods The study design was prospective sequential observational. Patients served as their own internal control. Patients with heart failure with reduced ejection fraction (HFrEF) receiving optimal medical therapy who were scheduled for a switch to ARNI therapy underwent echocardiography and a standardized 30-minute 12-lead Holter ECG recording before starting ARNI therapy. A monitoring of the parameters was performed 3 months after the start of therapy. Physicians were instructed to increase ARNI dose to the highest tolerated or maximum dose. Besides left ventricular ejection fraction (LVEF) we assessed heart rate (HR), standard deviation of normal-to-normal intervals (SDNN) and mean square of differences between consecutive R-R intervals (RMSSD). Results We recruited 55 patients and baseline characteristics were as follows: age 65±12 years, male sex 78%, NT-proBNP 4989±809 pg/ml, LVEF 28±6%, HR 75±9 bpm, SDNN 43±2 ms, RMSSD 19±2 ms. All patients received beta-blocker therapy and the dosage was similar at baseline and follow-up. After 3 months of ARNI therapy, heart rate showed a significant reduction of 7% (74±14 bpm vs. 69±11 min, P=0.005). SDNN increased by 49% (43±2 ms vs. 64±4 ms, P Conclusion After changing from ACE/AT1-I to ARNI, significant improvement of autonomic cardiac nervous system function could be observed. ARNI apparently activates the parasympathetic nervous system as suggested by decreased HR and increased SDNN and RMSSD. Therefore, part of its cardioprotective and beneficial effects may relate to the restoration of autonomic cardiac nervous system function. Potential beneficial effects regarding incidence of sudden cardiac arrest may relate to these observations. Funding Acknowledgement Type of funding sources: None.

The second most common histological subtype of invasive breast carcinoma is invasive lobular carcinoma (ILC) occuring with a frequency 10-15% in Western countries and approximately 5%, in Africa, the Middle East and Asia (AMA). Combined hormone replacement therapy (CHRT) is a risk factor for the development of ILC which is infrequently diagnosed at our centre.This study aimed to investigate the incidence and clinicopathological characteristics of ILC as compared to invasive breast carcinoma of no special type (IBC-NST).Clinical and pathological data on breast carcinoma patients attending the breast and endocrine unit at Tygerberg Academic Hospital since 2017 have been recorded on a Stellenbosch University REDCapIBC-NST was the most frequent subtype diagnosed (83.9%) and ILC the second most common subtype (5.2%). Most ILCs were of luminal B intrinsic subtype, and the median size was slightly smaller than IBC-NST. There were significantly more grade 2 ILCs than IBC-NSTs (81.5% vs 50.9%). There was no statistical difference between stage and histological subtype.ILC has clinicopathological differences when compared to IBC-NST, although these were less pronounced in this study. The prevalence of ILC was similar to numbers reported in AMA. We hypothesise that there may be a discrepancy in the prevalence of ILC between public and private healthcare systems in South Africa, and that it may be due to differing trends in prescribing CHRT.

The sexual strain of the planarian Schmidtea mediterranea, indigenous to Tunisia and several Mediterranean islands, is a hermaphrodite1,2. Here we isolate individual chromosomes and use sequencing, Hi-C3,4 and linkage mapping to assemble a chromosome-scale genome reference. The linkage map reveals an extremely low rate of recombination on chromosome 1. We confirm suppression of recombination on chromosome 1 by genotyping individual sperm cells and oocytes. We show that previously identified genomic regions that maintain heterozygosity even after prolonged inbreeding make up essentially all of chromosome 1. Genome sequencing of individuals isolated in the wild indicates that this phenomenon has evolved specifically in populations from Sardinia and Corsica. We find that most known master regulators5–13 of the reproductive system are located on chromosome 1. We used RNA interference14,15 to knock down a gene with haplotype-biased expression, which led to the formation of a more pronounced female mating organ. On the basis of these observations, we propose that chromosome 1 is a sex-primed autosome primed for evolution into a sex chromosome.

Anxiety is common in older adults with mild cognitive impairment (MCI), and Alzheimer's disease and related dementias (ADRD). Anxiety has also been identified as a risk factor for cognitive decline. Brief interventions targeting risk mechanisms of anxiety, such as anxiety sensitivity (AS), have been effective in reducing overall anxiety in a variety of populations. This case series investigated the feasibility and efficacy of a brief AS intervention in anxious older adults with MCI (n = 9). Paired samples t-test results indicate that this intervention is capable of significantly reducing AS as measured by the Anxiety Sensitivity Index-3 (Δ = 5.11, Hedges g = 0.82, P

The reported prevalence of tuberculous bronchial stenosis in children is unknown and rarely reported in English-speaking literature. In adult patients with pulmonary tuberculosis, it varies from 40% in an autopsied series in the preantibiotic era to 10% in patients who have undergone routine bronchofibroscopy in modern times. We describe our experience of four cases of confirmed bronchial stenosis due to MTB collected between January 2000 and June 2021 in this case series descriptive study. The diagnosis of bronchial stenosis due to TB was made on flexible bronchoscopy. A TB diagnosis was made if MTB was cultured from respiratory secretions, when Ziehl-Neelsen smear or GeneXpert MTB/RIF test was positive, or if a chest radiograph revealed radiographic features typical of MTB. Bronchial stenosis due to TB is rare even if airway compression is frequently seen. Although an early diagnosis of bronchial stenosis due to TB is difficult on chest X-rays, all children in this series demonstrated parenchymal changes distal to the stenosis ranging from hyperinflation and lobar collaps to bronchiectasis. If bronchial stenosis resulting from TB disease is diagnosed early, balloon dilatation as described in this report, may be an effective and safe intervention, preventing long-term complications such as irreversible lung destruction, that may require pneumonectomy.

Resumen Los injertos oseos y cartilaginosos forman parte del arsenal terapeutico en cirugia del aparato locomotor. En este articulo se describen las propiedades de estos distintos tejidos humanos. Los autoinjertos oseo y cartilaginoso siguen siendo los injertos de referencia debido a su vitalidad persistente despues de la implantacion, al contrario de lo que sucede con los aloinjertos. Estos ultimos se desvitalizan despues de su conservacion por frio o por liofilizacion. Esta conservacion se realiza en unidades tecnicas denominadas bancos de tejidos. Su actividad esta reglamentada juridicamente. Esta conservacion del tejido despues de su movilizacion le confiere la ventaja de ofrecer un material de reconstruccion apropiado para el aparato locomotor y de permitir muchas posibilidades de montaje que se revisaran aqui. La desvitalizacion de los aloinjertos provoca tambien una serie de complicaciones, como la seudoartrosis y la fractura por estres, que el cirujano debe prever. Los aloinjertos de hueso cortical permiten tambien aprovechar su contenido en factores osteoinductores, que se pueden utilizar para favorecer la consolidacion osea. Los progresos de las pruebas de imagen, de la informatica y de la ingenieria permiten en la actualidad seleccionar y adaptar un aloinjerto oseo cuya morfologia osea sea la mas apropiada para una reconstruccion precisa y mejorar la calidad del acto planificado durante la intervencion. El autoinjerto y el aloinjerto oseos u osteoarticulares siguen siendo elementos basicos en cirugia ortopedica y se deben conocer estas tecnicas fundamentales. Cuando el cirujano dispone de aloinjertos oseos, proporcionan posibilidades suplementarias de reconstruccion osea u osteoarticular.

Purpose The aim of this study was to demonstrate the value of DCE MRI with high spatiotemporal resolution (GRASP) for differentiating paragangliomas and schwannomas in the head and neck. Methods In a retrospective PACS search of in total 410 patients who had undergone head & neck GRASP-MRI, we identified 6 patients with biopsy proven cervical paragangliomas (n = 3) and schwannomas (n = 3). Conventional MRI features were evaluated, lesion size was determined. Postprocessing in 4D-GRASP datasets was performed (1) based on reconstructions with a temporal resolution (Tres) of 4.1 s, qualitative time-intensity curve classification and semiquantitative parameter (Tpeak, PH, ERmax and Slopemax) analysis, and (2) voxel-based mapping and qualitative and semiquantitative perfusion modeling based on reconstructions with a Tres of 1.6 s. Additionally, GRASP perfusion analysis was performed in another set of 5 patients with presumed cervical paragangliomas (n = 3) and schwannomas (n = 2) based on conventional imaging criteria and was correlated with conventional imaging findings. Due to the small sample size, both groups were compared qualitatively. Results In the time intensity curve classification of 4D GRASP reconstructions (Tres 4.1 s), biopsy proven paragangliomas were consistently characterized by a type-III rapid inflow wash-out pattern, compared to a type-I inflow pattern in the schwannoma group. In both temporal resolutions, semiquantitative analysis of time intensity curves demonstrated rapid wash-in, wash-out, and higher peak signal intensities in paragangliomas compared to schwannomas. In 5 presumed (non-biopsy-proven) paragangliomas and schwannomas, time intensity curves improved diagnostic certainty. Conclusions Visual time intensity curve classification and semi-quantitative analysis of GRASP-MRI were, in this small retrospective series, sufficient to differentiate cervical paragangliomas from schwannomas. Utilization of this technique may further improve diagnostic confidence in lesions lacking conventional imaging features.

Biocatalysis offers a promising path for plastic waste management and valorization, especially for hydrolysable plastics such as polyethylene terephthalate (PET). Microbial whole-cell biocatalysts for simultaneous PET degradation and growth on PET monomers would offer a one-step solution toward PET recycling or upcycling. We set out to engineer the industry-proven bacterium Pseudomonas putida for (i) metabolism of PET monomers as sole carbon sources, and (ii) efficient extracellular expression of PET hydrolases. We pursued this approach for both PET and the related polyester polybutylene adipate co-terephthalate (PBAT), aiming to learn about the determinants and potential applications of bacterial polyester-degrading biocatalysts.P. putida was engineered to metabolize the PET and PBAT monomer terephthalic acid (TA) through genomic integration of four tphII operon genes from Comamonas sp. E6. Efficient cellular TA uptake was enabled by a point mutation in the native P. putida membrane transporter MhpT. Metabolism of the PET and PBAT monomers ethylene glycol and 1,4-butanediol was achieved through adaptive laboratory evolution. We then used fast design-build-test-learn cycles to engineer extracellular PET hydrolase expression, including tests of (i) the three PET hydrolases LCC, HiC, and IsPETase; (ii) genomic versus plasmid-based expression, using expression plasmids with high, medium, and low cellular copy number; (iii) three different promoter systems; (iv) three membrane anchor proteins for PET hydrolase cell surface display; and (v) a 30-mer signal peptide library for PET hydrolase secretion. PET hydrolase surface display and secretion was successfully engineered but often resulted in host cell fitness costs, which could be mitigated by promoter choice and altering construct copy number. Plastic biodegradation assays with the best PET hydrolase expression constructs genomically integrated into our monomer-metabolizing P. putida strains resulted in various degrees of plastic depolymerization, although self-sustaining bacterial growth remained elusive.Our results show that balancing extracellular PET hydrolase expression with cellular fitness under nutrient-limiting conditions is a challenge. The precise knowledge of such bottlenecks, together with the vast array of PET hydrolase expression tools generated and tested here, may serve as a baseline for future efforts to engineer P. putida or other bacterial hosts towards becoming efficient whole-cell polyester-degrading biocatalysts.

Placental pathology is an important contributor to the understanding of preterm birth and reveals major differences between spontaneous preterm birth (SPTB) and iatrogenic preterm birth (IPTB). The aim of this study was to investigate these relationships.Research midwives collected placentas from 1101 women with singleton pregnancies who were enrolled in the Safe Passage Study. Trained pathology technologists prepared and processed placenta specimens for macroscopic and microscopic examination by designated pathologists. Statistical analyses were done with STATISTICA version 13.In SPTB we found more cases of accelerated villous maturation; however, the other features of maternal vascular malperfusion (MVM) were not present. The prevalence rate of funisitis was also increased. In IPTB, multiple features of MVM - accelerated villous maturation, distal villous hypoplasia, decidual arteriopathy, increased syncytial knots, increased perivillous fibrin, and prominent extravillous trophoblast were increased, as were features of fetal vascular malperfusion (FVM) - umbilical cord vessel thrombosis, avascular villi, and fetal vascular thrombosis. Increased syncytial knots were found in 26% of preterm stillbirths and in 29% of preterm infant demises as compared to 81% of IPTB infants alive at one year.SPTB and IPTB differ. The detected "abnormal" accelerated villous maturation pattern in SPTB and preterm demises, suggests an inability of the placenta to adapt and may be a trigger for SPTB. Funisitis was the only inflammatory response significant for SPTB. MVM and FVM are implicated in IPTB, but not an inflammatory process.

Genomic variation impacts on cellular networks by affecting the abundance (e.g., protein levels) and the functional states (e.g., protein phosphorylation) of their components. Previous work has focused on the former, while in this context, the functional states of proteins have largely remained neglected. Here, we generated high-quality transcriptome, proteome, and phosphoproteome data for a panel of 112 genomically well-defined yeast strains. Genetic effects on transcripts were generally transmitted to the protein layer, but specific gene groups, such as ribosomal proteins, showed diverging effects on protein levels compared with RNA levels. Phosphorylation states proved crucial to unravel genetic effects on signaling networks. Correspondingly, genetic variants that cause phosphorylation changes were mostly different from those causing abundance changes in the respective proteins. Underscoring their relevance for cell physiology, phosphorylation traits were more strongly correlated with cell physiological traits such as chemical compound resistance or cell morphology, compared with transcript or protein abundance. This study demonstrates how molecular networks mediate the effects of genomic variants to cellular traits and highlights the particular importance of protein phosphorylation., Molecular Systems Biology, 18 (5), ISSN:1744-4292

PurposeThe current literature on the use of brachial artery access is controversial. Some studies found increased puncture site complications. Others found no higher complication rates than in patients with femoral or radial access. The purpose of this study was to determine the impact of ultrasound (US)-guidance on access site complications.Materials and methodsThis is a single-center retrospective study of all consecutive patients with brachial arterial access for interventional procedures. Complications were classified into minor complications (conservative treatment only) and major complications (requiring surgical intervention). The brachial artery was cannulated in the antecubital fossa under US-guidance. After the intervention, manual compression or closure devices, both followed by a compression bandage for 3 h, either achieved hemostasis.ResultsSeventy-five procedures in seventy-one patients were performed in the study period using brachial access. Access was successful in all cases (100%). Procedures in different vascular territories were performed: neurovascular (10/13.5%), upper extremity (32/43.2%), visceral (20/27.0%), and lower extremity (12/16.3%). Sheath size ranged from 3.2F to 8F (mean: 5F). Closure devices were used in 17 cases (22.7%). In total, six complications were observed (8.0%), four minor complications (5.3%, mostly puncture site hematomas), and two major complications, that needed surgical treatment (2.7%). No brachial artery thrombosis or upper extremity ischemia occurred.ConclusionExclusive use of US-guidance resulted in a low risk of brachial artery access site complications in our study compared to the literature. US-guidance has been proven to reduce the risk of access site complications in several studies in femoral access. In addition, brachial artery access yields a high technical success rate and requires no additional injection of spasmolytic medication. Sheath size was the single significant predictor for complications.

The sexual biotype of the planarianSchmidtea mediterraneais a hermaphrodite indigenous to Tunisia and several Mediterranean islands. Here, we isolated individual chromosomes and used sequencing, Hi-C and linkage mapping to assemble a chromosome-scale genome reference. The linkage map revealed an extremely low rate of recombination on chromosome 1. We confirmed suppression of recombination on chromosome 1 by quantifying recombination events in individual sperm and oocytes. We showed that the extensive heterozygous regions, previously designated as J and V haplotypes, comprise essentially all of chromosome 1. Genome sequencing of individuals isolated in the wild indicated that this heterozygosity has evolved specifically in populations from Sardinia and Corsica. We found that chromosome 1 acquired many genes that determine the development of female and male reproductive systems, along with haplotype-specific expression of such sex specific genes. These molecular signatures and restricted recombination in a hermaphrodite led us to propose that chromosome 1 is a sex-primed autosome, providing direct molecular evidence for the traditional model of how sex chromosomes may have evolved from autosomes.

The COVID-19 pandemic has disrupted cancer diagnostic services. A decline in the number of new cancers being diagnosed over a relatively short term implies a delay in diagnosis and subsequent treatment. This delay is expected to have a negative effect on cancerrelated morbidity and mortality. The impact of the pandemic on the number of new cancer diagnoses in our setting is unknown.To assess the impact of COVID-19 on the number of new cancers diagnosed at our institution in the first 3 months following the implementation of lockdown restrictions, by focusing on common non-cutaneous cancers.A retrospective laboratory-based audit was performed at a large anatomical pathology laboratory in Western Cape Province, South Africa. The numbers of new diagnoses for six common cancers (breast, prostate, cervix, large bowel, oesophagus and stomach) from 1 April 2020 to 30 June 2020 were compared with the corresponding period in 2019.Histopathological diagnoses for the six cancers combined decreased by 192 (-36.2%), from 531 new cases in the 2019 study period to 339 in the corresponding period in 2020. Substantial declines were seen for prostate (-58.2%), oesophageal (-44.1%), breast (-32.9%), gastric (-32.6%) and colorectal cancer (-29.2%). The smallest decline was seen in cervical cancer (-7%). New breast cancers diagnosed by cytopathology declined by 61.1%.The first wave of the COVID-19 pandemic and the associated response resulted in a substantial decline in the number of new cancer diagnoses, implying a delay in diagnosis. Cancer-related morbidity and mortality is expected to rise as a result, with the greatest increase in mortality expected from breast and colorectal cancer.

Accurate measurements of cellular protein concentrations are invaluable to quantitative studies of gene expression and physiology in living cells. Here, we developed a versatile mass spectrometric workflow based on data‐independent acquisition proteomics (DIA/SWATH) together with a novel protein inference algorithm (xTop). We used this workflow to accurately quantify absolute protein abundances in Escherichia coli for > 2,000 proteins over > 60 growth conditions, including nutrient limitations, non‐metabolic stresses, and non‐planktonic states. The resulting high‐quality dataset of protein mass fractions allowed us to characterize proteome responses from a coarse (groups of related proteins) to a fine (individual) protein level. Hereby, a plethora of novel biological findings could be elucidated, including the generic upregulation of low‐abundant proteins under various metabolic limitations, the non‐specificity of catabolic enzymes upregulated under carbon limitation, the lack of large‐scale proteome reallocation under stress compared to nutrient limitations, as well as surprising strain‐dependent effects important for biofilm formation. These results present valuable resources for the systems biology community and can be used for future multi‐omics studies of gene regulation and metabolic control in E. coli., Accurate proteomic measurements of absolute protein mass fractions in Escherichia coli allowed the characterization of proteome responses under > 60 diverse growth conditions from a coarse (groups of related proteins) to a fine (individual) protein level.

For the assessment of the precipitation state in aluminum-based alloys by transmission electron microscopy (TEM), the sample must have an orientation in the [100] direction of the matrix. TEMs equipped with objective lenses that are optimized for high resolution are mostly characterized by limited sample tilt angles. The required crystal orientation must thus be taken into account during sampling. A favorably oriented grain was chosen in a coarse-grained material using electron backscatter diffraction and prepared in a suitable direction applying the in-situ lift-out method in the focused ion beam device. After that, the final correction of the orientation in the TEM amounts to less than 12°.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

SummaryThe Mycobacterium tuberculosis (Mtb) complex comprises seven phylogenetically distinct human-adapted lineages exhibiting different geographical distribution and degrees of pathogenicity. Among these, Lineage 1 (L1) has been associated with low virulence whereas Lineage 2 (L2) has been linked to hyper-virulence, enhanced transmission and drug resistance. Here, we conducted multi-layer comparative analyses using whole genome sequencing data combined with quantitative transcriptomic and proteomic profiling of a set of L1 and L2 clinical strains, each grown under two different conditions in vitro. Our data revealed different degrees of correlation between transcript and protein abundances across clinical strains and functional gene categories, indicating variable levels of post-transcriptional regulation in the tested lineages. Contrasting genomic and gene expression data showed that the magnitude of the transcriptional and translational changes was proportional to the phylogenetic distance between strains, with one out of three single nucleotide polymorphisms leading to a transcriptional and/or translational change on average. We devised a new genome-scale transcriptional regulatory model and identified several master transcription factors, strongly linked to the sigma factor network, whose targets were differentially regulated between the two lineages. These differences resulted in a higher basal expression of DosR proteins and a stronger response to nitric oxide (NO) exposure in L2 compared to L1. These patterns are most likely responsible for the shorter NO-induced growth arrest in L2 observed. Given the limited genetic variation between strains, it appears that phenotypic differences in Mtb are substantially driven by differences in the regulation of biochemical networks through master transcriptional regulators.HighlightsProteomic and transcriptomic characterization of fully sequenced diverse L1 and L2 clinical isolates of Mtb.Post-transcriptional control mechanisms for regulatory and virulence genes are mitigated in Mtb L2.By applying a genome-scale transcriptional framework, DosR, Rv1985c, Lsr2 and Rv0691c are identified as master transcription factors responsible for differential target gene expression in L2 strains compared to L1.L1 and L2 DosR proteins respond differently to nitric oxide stress, thus determining a relevant phenotype.

Tungsten carbide-cobalt hard metal produced by additive manufacturing offers opportunities to meet the increasingly complex requirements of high-performance machining. Besides a high level of design freedom and the easy integration of functional properties, the additive manufacturing of hard metals also offers potential for cost savings and conservation of resources. A window of favorable process parameters for laser beam melting was established using commercially available carbide powder with 17 % Co content, which serves to build carbide samples by laser-based additive manufacturing. Compared to conventionally manufactured carbides, deviations can still be noticed with regard to microstructural and mechanical properties. However, bending strengths of > 1 000 MPa and fracture toughness in the range of 10–12 Mpa √m are promising for the future additive manufacturing of WCCo hard metals.

Genomic variation affects cellular networks by altering diverse molecular layers such as RNA levels, protein abundance, and post-translational protein modifications. However, it remains unclear how these different layers are affected by genetic polymorphisms and give rise to complex physiological phenotypes. To address these questions, we generated high-quality transcriptome, proteome, and phosphoproteome data for a panel of 112 genetically diverse yeast strains. While genetic effects on transcript abundances were generally transmitted to the protein level, we found a significant uncoupling of the transcript-protein relationship for certain protein classes, such as subunits of protein complexes. The additional phosphoproteomics data suggests that the same genetic locus often affects distinct sets of genes within each of these layers. In particular, QTLs tended to affect upstream regulatory proteins at the phosphorylation layer, whereas downstream pathway targets were typically affected at the transcript and protein abundance layers. Underscoring the importance of regulatory protein phosphorylation in linking genetic to phenotypic variation is the finding that the number of protein phosphosites associated with a given genetic locus was more predictive for its influence on cellular growth traits than the number of transcripts or proteins.This study shows how multi-layered molecular networks mediate the effects of genomic variants to more complex physiological traits and highlights the important role of protein phosphorylation in mediating these effects.

Contains fulltext : 208201.pdf (Publisher’s version ) (Closed access) BACKGROUND: Diffuse-type tenosynovial giant-cell tumour is a rare, locally aggressive, and difficult-to-treat soft tissue tumour. Clinical and surgical outcomes depend on multiple factors, including preoperative diagnostic assessment, the localisation and extent of disease, and possibly the choice of treatment modalities by orthopaedic surgeons. We did a retrospective cohort study to characterise global surgical treatment protocols, and assess surgical outcomes, complications, and functional results in patients with diffuse-type tenosynovial giant-cell tumours. METHODS: In this international, multicentre, retrospective cohort study, we included consecutive patients treated in 31 sarcoma reference centres between Jan 1, 1990, and Dec 31, 2017. Eligible patients were of any age and had histologically proven diffuse-type tenosynovial giant-cell tumour of large joints. Patient data were retrieved from the local databases of participating centres. Patients with localised-type tenosynovial giant-cell tumour were excluded. In the analysis, we only included patients with complete core criteria data regarding admission status, date of treatment, type of treatment at participating centre, and first local recurrence after treatment. We used a non-parametric method to estimate recurrence-free survival at 3, 5, and 10 years after initial surgical resection in a tertiary centre. We used a multivariate Cox regression model to estimate the effect of risk factors. We also present subgroup analyses of disease status at presentation (primary vs recurrent disease) and recurrence-free survival by surgery type (open surgery vs arthroscopic synovectomy), and prespecified risk factors were tested in a univariate and multivariable analyses, with an endpoint of first local recurrence after treatment in a tertiary centre. FINDINGS: Data collection for these analyses occurred between January, 2016, and May, 2018. We received the records of 1192 patients, of which 966 (81%) were surgically treated and had complete information on core criteria. 445 patients were admitted with therapy-naive disease of the knee and were primarily treated in a tertiary centre. Since patients with wait and see treatment do not have a starting date of treatment, these patients were excluded in the calculation of median follow-up time for all patients. For this calculation we used time of surgery as a starting date. 758 (64%) of 1192 patients had knee involvement and 628 (54%) of 1163 patients with complete data on type of surgery had one-staged open synovectomy. At a median follow-up of 54 months (IQR 27-97), recurrent disease developed in 425 (44%) of all 966 surgically treated cases, and recurrence-free survival was 62% (95% CI 59-65) at 3 years, 55% (51-58) at 5 years, and 40% (35-45) at 10 years. Surgical complications were reported in 105 (12%) of 906 patients who had complete data on surgical complications. Pain improved after surgical treatment in 255 (59%) of 434 patients and swelling improved in 328 (72%) of 453 patients who had complete data. INTERPRETATION: This study of patients with diffuse-type tenosynovial giant-cell tumour provides a comprehensive and up-to-date disease overview, assessing the clinical profile and management of the disease in multiple specialised referral centres. Surgical treatment of diffuse-type tenosynovial giant cell tumours is not a definitive treatment for every patient because it involves a high risk for local recurrent disease and a relatively high risk for postoperative complications. After surgical treatment in treatment-naive patients, risk factors for recurrent disease in individual patients were not identified in what we believe is the largest cohort to date. FUNDING: Daiichi Sankyo.

Summary Accurate classification of breast tumors is vital for patient management decisions and enables more precise cancer treatment. Here, we present a quantitative proteotyping approach based on sequential windowed acquisition of all theoretical fragment ion spectra (SWATH) mass spectrometry and establish key proteins for breast tumor classification. The study is based on 96 tissue samples representing five conventional breast cancer subtypes. SWATH proteotype patterns largely recapitulate these subtypes; however, they also reveal varying heterogeneity within the conventional subtypes, with triple negative tumors being the most heterogeneous. Proteins that contribute most strongly to the proteotype-based classification include INPP4B, CDK1, and ERBB2 and are associated with estrogen receptor (ER) status, tumor grade status, and HER2 status. Although these three key proteins exhibit high levels of correlation with transcript levels (R > 0.67), general correlation did not exceed R = 0.29, indicating the value of protein-level measurements of disease-regulated genes. Overall, this study highlights how cancer tissue proteotyping can lead to more accurate patient stratification., Graphical Abstract, Highlights • Proteotyping of 96 breast tumors by SWATH mass spectrometry • Three key proteins for breast tumor classification • Varying degrees of heterogeneity within conventional breast cancer subtypes • Generally modest correlation between protein and transcript levels in tumor tissue, Bouchal et al. explore and confirm the suitability of SWATH-MS for proteotyping of human tumor samples at relatively high throughput. Results indicate that proteotype-based classification resolves more variability than is apparent from conventional subtyping and potentially improves current classification.

In this manuscript we report about the realization and testing of a high-voltage electrochemical double layer capacitor (EDLC) prototype (IES prototype), which has been assembled using innovative electrode and electrolyte components. The IES prototype displays a nominal capacitance of 4 F, a maximum voltage of 3.2 V and its maximal energy and power are in the order of 37 Wh kg −1 and 65 kW kg −1 , respectively. Furthermore, it also displays good cycling stability, high capacitance retention after 80 h float test and acceptable self-discharge. Taking into account substantial improvements of the cell design and assembly procedure, the performance of the IES prototype indicates that the components utilized in this device might be suitable alternatives to the state-of-the-art materials used in high energy EDLCs.

As a result of their outstanding properties hard metals offer great potential in the tool industry. They are however expensive and geometrically limited when manufactured using conventional machining techniques. Additive manufacturing has the possibility to revolutionise the manufacture of such tools. The composition of hard metals consisting of a hard component within a binder phase in combination with laser based additive manufacturing can produce particular effects in the microstructural development of such materials. This article describes those particular microstructural developments which can be achieved in the powder metallurgical additive manufacturing of hard metals.

Microplastic pollution in floodplains and river channels in 14 locations at six sites along three rivers in Virginia was measured to test the hypotheses that microplastics concentrate in floodplains, exist as larger aggregates with other natural and synthetic particles, and may be different than ocean microplastics. The results show that (1) microplastic concentrations were generally just as high or higher in the floodplain than in the stream channel, (2) microplastics aggregated with natural sediment particles into the “heteroaggregates” predicted theoretically, (3) microplastics were larger in the floodplain than in the stream channel with a wider particle size distribution, (4) microplastic particles were 80 % fragments, 15 % spherical particles, and 5% fibers, and (5) chemically identified microplastics were composed of common packaging plastics that were heavily oxidized or hydrolyzed. The shape and chemical compositions of microplastic particles found was very similar to those observed in and around other rivers studied in the literature but different from the ocean environment. The floodplain could be used to capture river microplastics.

Members of the Mycobacterium tuberculosis complex (MTBC) are the causative agents of tuberculosis in a range of mammals, including humans. A key feature of MTBC pathogens is their high degree of genetic identity, yet distinct host tropism. Notably, while Mycobacterium bovis is highly virulent and pathogenic for cattle, the human pathogen M. tuberculosis is attenuated in cattle. Previous research also suggests that host preference amongst MTBC members has a basis in host innate immune responses. To explore MTBC host tropism, we present in-depth profiling of the MTBC reference strains M. bovis AF2122/97 and M. tuberculosis H37Rv at both the global transcriptional and translational level via RNA-sequencing and SWATH mass spectrometry. Furthermore, a bovine alveolar macrophage infection time course model was employed to investigate the shared and divergent host transcriptomic response to infection with M. tuberculosis or M. bovis. Significant differential expression of virulence-associated pathways between the two bacilli was revealed, including the ESX-1 secretion system. A divergent transcriptional response was observed between M. tuberculosis and M. bovis infection of bovine alveolar macrophages, in particular cytosolic DNA-sensing pathways at 48 hours post-infection, and highlights a distinct engagement of M. bovis with the bovine innate immune system. The work presented here therefore provides a basis for the identification of host innate immune mechanisms subverted by virulent host-adapted mycobacteria to promote their survival during the early stages of infection.ImportanceThe Mycobacterium tuberculosis complex (MTBC) includes the most important global pathogens for humans and animals, namely Mycobacterium tuberculosis and Mycobacterium bovis, respectively. These two exemplar mycobacterial pathogens share a high degree of genetic identity, but the molecular basis for their distinct host preference is unknown. In this work we integrated transcriptomic and proteomic analyses of the pathogens to elucidate global quantitative differences between them at the mRNA and protein level. We then integrated this data with transcriptome analysis of the bovine macrophage response to infection with either pathogen. Increased expression of the ESX-1 virulence system in M. bovis appeared a key driver of an increased cytosolic nucleic acid sensing and interferon response in bovine macrophages infected with M. bovis compared to M. tuberculosis. Our work demonstrates the specificity of host-pathogen interaction and how the subtle interplay between mycobacterial phenotype and host response may underpin host specificity amongst MTBC members.

Cell-surface proteins are of great biomedical importance, as demonstrated by the fact that 66% of approved human drugs listed in the DrugBank database target a cell-surface protein. Despite this biomedical relevance, there has been no comprehensive assessment of the human surfaceome, and only a fraction of the predicted 5,000 human transmembrane proteins have been shown to be located at the plasma membrane. To enable analysis of the human surfaceome, we developed the surfaceome predictor SURFY, based on machine learning. As a training set, we used experimentally verified high-confidence cell-surface proteins from the Cell Surface Protein Atlas (CSPA) and trained a random forest classifier on 131 features per protein and, specifically, per topological domain. SURFY was used to predict a human surfaceome of 2,886 proteins with an accuracy of 93.5%, which shows excellent overlap with known cell-surface protein classes (i.e., receptors). In deposited mRNA data, we found that between 543 and 1,100 surfaceome genes were expressed in cancer cell lines and maximally 1,700 surfaceome genes were expressed in embryonic stem cells and derivative lines. Thus, the surfaceome diversity depends on cell type and appears to be more dynamic than the nonsurface proteome. To make the predicted surfaceome readily accessible to the research community, we provide visualization tools for intuitive interrogation (wlab.ethz.ch/surfaceome). The in silico surfaceome enables the filtering of data generated by multiomics screens and supports the elucidation of the surfaceome nanoscale organization., Proceedings of the National Academy of Sciences of the United States of America, 115 (46), ISSN:0027-8424, ISSN:1091-6490

Eukaryotic ribosome precursors acquire translation competence in the cytoplasm through stepwise release of bound assembly factors, and proofreading of their functional centers. In case of the large subunit precursor (pre-60S), these essential steps include eviction of placeholders Arx1 and Mrt4 that prevent premature loading of the protein-folding machinery at the polypeptide exit tunnel (PET), and the ribosomal stalk, respectively. Here, we reveal that sequential ATPase and GTPase activities license release factors Rei1 and Yvh1 recruitment to the pre-60S in order to trigger Arx1 and Mrt4 removal. Drg1-ATPase activity extracts the C-terminal tail of Nog1 from the PET, enabling Rei1 to probe PET integrity, and then catalyze Arx1 release. Subsequently, GTPase hydrolysis stimulates Nog1 removal from the pre-60S, permitting Yvh1 to mediate Mrt4 release, and initiate ribosomal stalk assembly. Thus, Nog1 couples quality control and assembly of spatially distant functional centers during ribosome formation.

Zielsetzung: Das Ziel der vorliegenden Studie ist die Evaluation eines Versorgungsmanagementprogramms innerhalb der mhplus Betriebskrankenkasse (mhplus BKK) fur psychische und Verhaltensstorungen, das mittels eines telefonbasierten Ansatzes durchgefuhrt wurde. Methodik: Randomisierte kontrollierte Studie im Rahmen einer gesundheitsokonomischen Kosteneffektivitatsevaluation. Ergebnisse: 424 Teilnehmer und 114 Kontrollpersonen wurden in der Auswertung berucksichtigt. In der Interventionsgruppe (IG) konnte verglichen mit der Kontrollgruppe (KG) die Chance, innerhalb eines Jahres rehospitalisiert zu werden, statistisch signifikant nahezu halbiert werden (Odds Ratio 0,52; 95 % KI: 0,27 – 0,99). Die Zufriedenheit mit der mhplus BKK war in der IG statistisch signifikant hoher. Die durchschnittlichen Kosten pro Versichertem waren in der IG mit 3703 Euro niedriger als in der Kontrollgruppe (4057 Euro). Dieser Unterschied war statistisch nicht signifikant (p = 0,56). Schlussfolgerung: Die Studie belegt die Wirksamkeit eines Versorgungsmanagementprogramms fur psychische Erkrankungen innerhalb einer Krankenkasse. Aufgrund erster Kostenersparnisse ist das Programm als dauerhafte Mehrleistung der mhplus BKK eingefuhrt worden.

SummaryMycobacterium tuberculosis remains a health concern due to its ability to enter a non-replicative dormant state linked to drug resistance. Understanding transitions into and out of dormancy will inform therapeutic strategies. We implemented a universally applicable, label-free approach to estimate absolute cellular protein concentrations on a proteome-wide scale based on SWATH mass spectrometry. We applied this approach to examine proteomic reorganization of M. tuberculosis during exponential growth, hypoxia-induced dormancy, and resuscitation. The resulting data set covering >2,000 proteins reveals how protein biomass is distributed among cellular functions during these states. The stress-induced DosR regulon contributes 20% to cellular protein content during dormancy, whereas ribosomal proteins remain largely unchanged at 5%–7%. Absolute protein concentrations furthermore allow protein alterations to be translated into changes in maximal enzymatic reaction velocities, enhancing understanding of metabolic adaptations. Thus, global absolute protein measurements provide a quantitative description of microbial states, which can support the development of therapeutic interventions.

Background Granulomatous inflammation on transbronchial needle aspirates from mediastinal lymph nodes is an infrequent yet important finding. We determined associations between cytomorphological features and underlying aetiology in an area of high prevalence of HIV-infection and tuberculosis. Methods We identified cases with granulomatous inflammation on mediastinal aspirates from January 2003 to July 2010. Cytomorphological features were evaluated and graded according to a simple and reproducible system including the presence, quality (discrete or vague), and number (≤5 or more) of granulomas as well as the presence of necrosis, lymphocytes, multinucleated giant cells, and neutrophils. Results In 81 patients (36 male, 9 HIV-positive) the final diagnosis was tuberculosis in 37 (46%), sarcoidosis in 40 (49%), fibrosing mediastinitis in 1 (1%), and unknown in 3 (4%). The presence of necrosis (P

Entscheidend fur den Erfolg der Strahlentherapie ist die zeitgerechte Applikation ohne toxizitatsbedingte Pausen; eine effektive Supportivtherapie ist obligat. Es werden Prophylaxe und Therapie akuter/subakuter Strahlenfolgen beschrieben. Von 1995 bis 2011 publizierte Studien wurden systematisch analysiert und die Leitlinie „Supportive Masnahmen der Radioonkologie“ der Deutschen Gesellschaft fur Radioonkologie erstellt. Prophylaxe und Therapie der (sub)akuten Strahlenreaktion werden fur Bestrahlungen des Zerebrums, im Kopf-Hals-Bereich, der Lunge und der Haut dargestellt. Strahlentherapiepausen konnen durch leitliniengerechte Supportivtherapie vermieden werden. Bei Verdacht auf Nebenwirkungen sollten die Patienten in der Radioonkologie vorgestellt werden.

Targeted proteomics by selected/multiple reaction monitoring (S/MRM) or, on a larger scale, by SWATH (sequential window acquisition of all theoretical spectra) MS (mass spectrometry) typically relies on spectral reference libraries for peptide identification. Quality and coverage of these libraries are therefore of crucial importance for the performance of the methods. Here we present a detailed protocol that has been successfully used to build high-quality, extensive reference libraries supporting targeted proteomics by SWATH MS. We describe each step of the process, including data acquisition by discovery proteomics, assertion of peptide-spectrum matches (PSMs), generation of consensus spectra and compilation of MS coordinates that uniquely define each targeted peptide. Crucial steps such as false discovery rate (FDR) control, retention time normalization and handling of post-translationally modified peptides are detailed. Finally, we show how to use the library to extract SWATH data with the open-source software Skyline. The protocol takes 2-3 d to complete, depending on the extent of the library and the computational resources available.