Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Radiomic Models Based on Low-Dose and Standard-Dose CT for Prediction of Adenocarcinomas and Benign Lesions in Solid Pulmonary Nodules

Objectives This study aimed to develop radiomic models based on low-dose CT (LDCT) and standard-dose CT to distinguish adenocarcinomas from benign lesions in patients with solid solitary pulmonary nodules and compare the performance among these radiomic models and Lung CT Screening Reporting and Data System (Lung-RADS). The reproducibility of radiomic features between LDCT and standard-dose CT were also evaluated. Methods A total of 141 consecutive pathologically confirmed solid solitary pulmonary nodules were enrolled including 50 adenocarcinomas and 48 benign nodules in primary cohort and 22 adenocarcinomas and 21 benign nodules in validation cohort. LDCT and standard-dose CT scans were conducted using same acquisition parameters and reconstruction method except for radiation dose. All nodules were automatically segmented and 104 original radiomic features were extracted. The concordance correlation coefficient was used to quantify reproducibility of radiomic features between LDCT and standard-dose CT. Radiomic features were selected to build radiomic signature, and clinical characteristics and radiomic signature were combined to develop radiomic nomogram for LDCT and standard-dose CT, respectively. The performance of radiomic models and Lung-RADS was assessed by area under curve (AUC) of receiver operating characteristic curve, sensitivity, and specificity. Results Shape and first order features, and neighboring gray tone difference matrix features were highly reproducible between LDCT and standard-dose CT. No significant differences of AUCs were found among radiomic signature and nomogram of LDCT and standard-dose CT in both primary and validation cohort (0.915 vs. 0.919 vs. 0.898 vs. 0.909 and 0.976 vs. 0.976 vs. 0.985 vs. 0.987, respectively). These radiomic models had higher specificity than Lung-RADS (all correct P < 0.05), while there were no significant differences of sensitivity between Lung-RADS and radiomic models. Conclusions The diagnostic performance of LDCT-based radiomic models to differentiate adenocarcinomas from benign lesions in solid pulmonary nodules were equivalent to that of standard-dose CT. The LDCT-based radiomic model with higher specificity and lower false-positive rate than Lung-RADS might help reduce overdiagnosis and overtreatment of solid pulmonary nodules in lung cancer screening.
Automatic Detection and Classification of Focal Liver Lesions Based on Deep Convolutional Neural Networks: A Preliminary Study

With the increasing daily workload of physicians, computer-aided diagnosis (CAD) systems based on deep learning play an increasingly important role in pattern recognition of diagnostic medical images. In this paper, we propose a framework based on hierarchical convolutional neural networks (CNNs) for automatic detection and classification of focal liver lesions (FLLs) in multi-phasic computed tomography (CT). A total of 616 nodules, composed of three types of malignant lesions (hepatocellular carcinoma, intrahepatic cholangiocarcinoma, and metastasis) and benign lesions (hemangioma, focal nodular hyperplasia, and cyst), were randomly divided into training and test sets at an approximate ratio of 3:1. To evaluate the performance of our model, other commonly adopted CNN models and two physicians were included for comparison. Our model achieved the best results to detect FLLs, with an average test precision of 82.8%, recall of 93.4%, and F1-score of 87.8%. Our model initially classified FLLs into malignant and benign and then classified them into more detailed classes. For the binary and six-class classification, our model achieved average accuracy results of 82.5 and73.4%, respectively, which were better than the other three classification neural networks. Interestingly, the classification performance of the model was placed between a junior physician and a senior physician. Overall, this preliminary study demonstrates that our proposed multi-modality and multi-scale CNN structure can locate and classify FLLs accurately in a limited dataset, and would help inexperienced physicians to reach a diagnosis in clinical practice.
Proteomic Analysis of Listeria monocytogenes FBUNT During Biofilm Formation at 10°C in Response to Lactocin AL705

Listeria monocytogenes is one of the major food-related pathogens and is able to survive and multiply under different stress conditions. Its persistence in industrial premises and foods is partially due to its ability to form biofilm. Thus, as a natural strategy to overcome L. monocytogenes biofilm formation, the treatment with lactocin AL705 using a sublethal dose (20AU/ml) was explored. The effect of the presence of the bacteriocin on the biofilm formation at 10°C of L. monocytogenes FBUNT was evaluated for its proteome and compared to the proteomes of planktonic and sessile cells grown at 10°C in the absence of lactocin. Compared to planktonic cells, adaptation of sessile cells during cold stress involved protein abundance shifts associated with ribosomes function and biogenesis, cell membrane functionality, carbohydrate and amino acid metabolism, and transport. When sessile cells were treated with lactocin AL705, proteins’ up-regulation were mostly related to carbohydrate metabolism and nutrient transport in an attempt to compensate for impaired energy generation caused by bacteriocin interacting with the cytoplasmic membrane. Notably, transport systems such as β-glucosidase IIABC (lmo0027), cellobiose (lmo2763), and trehalose (lmo1255) specific PTS proteins were highly overexpressed. In addition, mannose (lmo0098), a specific PTS protein indicating the adaptive response of sessile cells to the bacteriocin, was downregulated as this PTS system acts as a class IIa bacteriocin receptor. A sublethal dose of lactocin AL705 was able to reduce the biofilm formation in L. monocytogenes FBUNT and this bacteriocin induced adaptation mechanisms in treated sessile cells. These results constitute valuable data related to specific proteins targeting the control of L. monocytogenes biofilm upon bacteriocin treatment.
Walking Speed Reliably Measures Clinically Significant Changes in Gait by Directional Deep Brain Stimulation

Introduction: Although deep brain stimulation (DBS) often improves levodopa-responsive gait symptoms, robust therapies for gait dysfunction from Parkinson's disease (PD) remain a major unmet need. Walking speed could represent a simple, integrated tool to assess DBS efficacy but is often not examined systematically or quantitatively during DBS programming. Here we investigate the reliability and functional significance of changes in gait by directional DBS in the subthalamic nucleus. Methods: Nineteen patients underwent unilateral subthalamic nucleus DBS surgery with an eight-contact directional lead (1-3-3-1 configuration) in the most severely affected hemisphere. They arrived off dopaminergic medications >12 h preoperatively and for device activation 1 month after surgery. We measured a comfortable walking speed using an instrumented walkway with DBS off and at each of 10 stimulation configurations (six directional contacts, two virtual rings, and two circular rings) at the midpoint of the therapeutic window. Repeated measures of ANOVA contrasted preoperative vs. maximum and minimum walking speeds across DBS configurations during device activation. Intraclass correlation coefficients examined walking speed reliability across the four trials within each DBS configuration. We also investigated whether changes in walking speed related to modification of step length vs. cadence with a one-sample t-test. Results: Mean comfortable walking speed improved significantly with DBS on vs. both DBS off and minimum speeds with DBS on (p < 0.001, respectively). Pairwise comparisons showed no significant difference between DBS off and minimum comfortable walking speed with DBS on (p = 1.000). Intraclass correlations were ≥0.949 within each condition. Changes in comfortable walk speed were conferred primarily by changes in step length (p < 0.004). Conclusion: Acute assessment of walking speed is a reliable, clinically meaningful measure of gait function during DBS activation. Directional and circular unilateral subthalamic DBS in appropriate configurations elicit acute and clinically significant improvements in gait dysfunction related to PD. Next-generation directional DBS technologies have significant potential to enhance gait by individually tailoring stimulation parameters to optimize efficacy.
Insights on the Control of Yeast Single-Cell Growth Variability by Members of the Trehalose Phosphate Synthase (TPS) Complex

Single-cell variability of growth is a biological phenomenon that has attracted growing interest in recent years. Important progress has been made in the knowledge of the origin of cell-to-cell heterogeneity of growth, especially in microbial cells. To better understand the origins of such heterogeneity at the single-cell level, we developed a new methodological pipeline that coupled cytometry-based cell sorting with automatized microscopy and image analysis to score the growth rate of thousands of single cells. This allowed investigating the influence of the initial amount of proteins of interest on the subsequent growth of the microcolony. As a preliminary step to validate this experimental setup, we referred to previous findings in yeast where the expression level of Tsl1, a member of the Trehalose Phosphate Synthase (TPS) complex, negatively correlated with cell division rate. We unfortunately could not find any influence of the initial TSL1 expression level on the growth rate of the microcolonies. We also analyzed the effect of the natural variations of trehalose-6-phosphate synthase (TPS1) expression on cell-to-cell growth heterogeneity, but we did not find any correlation. However, due to the already known altered growth of the tps1Δ mutants, we tested this strain at the single-cell level on a permissive carbon source. This mutant showed an outstanding lack of reproducibility of growth rate distributions as compared to the wild-type strain, with variable proportions of non-growing cells between cultivations and more heterogeneous microcolonies in terms of individual growth rates. Interestingly, this variable behavior at the single-cell level was reminiscent to the high variability that is also stochastically suffered at the population level when cultivating this tps1Δ strain, even when using controlled bioreactors.
Reduced Facilitation of Parietal-Motor Functional Connections in Older Adults

Age-related changes in cortico-cortical connectivity in the human motor network in older adults are associated with declines in hand dexterity. Posterior parietal cortex (PPC) is strongly interconnected with motor areas and plays a critical role in many aspects of motor planning. Functional connectivity measures derived from dual-site transcranial magnetic stimulation (dsTMS) studies have found facilitatory inputs from PPC to ipsilateral primary motor cortex (M1) in younger adults. In this study, we investigated whether facilitatory inputs from PPC to M1 are altered by age. We used dsTMS in a conditioning-test paradigm to characterize patterns of functional connectivity between the left PPC and ipsilateral M1 and a standard pegboard test to assess skilled hand motor function in 13 young and 13 older adults. We found a PPC-M1 facilitation in young adults but not older adults. Older adults also showed a decline in motor performance compared to young adults. We conclude that the reduced PPC-M1 facilitation in older adults may be an early marker of age-related decline in the neural control of movement.
Using Muse: Rapid Mobile Assessment of Brain Performance

The advent of mobile electroencephalography (mEEG) has created a means for large scale collection of neural data thus affording a deeper insight into cognitive phenomena such as cognitive fatigue. Cognitive fatigue – a neural state that is associated with an increased incidence of errorful performance – is responsible for accidents on a daily basis which at times can cost human lives. To gain better insight into the neural signature of cognitive fatigue in the present study we used mEEG to examine the relationship between perceived cognitive fatigue and human-event related brain potentials (ERPs) and electroencephalographic (EEG) oscillations in a sample of 1,000 people. As a secondary goal, we wanted to further demonstrate the capability of mEEG to accurately measure ERP and EEG data. To accomplish these goals, participants performed a standard visual oddball task on an Apple iPad while EEG data were recorded from a Muse EEG headband. Counter to traditional EEG studies, experimental setup and data collection was completed in less than seven minutes on average. An analysis of our EEG data revealed robust N200 and P300 ERP components and neural oscillations in the delta, theta, alpha, and beta bands. In line with previous findings we observed correlations between ERP components and EEG power and perceived cognitive fatigue. Further, we demonstrate here that a linear combination of ERP and EEG features is a significantly better predictor of perceived cognitive fatigue than any ERP or EEG feature on its own. In sum, our results provide validation of mEEG as a viable tool for research and provide further insight into the impact of cognitive fatigue on the human brain.
Inonotus obliquus Polysaccharide Ameliorates Azoxymethane/Dextran Sulfate Sodium-Induced Colitis-Associated Cancer in Mice via Activation of the NLRP3 Inflammasome

Inonotus obliquus polysaccharide (IOP), the primary constituent of the parasitic fungus Inonotus obliquus, has anti-tumor, anti-inflammatory, anti-oxidation effects. However, the roles of IOP on colitis-associated cancer (CAC) are still unclear. Herein, we tested the efficacy of IOP using a mouse model of CAC induced by azoxymethane and dextran sulfate sodium (AOM/DSS). We confirmed that intragastric administration of IOP decreased CAC-induced body weight loss, colon tissue damage, colon shortening, and expression of proinflammatory mediators. Meanwhile, IOP treatment increased in expression of the NLRP3 inflammasome, IL-1β, and IL-18 in the colon of CAC mice. Moreover, in vitro, IOP inhibited the proliferation of SW620 colorectal cancer cells. Finally, overexpression of NLRP3 with plasmid transfection could further enhance the activation of NLRP3 inflammasome by IOP. Taken together, these results suggest that IOP suppresses the development of CAC, possibly by activation of the NLRP3 inflammasome, and reveal that IOP may be a therapeutic drug candidate for CAC.
Analysis of Hair Cortisol as an Indicator of Chronic Stress in Pigs in Two Different Farrowing Systems

Confinement to farrowing crates is known to prevent sows from performing natural behavior, impairing animal welfare and possibly causing chronic stress. Hair cortisol analyses are increasingly used to detect chronic stress in animals. In the present study, hair samples were collected in the neck of sows kept either in farrowing crates (FC, n = 31) or in a loose-housing system (LH, n = 30) in six batches. Cortisol was extracted and analyzed using chemiluminescence immunoassay. Mean hair cortisol concentrations (HCC) did not differ significantly between the systems (LH: 1.85 ± 0.82 pg/mg, FC: 2.13 ± 1.53 pg/mg, P = 0.631). HCC was also not affected by other factors, such as sows' parity, number of piglets, skin lesion score or sow's weight loss during the farrowing period. However, highly significant differences were found in hair growth rates between different regions within the 20 × 30 cm shaving area. While the hair in both lateral parts of the shaving area grew almost identically (left: 7.48 ± 3.52 mm, right: 7.44 ± 3.24 mm, P = 1.00), the hair grew more in the area above the spine (12.27 + 3.95 mm, P < 0.001). In both systems, the mean individual lesion score of sows declined from the beginning to the end of the housing period (P < 0.001). No difference was found between FC and LH sows at any time (P > 0.05). Since neither the amount of skin lesions nor HCC differed between LH and FC sows, it may be concluded that confining sows in farrowing crates did not affect chronic stress levels. However, results may be affected by a downregulation of the hypothalamic-pituitary-adrenal axis during long-term stress, resulting in lower cortisol levels over time. HCC in sows may also be influenced by a dominant stressor, such as farrowing or the presence of suckling piglets. Thus, for a comparison of different farrowing systems regarding chronic stress, the use of hair cortisol measurement seems to be limited. The present results revealed that differences in hair growth rate within the same body region exist. This important finding should be considered when collecting hair samples in pigs, since hair cortisol concentrations may vary depending on hair growth and length.
Impact of Zinc and/or Herbal Mixture on Ruminal Fermentation, Microbiota, and Histopathology in Lambs

We investigated the effect of diets containing organic zinc and a mixture of medicinal herbs on ruminal microbial fermentation and histopathology in lambs. Twenty-eight lambs were divided into four groups: unsupplemented animals (Control), animals supplemented with organic zinc (Zn, 70 mg Zn/kg diet), animals supplemented with a mixture of dry medicinal herbs (Herbs, 100 g dry matter (DM)/d) and animals supplemented with both zinc and herbs (Zn+Herbs). Each lamb was fed a basal diet composed of meadow hay (700 g DM/d) and barley (300 g DM/d). The herbs Fumaria officinalis L. (FO), Malva sylvestris L. (MS), Artemisia absinthium L. (AA) and Matricaria chamomilla L. (MC) were mixed in equal proportions. The lambs were slaughtered after 70 d. The ruminal contents were used to determine the parameters of fermentation in vitro and in vivo and to quantify the microbes by molecular and microscopic methods. Samples of fresh ruminal tissue were used for histopathological evaluation. Quantitative analyses of the bioactive compounds in FO, MS, AA, and MC identified 3.961, 0.654, 6.482, and 12.084 g/kg DM phenolic acids and 12.211, 6.479, 0.349, and 2.442 g/kg DM flavonoids, respectively. The alkaloid content in FO was 6.015 g/kg DM. The diets affected the levels of total gas, methane and n-butyrate in vitro (P < 0.046, < 0.001, and < 0.001, respectively). Relative quantification by real-time PCR indicated a lower total ruminal bacterial population in the lambs in the Zn and Zn+Herbs groups than the Control group (P < 0.05). The relative abundances of Ruminococcus albus, R. flavefaciens, Streptococcus bovis, and Butyrivibrio proteoclasticus shifted in the Zn group. Morphological observation found a focally mixed infiltration of inflammatory cells in the lamina propria of the rumen in the Zn+Herbs group. The effect of the organic zinc and the herbal mixture on the parameters of ruminal fermentation in vitro was not confirmed in vivo, perhaps because the ruminal microbiota of the lambs adapted to the zinc-supplemented diets. Long-term supplementation of a diet combining zinc and medicinal herbs, however, may negatively affect the health of the ruminal epithelium of lambs.
Akkermansia muciniphila Improves Host Defense Against Influenza Virus Infection

Influenza virus infection can alter the composition of the gut microbiota, while its pathogenicity can, in turn, be highly influenced by the gut microbiota. However, the details underlying these associations remain to be determined. The H7N9 influenza virus is an emerging zoonotic pathogen which has caused the death of 616 humans and has incurred huge losses in the poultry industry. Here, we investigated the effects of infection with highly pathogenic H7N9 on gut microbiota and determined potential anti-influenza microbes. 16S rRNA sequencing results show that H7N9 infection alters the mouse gut microbiota by promoting the growth of Akkermansia, Ruminococcus 1, and Ruminococcaceae UCG-010, and reducing the abundance of Rikenellaceae RC9 gut group and Lachnoclostridium. Although the abundance of Akkermansia muciniphila is positively related to H7N9 infection, the oral administration of cultures, especially of pasteurized A. muciniphila, can significantly reduce weight loss and mortality caused by H7N9 infection in mice. Furthermore, oral administration of live or pasteurized A. muciniphila significantly reduces pulmonary viral titers and the levels IL-1β and IL-6 but enhances the levels of IFN-β, IFN-γ, and IL-10 in H7N9-infected mice, suggesting that the anti-influenza role of A. muciniphila is due to its anti-inflammatory and immunoregulatory properties. Taken together, we showed that the changes in the gut microbiota are associated with H7N9 infection and demonstrated the anti-influenza role of A. muciniphila, which enriches current knowledge about how specific gut bacterial strains protect against influenza infection and suggests a potential anti-influenza probiotic.
Veterinary Herd Health Consultancy and Antimicrobial Use in Dairy Herds

The globally increasing level of antimicrobial resistance affects both human and animal health, why it is necessary to identify ways to change our current use of antimicrobials. The veterinary herd health collaboration between veterinarians and dairy farmers provides a useful setting for changing antimicrobial use in livestock. However, farmers and veterinarians work in a complex agricultural setting influenced by socio-economic factors, which complicates their choices regarding antimicrobial usage. It is therefore necessary to be aware of the range of potential influencing factors and to integrate this knowledge in the relevant local settings. This manuscript presents a literature review of relevant factors relating to antimicrobial use within the veterinary herd health consultancy setting, including knowledge gaps of relevance for changing the use of antimicrobials. An enriched version of the framework of the Theory of Planned Behaviour was used to organise the literature review. We identified diverging attitudes on correct treatment practices and perceptions of antimicrobial resistance among veterinarians and farmers, influenced by individual risk perception as well as social norms. Furthermore, disagreements in terms of goal setting and in the frequency of herd visits in relation to herd health consultancy can negatively influence the collaboration and the intention to change antimicrobial use. Farmers and veterinarians emphasise the importance of legislation and the role of the dairy industry in changing antimicrobial use, but the relevance of specific factors depends on the country-specific context. Overall, farmers and veterinarians must communicate better to understand each other's perspectives and establish common goals within the collaboration if they are to work efficiently to reduce antimicrobial use. Farmers and veterinarians both requested changes in individual behaviour; however, they also called for national and structural solutions in terms of balanced legislation and the availability of better diagnostics to facilitate a change in antimicrobial use practices. These various paths to achieving the desired changes in antimicrobial use illustrate the need to bridge methodological research approaches of veterinary science and social sciences for a better understanding of our potential to change antimicrobial use within the dairy farm animal sector.