Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-View Spatial Aggregation Framework for Joint Localization and Segmentation of Organs at Risk in Head and Neck CT Images

Accurate segmentation of organs at risk (OARs) from head and neck (H&N) CT images is crucial for effective H&N cancer radiotherapy. However, the existing deep learning methods are often not trained in an end-to-end fashion, i.e., they independently predetermine the regions of target organs before organ segmentation, causing limited information sharing between related tasks and thus leading to suboptimal segmentation results. Furthermore, when conventional segmentation network is used to segment all the OARs simultaneously, the results often favor big OARs over small OARs. Thus, the existing methods often train a specific model for each OAR, ignoring the correlation between different segmentation tasks. To address these issues, we propose a new multi-view spatial aggregation framework for joint localization and segmentation of multiple OARs using H&N CT images. The core of our framework is a proposed region-of-interest (ROI)-based fine-grained representation convolutional neural network (CNN), which is used to generate multi-OAR probability maps from each 2D view (i.e., axial, coronal, and sagittal view) of CT images. Specifically, our ROI-based fine-grained representation CNN (1) unifies the OARs localization and segmentation tasks and trains them in an end-to-end fashion, and (2) improves the segmentation results of various-sized OARs via a novel ROI-based fine-grained representation. Our multi-view spatial aggregation framework then spatially aggregates and assembles the generated multi-view multi-OAR probability maps to segment all the OARs simultaneously. We evaluate our framework using two sets of H&N CT images and achieve competitive and highly robust segmentation performance for OARs of various sizes.
Investigation of Doubly Salient Structure for Permanent Magnet Vernier Machines Using Flux Modulation Effects

Recently, the permanent magnet vernier machine (PMVM) is studied extensively because of its merits such as the high torque density. Similar to the magnetic gears, the PMVM operates on the principle of flux modulation. However, there is a distinct difference in between the two as unlike the magnetic gear, in case of PMVM, the winding MMF harmonics rotates with different speed as that of the fundamental. As a result, these harmonics are capable of making a working magnetic field by interacting with different permeance harmonics. Therefore, this paper aims to provide an analytical explanation of this whole process, which is helpful to understand the effect of the flux modulation on the output torque. Furthermore, using the analytical formulation, this work finds the optimal geometric parameters which maximize the working magnetic field and hence the torque. A detailed analysis of the PMVM with the doubly salient structure is studied and the performance is analyzed using the finite element method (FEM) and the experimental setup. The FEM and experimental results verify the maximum torque production by using the optimal geometric parameters in the PMVM modeling, obtained using the analytical formulation.
Hepatocellular carcinoma surveillance in Australia: time to improve the diagnosis of cirrhosis and use liver ultrasound

Hepatocellular carcinoma (HCC) is an important cause of cancer death in Australia (Box 1). A 2019 report on cancer in Australia, based on data from 1982 to 2015, showed that liver cancer (90% HCC) had the second largest increase (378%) in age‐standardised incidence rates from 1.8 to 8.6 per 100 000 population.1 Unfortunately, there was a matching threefold increase in liver cancer mortality rate from 2.3 deaths to 7.0 per 100 000 population. This was the largest increase for any cancer and, unlike other cancers, is likely an underestimate owing to under‐reporting by some state cancer registries.2 An Australia‐wide epidemiological study found survival from HCC had improved from a median of 2.1 months (95% CI, 1.6–2.6 months) between 1982 and 1984 to 12.1 months (95% CI, 11.2–13.0 months) between 2010 and 2014 (P < 0.001). 3 However, survival remains poor and HCC is the only low survival cancer of all the cancers that are rapidly increasing in incidence in Australia.1 The average cost to treat HCC is $50 000 and liver transplantation costs $166 000.4, 5 Therefore, with incidence showing no signs of slowing, health system costs will continue to increase substantially in the absence of preventive actions. This article reviews the present evidence for liver ultrasound surveillance in patients with cirrhosis, a major risk factor for the development of HCC.
Draft Genome Resource for Macrophomina phaseolina associated with Charcoal Rot in Sorghum.

Macrophomina phaseolina is a soil-borne phytopathogenic fungus, which causes charcoal rot in several plant species including sorghum. We constructed a draft genome of M. phaseolina isolate BRIP 70780a from sorghum, using long-read native DNA from MinION Sequencing (Oxford Nanopore Technology), which was error-corrected using short-read Illumina MiSeq reads. The draft genome, consisting of 22 contigs with an N50 of 4,257,441 bp, 99.3% complete Benchmarking Universal Single-Copy Orthologs (BUSCOs), and 14,471 genes is a valuable resource to aid future studies in population genomics and molecular diagnostic marker development for rapid detection of the pathogen.
Epidemiology of Staphylococcus epidermidis Keratitis

Purposes : Staphylococcus epidermidis is a causative agent of bacterial keratitis and the authors performed an epidemiologic study to identify the risk factors, clinical features and treatment results. Methods : Epidemiologic study on Staphylococcus epidermidis keratitis, which were confirmed by cultures in 6 university hospitals, was performed prospectively under the identical protocol. Results : Seventeen cases of Staphylococcus epidermidis keratitis were diagnosed by culture with corneal scraping and comprised 4.1% of 401 cases of confirmed bacterial keratitis. Male patients were affected more than female patients and the highest prevalent age was in the seventies. Most of their occupation was farming. The most prevalent season was fall and it mostly occurred after corneal trauma. Conclusions : Staphylococcus epidermidis keratitis usually occurred in a relatively old age group followed by corneal trauma. Its prevention along with early and proper antimicrobial therapy based on sensitivity results is important.
MicroRNA-34a suppresses neuronal apoptosis and alleviates microglia inflammation by negatively targeting the Notch pathway in spinal cord injury.

OBJECTIVE The purpose of this study was to investigate role of inhibition of microRNA-34a (miR-34a) in neural damage and repair after spinal cord injury, and to explore the underlying mechanism. MATERIALS AND METHODS In BV2 microglia, we conducted classical activation using lipopolysaccharide (LPS) and pre-treatment using miR-34a mimics. The expressions of miR-34a, Notch 1, and Jagged 1 were detected by quantitative Real Time-Polymerase Chain Reaction (qRT-PCR). Moreover, the protein expressions of inflammatory microglia markers were evaluated by Western blotting. In vivo, SCI model was successfully established in rats. Subsequently, the expression levels of miR-34a, Notch 1, and Jagged 1 levels within 1 week were measured by qRT-PCR. Meanwhile, protein expressions of inflammatory mediators were determined by enzyme-linked immunosorbent assay (ELISA) assay. Immunofluorescence was conducted to display the activation degree of microglia and residual neural structure. Furthermore, locomotor function recovery was estimated using BBB rating scale. RESULTS Compared with the only LPS-activated group, pre-treatment of miR-34a mimics significantly decreased the expressions of Notch 1 and Jagged 1. Similarly, the protein expressions of CD11b and iNOS were significantly down-regulated. In vivo, the levels of Notch 1 and Jagged 1 within 1 week increased significantly, while miR-34a was negatively regulated following spinal cord injury (SCI). Furthermore, the contents of interleukin-1 beta (IL-1β) and IL-6 were reduced with the treatment of miR-34a mimics when compared with SCI group. With the treatment of miR-34a, the number of inflammatory microglia decreased significantly, and the remaining neural structure was similarly improved. In addition, locomotor function recovery of hindlimbs in rats was significantly ameliorated after the administration of miR-34a mimics. CONCLUSIONS Increase of miR-34a suppresses neuronal apoptosis and alleviates microglia inflammation by negatively targeting the Notch pathway, thereby improving neural recovery and locomotor function.
Cryo-EM structure of the Shigella type III needle complex

The Type III Secretion Systems (T3SS) needle complex is a conserved syringe-shaped protein translocation nanomachine with a mass of about 3.5 MDa essential for the survival and virulence of many Gram-negative bacterial pathogens. This system is composed of a membrane-embedded basal body and an extracellular needle that deliver effector proteins into host cells. High-resolution structures of the T3SS from different organisms and infection stages are needed to understand the underlying molecular mechanisms of effector translocation. Here, we present the cryo-electron microscopy structure of the isolated Shigella T3SS needle complex. The inner membrane (IM) region of the basal body adopts 24-fold rotational symmetry and forms a channel system that connects the bacterial periplasm with the export apparatus cage. The secretin oligomer adopts a heterogeneous architecture with 16- and 15-fold cyclic symmetry in the periplasmic N-terminal connector and C-terminal outer membrane ring, respectively. Two out of three IM subunits bind the secretin connector via a β-sheet augmentation. The cryo-EM map also reveals the helical architecture of the export apparatus core, the inner rod, the needle and their intervening interfaces.
FADS Genetic Variants in Taiwanese Modify Association of DHA Intake and Its Proportions in Human Milk

Our objective was to determine how docosahexaenoic acid (DHA) proportions in human milk are modulated by maternal FADS gene variants and dietary intake in Taiwanese women. Inclusion criteria included being healthy, 20–40 y old, having had a full-term baby that they intended to breast feed for at least 1 month, and willingness to participate in this study. Intake of DHA was assessed by food frequency questionnaire and fatty acids were analyzed in human milk samples collected 3–4 weeks postpartum. Based on multiple linear regression of data from 164 mothers that completed this study, there was 0.28% (FA%) reduction in milk DHA in high versus low genetic risk (stratified by whether minor allele numbers were ≥ 3 in rs1535 and rs174448) and 0.45% reduction in low versus high intake (stratified by whether DHA intake reached 200 mg/d). There was a significant gene–diet interaction; mothers with low genetic risk only had high milk DHA proportions with high DHA intake, whereas for mothers with high genetic risk, dietary effects were quite limited. Therefore, for FADS single nucleotide polymorphism in Taiwanese women, increasing DHA intake did not correct low milk DHA proportions in those with a high-risk genotype. Diet only conferred benefits to those with a low-risk genotype. Trial registration: This trial was retrospectively registered (Feb 12, 2019) in ClinicalTrials.gov (No. NCT03842891, https://clinicaltrials.gov/ct2/show/NCT03842891).
Monostability and Multistability for Almost-Periodic Solutions of Fractional-Order Neural Networks With Unsaturating Piecewise Linear Activation Functions

Since the unsaturating activation function is unbounded, more complex dynamics may exist in neural networks with this kind of activation function. In this article, monostability and multistability results of almost-periodic solutions are developed for fractional-order neural networks with unsaturating piecewise linear activation functions. Some globally Mittag-Leffler attractive sets are given, and the existence of globally Mittag-Leffler stable almost-periodic solution is demonstrated by using Ascoli–Arzela theorem. In particular, some sufficient conditions are provided to ascertain the multistability of almost-periodic solutions based on locally positively invariant set. It shows that there exists an almost-periodic solution in each positively invariant set, and all trajectories converge to this periodic trajectory in that rectangular area. Two illustrative examples are provided to demonstrate the effectiveness of the proposed sufficient criteria.
Surgical procedures in patients aged 90 years and older.

: During the past five years 75 patients aged 90 years or more had 85 major surgical procedures at the Metropolitan Nashville General and Vanderbilt University hospitals. The most common operation was exploratory laparotomy. The second was lower extremity amputation for peripheral vascular disease and/or gangrene. Fifty-seven percent had general endotracheal anesthesia. Associated medical problems were common, and included congestive heart failure (24%), hypertension (21%), diabetes mellitus (13%), chronic arrhythmias (9%), history of myocardial infarction (8%), and history of cerebrovascular accident (5%). Eleven patients (13.4%), six of whom had general anesthesia, died after operation. Of these, two had postoperative pneumonia, two did not recover from bowel perforation and peritonitis, one had a postoperative myocardial infarction, another had a cerebrovascular accident, and one had sepsis. One patient's sudden death was likely due to myocardial infarction or pulmonary embolus. The other three deaths occurred in patients with extensive carcinomas (gallbladder carcinoma in one and widely metastatic carcinoma of unknown origin in two). These three patients died of the disease for which they were operated upon when the operation failed to alter its course. When surgical procedures are necessary to prolong and/or improve the quality of life in elderly patients, these procedures may be done in most cases with acceptable results.
Memristors for Neuromorphic Circuits and Artificial Intelligence Applications

Artificial Intelligence has found many applications in the last decade due to increased computing power. Artificial Neural Networks are inspired in the brain structure and consist in the interconnection of artificial neurons through artificial synapses in the so-called Deep Neural Networks (DNNs). Training these systems requires huge amounts of data and, after the network is trained, it can recognize unforeseen data and provide useful information. As far as the training is concerned, we can distinguish between supervised and unsupervised learning. The former requires labelled data and is based on the iterative minimization of the output error using the stochastic gradient descent method followed by the recalculation of the strength of the synaptic connections (weights) with the backpropagation algorithm. On the other hand, unsupervised learning does not require data labeling and it is not based on explicit output error minimization. Conventional ANNs can function with supervised learning algorithms (perceptrons, multi-layer perceptrons, convolutional networks, etc.) but also with unsupervised learning rules (Kohonen networks, self-organizing maps, etc.). Besides, another type of neural networks are the so-called Spiking Neural Networks (SNNs) in which learning takes place through the superposition of voltage spikes launched by the neurons. Their behavior is much closer to the brain functioning mechanisms they can be used with supervised and unsupervised learning rules. Since learning and inference is based on short voltage spikes, energy efficiency improves substantially. Up to this moment, all these ANNs (spiking and conventional) have been implemented as software tools running on conventional computing units based on the von Neumann architecture. However, this approach reaches important limits due to the required computing power, physical size and energy consumption. This is particularly true for applications at the edge of the internet. Thus, there is an increasing interest in developing AI tools directly implemented in hardware for this type of applications. The first hardware demonstrations have been based on Complementary Metal-Oxide-Semiconductor (CMOS) circuits and specific communication protocols. However, to further increase training speed andenergy efficiency while reducing the system size, the combination of CMOS neuron circuits with memristor synapses is now being explored. It has also been pointed out that the short time non-volatility of some memristors may even allow fabricating purely memristive ANNs. The memristor is a new device (first demonstrated in solid-state in 2008) which behaves as a resistor with memory and which has been shown to have potentiation and depression properties similar to those of biological synapses. In this Special Issue, we explore the state of the art of neuromorphic circuits implementing neural networks with memristors for AI applications.
Bladder Cancer Chemosensitivity Is Affected by Paraoxonase-2 Expression

The goal of the current study was to identify potential roles of paraoxonase-2 in bladder carcinogenesis. T24 bladder cancer cells were transfected with plasmids inducing paraoxonase-2 silencing or overexpression. Upon the selection of clones stably down- or upregulating paraoxonase-2, cell proliferation, migration, and the production of reactive oxygen species were evaluated, before and after treatment with cisplatin and gemcitabine, used alone or in combination. The activity levels of both caspase-3 and caspase-8 were also analyzed. shRNA-mediated gene silencing and the overexpression of paraoxonase-2 revealed that the enzyme was able to promote both the proliferation and migration of T24 cells. Moreover, the knockdown of paraoxonase-2 was significantly associated with a reduced cell viability of T24 cells treated with chemotherapeutic drugs and led to both an increase of reactive oxygen species production and caspase-3 and caspase-8 activation. Conversely, under treatment with anti-neoplastic compounds, a higher proliferative capacity was found in T24 cells overexpressing paraoxonase-2 compared with controls. In addition, upon enzyme upregulation, both the production of reactive oxygen species and activation of caspase-3 and caspase-8 were reduced. Although further analyses will be required to fully understand the involvement of paraoxonase-2 in bladder tumorigenesis and in mechanisms leading to the development of chemoresistance, the data reported in this study seem to demonstrate that the enzyme could exert a great impact on tumor progression and susceptibility to chemotherapy, thus suggesting paraoxonase-2 as a novel and interesting molecular target for effective bladder cancer treatment.
Nutritional ketosis as an intervention to relieve astrogliosis: Possible therapeutic applications in the treatment of neurodegenerative and neuroprogressive disorders

Abstract Nutritional ketosis, induced via either the classical ketogenic diet or the use of emulsified medium-chain triglycerides, is an established treatment for pharmaceutical resistant epilepsy in children and more recently in adults. In addition, the use of oral ketogenic compounds, fractionated coconut oil, very low carbohydrate intake, or ketone monoester supplementation has been reported to be potentially helpful in mild cognitive impairment, Parkinson’s disease, schizophrenia, bipolar disorder, and autistic spectrum disorder. In these and other neurodegenerative and neuroprogressive disorders, there are detrimental effects of oxidative stress, mitochondrial dysfunction, and neuroinflammation on neuronal function. However, they also adversely impact on neurone–glia interactions, disrupting the role of microglia and astrocytes in central nervous system (CNS) homeostasis. Astrocytes are the main site of CNS fatty acid oxidation; the resulting ketone bodies constitute an important source of oxidative fuel for neurones in an environment of glucose restriction. Importantly, the lactate shuttle between astrocytes and neurones is dependent on glycogenolysis and glycolysis, resulting from the fact that the astrocytic filopodia responsible for lactate release are too narrow to accommodate mitochondria. The entry into the CNS of ketone bodies and fatty acids, as a result of nutritional ketosis, has effects on the astrocytic glutamate–glutamine cycle, glutamate synthase activity, and on the function of vesicular glutamate transporters, EAAT, Na+, K+-ATPase, Kir4.1, aquaporin-4, Cx34 and KATP channels, as well as on astrogliosis. These mechanisms are detailed and it is suggested that they would tend to mitigate the changes seen in many neurodegenerative and neuroprogressive disorders. Hence, it is hypothesized that nutritional ketosis may have therapeutic applications in such disorders.
Life has given me suffering and desire - A study of older men's lives after the loss of their life partners.

BACKGROUND AND AIM All human beings have the need to feel connected with others. However, researchers have found that for those aged 80+, loneliness markedly increases and that such loneliness is often linked to life changes or the loss of a close relative. The loss of a life partner is considered to have a greater impact on men's identify, social engagement and management of life. The aim of this study was to deepen understanding of older (80+) men's life after the loss of their life partners. THEORETICAL FRAMEWORK Caring science and Eriksson's theory of caritative caring form the theoretical base for the study and its interpretative framework. The central concepts are suffering of life and desire of life. INFORMANTS, METHODOLOGY AND METHODS A total of five men aged 81-91 gave thereby consent for participation in the study. Emanating from hermeneutical methodology, qualitative deep interviews with a narrative approach were used to collect data. Thereafter, a six-step qualitative thematic analysis in accordance with Braun and Clarke was used to analyse the text. INTERPRETATION AND CONCLUSION Four themes emerged: reconciliation with one's lived life, living in the present with uncertainty about the future, a reorientation in life including new living conditions and living with the hope of finding a new life partner and feeling loved. We found that loss can lead to suffering in life. The life can be filled with loneliness, emptiness, life weariness and an absence of desire, hope and longing. Yet there is a vitality in suffering that enables to find new meaning contexts and desire for life. Here, the fundamental choice underpinning the movement between life suffering and desire for life is comprised of reconciliation with one's lived life, living in the present, daily habits and routines, being seen, participation, love and thoughtfulness.