3D CATBraTS: Channel Attention Transformer for Brain Tumour Semantic Segmentation

Brain tumour diagnosis is a challenging task yet crucial for planning treatments to stop or slow the growth of a tumour. In the last decade, there has been a dramatic increase in the use of convolutional neural networks (CNN) for their high performance in the automatic segmentation of tumours in medical images. More recently, Vision Transformer (ViT) has become a central focus of medical imaging for its robustness and efficiency when compared to CNNs. In this paper, we propose a novel 3D transformer named 3D CATBraTS for brain tumour semantic segmentation on magnetic resonance images (MRIs) based on the state-of-the-art Swin transformer with a modified CNN-encoder architecture using residual blocks and a channel attention module. The proposed approach is evaluated on the BraTS 2021 dataset and achieved quantitative measures of the mean Dice similarity coefficient (DSC) that surpasses the current state-of-the-art approaches in the validation phase

Milling cutting tool diagnosis using comparisons of the excitation identified by cepstral techniques

This paper investigates the diagnosis of cutting tools in a milling operation using vibration signals and proposes a signal processing algorithm to achieve that. In the proposed algorithm, the impulse response of the measured vibration signal is firstly identified using the random decrement technique. This is then converted to a cepstrum and subtracted from the measured signal in the quefrency domain using the additive properties of cepstra. The residual signal representing the forcing function is then transformed back into the time domain using the inverse cepstrum. Finally the power spectral density is estimated, and a comparison is made between the different states of the cutting tool. For a good estimation of the force, four measurement points are used, and the identified excitation sources are then averaged. By comparing the spectra of the forcing functions, the efficiency of the method is demonstrated, and the faulty case is clearly distinguished from the fault-free case. This was not the case with the original response signals

Impact of hemodialysis on P-wave amplitude, duration, and dispersion

Atrial fibrillation (AF) is a frequent arrhythmia in patients undergoing hemodialysis (HD). P wave duration (PWdu) and P wave dispersion (PWdi) have been shown to be predictors of emerging AF in different clinical conditions. We sought to study the impact of HD on PWdu, PWdi, and P wave amplitude in a cohort of patients undergoing HD. Seventeen patients (8 men, 31±10 years) were studied. Echocardiography parameters, the sum of the amplitude of P waves in all 12 ECG leads (SP), mean PWdu, and PWdi, along with a host of other parameters (body weight, heart rate, electrolytes and hemoglobin/hematochrit) were measured 1/2h, before and after, HD. SP increased (11.8±3.9 vs 15.3±4.0 mm, p = 0.004), mean PWdu remained stable (82.7±11.1 vs 81.6±10.5 ms, p = 0.606), PWdi decreased (51.7±19.1 vs 41.7±19.1 ms, p = 0.03), and left atrial dimension decreased (37.96±3.90 vs 30.62±3.38 mm, p = 0.0001), after HD. The change in PWdi correlated with fluid removed by HD (r = -0.55, p = 0.022). Re-measurements of P-wave parameters in a random group of 11 of the 17 patients revealed augmented SP (p = 0.01), and stable mean PWdu (p = 0.36), and PWdi (p = 0.31), after HD. Fluid removed by HD leads to an increase in SP, a stable mean PWdu, and decrease (or stability on re-measurement in a subgroup of patients) in PWdi. Stability of PWdu may be due to the effects of augmentation of the P-wave amplitude and the reduction of the left atrial volume, cancelling each other. Variability of PWdi may stem from the occasional impossibility to measure PWdu (or measure it correctly) in minute P-waves in certain ECG leads, which in turn profoundly affects the PWdi

Structural basis of second-generation HIV integrase inhibitor action and viral resistance

Despite worldwide prescription, the mechanistic basis for superiority of second-generation HIV integrase (IN) strand transfer inhibitors (INSTIs) is poorly understood. We use single-particle cryo-electron microscopy to visualize the mode of action of the advanced INSTIs dolutegravir and bictegravir at near atomic resolution. Q148H/G140S amino acid substitutions in IN that pervade clinical INSTI failure perturb optimal magnesium ion coordination in the enzyme active site. The expanded chemical scaffolds of second-generation compounds mediate interactions with the protein backbone, which are critical for antagonizing Q148H/G140S mutant virus. Our results reveal that binding to magnesium ions underpins a fundamental weakness of the INSTI pharmacophore that is exploited by the virus to engender resistance and provide a structural framework for the development of this important class of anti-HIV/AIDS therapeutics

The structural basis for Z α1-antitrypsin polymerization in the liver

The serpinopathies are among a diverse set of conformational diseases that involve the aberrant self-association of proteins into ordered aggregates. α1-Antitrypsin deficiency is the archetypal serpinopathy and results from the formation and deposition of mutant forms of α1-antitrypsin as “polymer” chains in liver tissue. No detailed structural analysis has been performed of this material. Moreover, there is little information on the relevance of well-studied artificially induced polymers to these disease-associated molecules. We have isolated polymers from the liver tissue of Z α1-antitrypsin homozygotes (E342K) who have undergone transplantation, labeled them using a Fab fragment, and performed single-particle analysis of negative-stain electron micrographs. The data show structural equivalence between heat-induced and ex vivo polymers and that the intersubunit linkage is best explained by a carboxyl-terminal domain swap between molecules of α1-antitrypsin

Stapling and Section of the Nasogastric Tube during Sleeve Gastrectomy: How to Prevent and Recover?

Bariatric surgery has become an integral part of morbid obesity treatment with well-defined indications. Some complications, specific or not, due to laparoscopic sleeve gastrectomy (LSG) procedure have recently been described. We report a rare complication unpublished to date: a nasogastric section during great gastric curve stapling. A 44-year-old woman suffered of severe obesity (BMI 36.6 kg/m2) with failure of medical treatments for years. According to already published technique, a LSG was performed. Six hours postoperatively, a nurse removed the nasogastric tube according to the local protocol and the nasogastric tube was abnormally short, with staples at its extremity. Surgery was performed with peroperative endoscopy. In conclusion, this is the first publication of a nasogastric section during LSG. Therefore we report this case and propose a solution to prevent its occurrence. To avoid this kind of accident, we now systematically insert the nasogastric tube by mouth through a Guedel cannula. Then, to insert the calibrating bougie, we entirely withdraw the nasogastric tube

Why alternative teenagers self-harm: exploring the link between non-suicidal self-injury, attempted suicide and adolescent identity

Background: The term ‘self-harm’ encompasses both attempted suicide and non-suicidal self-injury (NSSI). Specific adolescent subpopulations such as ethnic or sexual minorities, and more controversially, those who identify as ‘Alternative’ (Goth, Emo) have been proposed as being more likely to self-harm, while other groups such as ‘Jocks’ are linked with protective coping behaviours (for example exercise). NSSI has autonomic (it reduces negative emotions) and social (it communicates distress or facilitates group ‘bonding’) functions. This study explores the links between such aspects of self-harm, primarily NSSI, and youth subculture.<p></p> Methods: An anonymous survey was carried out of 452 15 year old German school students. Measures included: identification with different youth cultures, i.e. Alternative (Goth, Emo, Punk), Nerd (academic) or Jock (athletic); social background, e.g. socioeconomic status; and experience of victimisation. Self-harm (suicide and NSSI) was assessed using Self-harm Behavior Questionnaire and the Functional Assessment of Self-Mutilation (FASM).<p></p> Results: An “Alternative” identity was directly (r ≈ 0.3) and a “Jock” identity inversely (r ≈ -0.1) correlated with self-harm. “Alternative” teenagers self-injured more frequently (NSSI 45.5% vs. 18.8%), repeatedly self-injured, and were 4–8 times more likely to attempt suicide (even after adjusting for social background) than their non-Alternative peers. They were also more likely to self-injure for autonomic, communicative and social reasons than other adolescents.<p></p> Conclusions: About half of ‘Alternative’ adolescents’ self-injure, primarily to regulate emotions and communicate distress. However, a minority self-injure to reinforce their group identity, i.e. ‘To feel more a part of a group’

Structural and functional annotation of the porcine immunome

Background: The domestic pig is known as an excellent model for human immunology and the two species share many pathogens. Susceptibility to infectious disease is one of the major constraints on swine performance, yet the structure and function of genes comprising the pig immunome are not well-characterized. The completion of the pig genome provides the opportunity to annotate the pig immunome, and compare and contrast pig and human immune systems.[br/] Results: The Immune Response Annotation Group (IRAG) used computational curation and manual annotation of the swine genome assembly 10.2 (Sscrofa10.2) to refine the currently available automated annotation of 1,369 immunity-related genes through sequence-based comparison to genes in other species. Within these genes, we annotated 3,472 transcripts. Annotation provided evidence for gene expansions in several immune response families, and identified artiodactyl-specific expansions in the cathelicidin and type 1 Interferon families. We found gene duplications for 18 genes, including 13 immune response genes and five non-immune response genes discovered in the annotation process. Manual annotation provided evidence for many new alternative splice variants and 8 gene duplications. Over 1,100 transcripts without porcine sequence evidence were detected using cross-species annotation. We used a functional approach to discover and accurately annotate porcine immune response genes. A co-expression clustering analysis of transcriptomic data from selected experimental infections or immune stimulations of blood, macrophages or lymph nodes identified a large cluster of genes that exhibited a correlated positive response upon infection across multiple pathogens or immune stimuli. Interestingly, this gene cluster (cluster 4) is enriched for known general human immune response genes, yet contains many un-annotated porcine genes. A phylogenetic analysis of the encoded proteins of cluster 4 genes showed that 15% exhibited an accelerated evolution as compared to 4.1% across the entire genome.[br/] Conclusions: This extensive annotation dramatically extends the genome-based knowledge of the molecular genetics and structure of a major portion of the porcine immunome. Our complementary functional approach using co-expression during immune response has provided new putative immune response annotation for over 500 porcine genes. Our phylogenetic analysis of this core immunome cluster confirms rapid evolutionary change in this set of genes, and that, as in other species, such genes are important components of the pig’s adaptation to pathogen challenge over evolutionary time. These comprehensive and integrated analyses increase the value of the porcine genome sequence and provide important tools for global analyses and data-mining of the porcine immune response

Agouti Revisited: Transcript Quantification of the ASIP Gene in Bovine Tissues Related to Protein Expression and Localization

Beside its role in melanogenesis, the agouti signaling protein (ASIP) has been related to obesity. The potentially crucial role in adipocyte development makes it a tempting candidate for economic relevant, fat related traits in farm animals. The objective of our study was to characterize the mRNA expression of different ASIP transcripts and of putative targets in different bovine tissues, as well as to study consequences on protein abundance and localization. ASIP mRNA abundance was determined by RT-qPCR in adipose and further tissues of cattle representing different breeds and crosses. ASIP mRNA was up-regulated more than 9-fold in intramuscular fat of Japanese Black cattle compared to Holstein (p<0.001). Further analyses revealed that a transposon-derived transcript was solely responsible for the increased ASIP mRNA abundance. This transcript was observed in single individuals of different breeds indicating a wide spread occurrence of this insertion at the ASIP locus in cattle. The protein was detected in different adipose tissues, skin, lung and liver, but not in skeletal muscle by Western blot with a bovine-specific ASIP antibody. However, the protein abundance was not related to the observed ASIP mRNA over-expression. Immuno-histochemical analyses revealed a putative nuclear localization of ASIP additionally to the expected cytosolic signal in different cell types. The expression of melanocortin receptors (MCR) 1 to 5 as potential targets for ASIP was analyzed by RT-PCR in subcutaneous fat. Only MC1R and MC4R were detected indicating a similar receptor expression like in human adipose tissue. Our results provide evidence for a widespread expression of ASIP in bovine tissues at mRNA and, for the first time, at protein level. ASIP protein is detectable in adipocytes as well as in further cells of adipose tissue. We generated a basis for a more detailed investigation of ASIP function in peripheral tissues of various mammalian species