Artificial intelligence uncovers carcinogenic human metabolites.

The genome of a eukaryotic cell is often vulnerable to both intrinsic and extrinsic threats owing to its constant exposure to a myriad of heterogeneous compounds. Despite the availability of innate DNA damage responses, some genomic lesions trigger malignant transformation of cells. Accurate prediction of carcinogens is an ever-challenging task owing to the limited information about bona fide (non-)carcinogens. We developed Metabokiller, an ensemble classifier that accurately recognizes carcinogens by quantitatively assessing their electrophilicity, their potential to induce proliferation, oxidative stress, genomic instability, epigenome alterations, and anti-apoptotic response. Concomitant with the carcinogenicity prediction, Metabokiller is fully interpretable and outperforms existing best-practice methods for carcinogenicity prediction. Metabokiller unraveled potential carcinogenic human metabolites. To cross-validate Metabokiller predictions, we performed multiple functional assays using Saccharomyces cerevisiae and human cells with two Metabokiller-flagged human metabolites, namely 4-nitrocatechol and 3,4-dihydroxyphenylacetic acid, and observed high synergy between Metabokiller predictions and experimental validations.

Driven-Dissipative Criticality within the Discrete Truncated Wigner Approximation.

We present an approach to the numerical simulation of open quantum many-body systems based on the semiclassical framework of the discrete truncated Wigner approximation. We establish a quantum jump formalism to integrate the quantum master equation describing the dynamics of the system, which we find to be exact in both the noninteracting limit and the limit where the system is described by classical rate equations. We apply our method to simulation of the paradigmatic dissipative Ising model, where we are able to capture the critical fluctuations of the system beyond the level of mean-field theory.

The Capability Maturity Model as a Measure of Culture of Care in Laboratory Animal Science.

Culture of care in Laboratory Animal Science (LAS) refers to a commitment toward improving animal welfare, scientific quality, staff wellbeing, and transparency for all stakeholders, ensuring that the animals and personnel involved are treated with compassion and respect. A strong culture of care can be established by the proactive implementation of the Three Rs, sharing best practices, caring for and respecting animals and colleagues, empowering staff, taking responsibility for our actions, and having a caring leadership. Culture of care, when established, should be evaluated continuously, in order to foster its progress and persistence. Even though several tools for assessing the culture of care within an institution have been proposed, an ultimate standard for measuring the concept is lacking. Here, we review the culture of care concept and propose the 'Capability Maturity Model' as a means of quantifying culture of care in the laboratory animal setting.

Adhatoda vasica rescues the hypoxia-dependent severe asthma symptoms and mitochondrial dysfunction.

Severe asthma is a chronic airway disease that exhibits poor response to conventional asthma therapies. Growing evidence suggests that elevated hypoxia increases the severity of asthmatic inflammation among patients and in model systems. In this study, we elucidate the therapeutic effects and mechanistic basis of Adhatoda vasica (AV) aqueous extract on mouse models of acute allergic as well as severe asthma subtypes at physiological, histopathological, and molecular levels. Oral administration of AV extract attenuates the increased airway resistance and inflammation in acute allergic asthmatic mice and alleviates the molecular signatures of steroid (dexamethasone) resistance like IL-17A, KC (murine IL-8 homologue), and HIF-1α (hypoxia-inducible factor-1α) in severe asthmatic mice. AV inhibits HIF-1α levels through restoration of expression of its negative regulator-PHD2 (prolyl hydroxylase domain-2). Alleviation of hypoxic response mediated by AV is further confirmed in the acute and severe asthma model. AV reverses cellular hypoxia-induced mitochondrial dysfunction in human bronchial epithelial cells-evident from bioenergetic profiles and morphological analysis of mitochondria. In silico docking of AV constituents reveal higher negative binding affinity for C and O-glycosides for HIF-1α, IL-6, Janus kinase 1/3, TNF-α, and TGF-ß-key players of hypoxia inflammation. This study for the first time provides a molecular basis of action and effect of AV whole extract that is widely used in Ayurveda practice for diverse respiratory ailments. Further, through its effect on hypoxia-induced mitochondrial dysfunction, the study highlights its potential to treat severe steroid-resistant asthma.

Risk assessment of heavy metals in milk from cows reared around industrial areas in India.

This study assessed the health risk associated with exposure to heavy metals through consumption of milk from cows reared around industrial areas in India. Heavy metals, namely Cu, Zn, Cr, Pb, and Cd, were determined in water and forage from four locations as well as in milk produced by dairy cattle raised in these locations, using inductively coupled plasma-mass spectrometry. A quantitative risk assessment using probabilistic approaches was performed to assess the exposure of adults and children to the heavy metals via milk consumption. In milk samples, the highest levels of Cd and Pb were 0.18 mg L-1 and 0.37 mg L-1, respectively, which were above the international permissible levels. Possible sources of Pb in the milk could be the industrial by-products and wastes or automobiles exhaust gas. Significant (P < 0.05) positive relationships were found between the concentration of Cu, Cr, Pb, and Cd in milk and in the environmental samples (water or forage). Exposure assessment showed that milk consumers were mostly exposed to Zn, Cd, and Pb, with 63.7%, 51.2%, and 41.2% of children exposed to a dose greater than the references dose for these metals, respectively. Our results suggest that industrial activities lead to possible transfer of heavy metals to cows from their rearing environment (water, plant), which can be accumulated and cause potential health risks to milk consumers. The outcome of this study can be used by policy makers to manage the potential health risk.

The Ser/Thr protein kinase PrkC imprints phenotypic memory in Bacillus anthracis spores by phosphorylating the glycolytic enzyme enolase.

Bacillus anthracis is the causative agent of anthrax in humans, bovine, and other animals. B. anthracis pathogenesis requires differentiation of dormant spores into vegetative cells. The spores inherit cellular components as phenotypic memory from the parent cell, and this memory plays a critical role in facilitating the spores' revival. Because metabolism initiates at the beginning of spore germination, here we metabolically reprogrammed B. anthracis cells to understand the role of glycolytic enzymes in this process. We show that increased expression of enolase (Eno) in the sporulating mother cell decreases germination efficiency. Eno is phosphorylated by the conserved Ser/Thr protein kinase PrkC which decreases the catalytic activity of Eno. We found that phosphorylation also regulates Eno expression and localization, thereby controlling the overall spore germination process. Using MS analysis, we identified the sites of phosphorylation in Eno, and substitution(s) of selected phosphorylation sites helped establish the functional correlation between phosphorylation and Eno activity. We propose that PrkC-mediated regulation of Eno may help sporulating B. anthracis cells in adapting to nutrient deprivation. In summary, to the best of our knowledge, our study provides the first evidence that in sporulating B. anthracis, PrkC imprints phenotypic memory that facilitates the germination process.

The Quality of Reporting Raises Questions on the Experimental Validity of Animal Studies Conducted in India and Sri Lanka: Preliminary Analysis of a Systematic Survey.

The quality of animal experiments in terms of appropriate reporting is a concern, particularly with regard to their validity and the recording of the measures taken to reduce various types of bias. A systematic survey of 1371 and 236 publications from India and Sri Lanka, respectively, which were published between 1905 and 2017 and indexed in NCBI-PubMed, Cinhal, MEDLINE and Scopus, was carried out. The level of detail in the descriptions of animals used and the measures taken to reduce bias were analysed in each article. Selected parameters from the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines, such as age, weight, sex, sample size calculation, blinding and randomisation were considered. The findings revealed poor reporting standards in animal experiments carried out in India and Sri Lanka, confirming the limited impact of the ARRIVE guidelines. These findings emphasise the urgent need for improvements in the peer review process, both prior to a study being set up and in the post-study reporting phase, and for more stringent adherence to the ARRIVE guidelines in the reporting of animal experiments.

Design and synthesis of cell selective α/ß-diastereomeric peptidomimetic with potent in vivo antibacterial activity against methicillin resistant S. Aureus.

Design of therapeutically viable antimicrobial peptides with cell selectivity against microorganisms is an important step towards the development of new antimicrobial agents. Here, we report four de novo designed, short amphipathic sequences based on a α-helical template comprising of Lys, Trp and Leu or their corresponding D-and/or ß-amino acids. Sequence A-12 was protease susceptible whereas its α/ß-diastereomeric analogue UNA-12 was resistant to trypsin and proteinase K up to 24 h. A-12 and UNA-12 exhibited broad-spectrum antibacterial activity (MIC: 2-32 µg/mL) against pathogens including methicillin resistant S. aureus (MRSA) and methicillin-resistant S. epidermidis (MRSE). Interestingly, A-12 was found to be most toxic (>50% haemolytic at 250 µg/mL) whereas UNA-12 was found to be non cytotoxic among the all analogues against hRBCs and human keratinocytes. Interaction studies with artificial membranes by tryptophan fluorescence and acrylamide quenching assay demonstrated A-12 interacted equally in bacterial as well as mammalian mimic membrane whereas UNA-12 was found to be more selective towards bacterial mimic membrane. Further microscopic tool has revealed membrane damaging ability of A-12 and UNA-12 with bactericidal mode of action against MRSA. Encouragingly, peptidomimetics analogue UNA-12 showed remarkable safety and efficacy against MRSA in in-vivo neutropenic mice thigh infection model. In summary, simultaneous replacement of the natural amino acids with D-/ß-congeners is a promising strategy for designing of potent, cell selective and protease stable peptide based antibiotics.

Impact of bariatric surgery on obstructive sleep apnoea-hypopnea syndrome in morbidly obese patients.

BACKGROUND: Obstructive sleep apnea (OSA) is commonly associated with morbid obesity. Weight loss following bariatric surgery results in resolution or improvement of OSA. However, few studies have done objective assessment of the impact of bariatric surgery on OSA. OBJECTIVE: The aim of this study was to assess the outcome of bariatric surgery on OSA. SETTING: The study was conducted in the teaching institution of a tertiary care centre. METHODS: Twenty-seven morbidly obese patients seeking bariatric surgery were administered Epworth Sleepiness Scale (ESS) health questionnaire and subjected to overnight polysomnography. Repeat assessment using ESS and polysomnography was done at 3-6 months after surgery. RESULTS: Mean age was 42.4 ± 10.5 years, and majority (77.8%) were female. The mean pre-operative weight and body mass index (BMI) were 126.4 ± 24.9 kg and 48.4 ± 8.2 kg/m2, respectively. Nearly 29.6% patients had symptoms of excessive daytime somnolence based on ESS score and overnight polysomnography detected the presence of OSA in 96.3% patients, of which 51.9% had severe OSA. At mean follow-up of 5.2 ± 2.5 months after surgery, mean weight and BMI decreased to 107.4 ± 24.5 kg and 41.2 ± 8.2 kg/m2, respectively. Mean ESS score and mean apnoea-hypopnea index declined from 8.9 ± 3.2 to 4.03 ± 2.15 (P < 0.001) and from 31.8 ± 20.4 to 20.2 ± 23.1 (P = 0.007), respectively. Number of patients requiring continuous positive airway pressure (CPAP) therapy declined from 15 to 3 and average CPAP requirement came down from 11.3 cm of H2O to 6 cm of H2O. CONCLUSION: OSA was present in a significant proportion of patients undergoing bariatric surgery. Bariatric surgery resulted in significant improvement in both subjective and objective parameters of OSA.

Downregulation of miRNAs during Delayed Wound Healing in Diabetes: Role of Dicer.

Delayed wound healing is a major complication associated with diabetes and is a result of a complex interplay among diverse deregulated cellular parameters. Although several genes and pathways have been identified to be mediating impaired wound closure, the role of microRNAs (miRNAs) in these events is not very well understood. Here, we identify an altered miRNA signature in the prolonged inflammatory phase in a wound during diabetes, with increased infiltration of inflammatory cells in the basal layer of the epidermis. Nineteen miRNAs were downregulated in diabetic rat wounds (as compared with normal rat wound, d 7 postwounding) together with inhibited levels of the central miRNA biosynthesis enzyme, Dicer, suggesting that in wounds of diabetic rats, the decreased levels of Dicer are presumably responsible for miRNA downregulation. Compared with unwounded skin, Dicer levels were significantly upregulated 12 d postwounding in normal rats, and this result was notably absent in diabetic rats that showed impaired wound closure. In a wound-healing specific quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) array, 10 genes were significantly altered in the diabetic rat wound and included growth factors and collagens. Network analyses demonstrated significant interactions and correlations between the miRNA predicted targets (regulators) and the 10 wound-healing specific genes, suggesting altered miRNAs might fine-tune the levels of these genes that determine wound closure. Dicer inhibition prevented HaCaT cell migration and affected wound closure. Altered levels of Dicer and miRNAs are critical during delayed wound closure and offer promising targets to address the issue of impaired wound healing.

A training course on laboratory animal science: an initiative to implement the Three Rs of animal research in India.

There is a current need for a change in the attitudes of researchers toward the care and use of experimental animals in India. This could be achieved through improvements in the provision of training, to further the integration of the Three Rs concept into scientific research and into the regulations of the Committee for the Purpose of Control and Supervision of Experiments on Animals (CPCSEA). A survey was performed after participants undertook the Federation of European Laboratory Animal Science Associations (FELASA) Category C-based course on Laboratory Animal Science (in 2013 and 2015). It revealed that the participants subsequently employed, in their future research, the practical and theoretical Three Rs approaches that they had learned. This is of great importance in terms of animal welfare, and also serves to benefit their research outcomes extensively. All the lectures, hands-on practical sessions and supplementary elements of the courses, which also involved the handling of small animals and procedures with live animals, were well appreciated by the participants. Insight into developments in practical handling and welfare procedures, norms, directives, and ethical use of laboratory animals in research, was also provided, through the comparison of results from the 2013 and 2015 post-course surveys.

Critical velocity in the BEC-BCS crossover.

We map out the critical velocity in the crossover from Bose-Einstein condensation to Bardeen-Cooper-Schrieffer superfluidity with ultracold ^{6}Li gases. A small attractive potential is dragged along lines of constant column density. The rate of the induced heating increases steeply above a critical velocity v_{c}. In the same samples, we measure the speed of sound v_{s} by exciting density waves and compare the results to the measured values of v_{c}. We perform numerical simulations in the Bose-Einstein condensation regime and find very good agreement, validating the approach. In the strongly correlated regime our measurements of v_{c} provide a testing ground for theoretical approaches.

Parabromophenacyl bromide inhibits subepithelial fibrosis by reducing TGF-ß1 in a chronic mouse model of allergic asthma.

BACKGROUND: Our previous study showed that parabromophenacyl bromide (PBPB) inhibits the features of allergic airway inflammation and airway hyperresponsiveness (AHR). However, its effect on airway remodeling, e.g. subepithelial fibrosis in a chronic allergic asthma model, was not investigated. We examined this issue in this study. METHODS: PBPB was administered to mice with an induced chronic asthmatic condition. AHR was estimated at the end of the experiment, followed by euthanasia. Lung sections were stained with hematoxylin and eosin, periodic acid-Schiff and Masson's trichrome to determine airway inflammation, goblet cell metaplasia and subepithelial fibrosis, respectively. Transforming growth factor-ß1 (TGF-ß1) was estimated in lung homogenates. To determine the effect of PBPB on smooth-muscle hyperplasia, immunohistochemistry against α-smooth-muscle actin was performed on the lung sections. RESULTS: Chronic ovalbumin challenges in a mouse model of allergic asthma caused significant subepithelial fibrosis and elevated TGF-ß1, along with significant AHR. PBPB attenuated subepithelial fibrosis with a reduction of lung TGF-ß1, airway inflammation and AHR without affecting goblet cell metaplasia. It also attenuated smooth-muscle hyperplasia with a reduction in the expression of α-smooth-muscle actin in the lungs. CONCLUSION: Our findings indicate that PBPB attenuates some crucial features of airway remodeling such as subepithelial fibrosis and smooth-muscle hyperplasia. These data suggest that PBPB could therefore be a therapeutic drug for chronic asthma.

Metabolic pathway for degradation of 2-chloro-4-aminophenol by Arthrobacter sp. SPG.

A degradation pathway of 2-chloro-4-aminophenol (2C4AP) was studied in an Arthrobacter sp. SPG that utilized 2C4AP as its sole source of carbon and energy. The 2C4AP degradation was initiated by a 2C4AP-deaminase that catalyzed the conversion of 2C4AP into chlorohydroquinone (CHQ) with removal of ammonium ion. In the next step, a CHQ-dehalogenase dehalogenated CHQ to hydroquinone (HQ) that cleaved into γ-hydroxymuconic semialdehyde by a HQ-dioxygenase. The 2C4AP degradation was also investigated in sterile and non-sterile soil microcosms using strain SPG. The results show that the SPG cells degraded 2C4AP more rapidly in sterile soil than non-sterile soil. Our studies showed that strain SPG may be used for bioremediation of 2C4AP-contaminated sites. This is the first report of the 2C4AP degradation by any bacteria.

Accessing the behavior and awareness of veterinary professionals towards antimicrobials use and antimicrobial resistance in Indian district.

Introduction: Antimicrobial resistance (AMR) poses a significant public health threat, and understanding the awareness and practices of healthcare professionals is crucial for its mitigation. Since the animal sector plays a key role in India's economy, we decided to explore the understanding of Antimicrobial Use (AMU) and AMR among veterinary professionals. Methods: The study aimed to evaluate the awareness and behavior of veterinarians and para-veterinarians working in the Jhunjhunu district, Rajasthan, India, concerning AMU and AMR. Questionnaire surveys were administered to them with closed-ended questions. The data was collected and subjected to statistical analysis to derive meaningful insights. The key findings highlight notable differences in certain behavioral aspects of antibiotic prescription among the two groups. Results and Discussion: It appears that 53.8% of veterinarians as compared to 25.8% para-veterinarians do not surely inform farmers about the importance of adhering to antibiotic withdrawal periods, thereby failing to raise awareness about proper antibiotic use. Moreover, para-veterinarians (46.6%) tend to engage less in evidence-based antibiotic prescription than veterinarians (81%). Furthermore, both groups exhibit a lower frequency of advice on Antimicrobial Susceptibility Testing (ABST), essential for informed prescribing decisions. Most significantly, both groups show a tendency to prefer critically important antibiotics for prescription, raising concerns about the escalating threat of AMR. This study thus emphasizes the areas that need targeted interventions to enhance responsible antimicrobial usage and curb the growth of AMR in the region.

Knowledge and practices related to antibiotics among poultry producers and veterinarians in two Indian states.

Background: Antibiotics are frequently utilized in livestock, particularly poultry, for therapy and growth promotion, resulting in antimicrobial resistance. Multidrug-resistant bacteria are frequent in poultry samples from India. The purpose of this study was to better understand main antibiotic consumption patterns in poultry value chains, as well as antibiotic knowledge and practices among the stakeholders. Methods: A cross-sectional survey was conducted in Assam and Karnataka, India. The poultry farmers were interviewed on antibiotic usage, antibiotic knowledge, feeding practices, and preventive measures on the farm. Poultry farmers reported their veterinarians, and we also interviewed them on knowledge and practices related to antimicrobial use in poultry and antimicrobial resistance. Item response theory (IRT) was used to assess the association between the answers and demographic factors. Results: This survey interviewed 62 poultry farmers and 11 veterinarians. Small poultry farms with fewer than 4000 birds were owned by 51.6% of farmers. Most poultry farmers had heard about antibiotics, and 62.9% thought they cured all diseases. If one chicken is sick, 72.6% said others should be given antibiotics to prevent the disease. All veterinarians utilized tetracyclines, aminoglycosides, and cephalexin on the poultry farms. Over half (54.5%) stated antibiotics prevent diseases, and 72.7% said they treat and prevent diseases. Some (45.5%) said antibiotics boost growth. IRT analysis showed that 8 questions assessed a knowledge scale well. Univariable analysis showed that Assam farmers and women were likely to have have more knowledge. Conclusion: The poultry farmers were mostly unaware of the relation between antibiotic use and antimicrobial resistance. Despite being aware, the veterinarians agreed with use antibiotics as a prophylactic measure. It is vital that these stakeholders understand the repercussions of such widespread antibiotic use. In order to increase knowledge, frequent trainings and antimicrobial stewardship programmes with effective communication and incentives for behaviour change should be conducted.

Towards identification of finger flexions using single channel surface electromyography--able bodied and amputee subjects.

BACKGROUND: This research has established a method for using single channel surface electromyogram (sEMG) recorded from the forearm to identify individual finger flexion. The technique uses the volume conduction properties of the tissues and uses the magnitude and density of the singularities in the signal as a measure of strength of the muscle activity. METHODS: SEMG was recorded from the flexor digitorum superficialis muscle during four different finger flexions. Based on the volume conduction properties of the tissues, sEMG was decomposed into wavelet maxima and grouped into four groups based on their magnitude. The mean magnitude and the density of each group were the inputs to the twin support vector machines (TSVM). The algorithm was tested on 11 able-bodied and one trans-radial amputated volunteer to determine the accuracy, sensitivity and specificity. The system was also tested to determine inter-experimental variations and variations due to difference in the electrode location. RESULTS: Accuracy and sensitivity of identification of finger actions from single channel sEMG signal was 93% and 94% for able-bodied and 81% and 84% for trans-radial amputated respectively, and there was only a small inter-experimental variation. CONCLUSIONS: Volume conduction properties based sEMG analysis provides a suitable basis for identifying finger flexions from single channel sEMG. The reported system requires supervised training and automatic classification.

Understanding Knowledge and Attitude of Farmers towards Antibiotic Use and Antimicrobial Resistance in Jhunjhunu District, Rajasthan India.

The misuse of antibiotics in veterinary practices by farmers is harming livestock production and food safety and leading to the rise of antibiotic resistance (AMR). This can also transfer resistant bacteria from animals to humans, posing a serious public health threat. However, we have not paid enough attention to understanding how farmers behave in this regard. Our study aims to explore farmers' behaviors and identify the factors that influence their choices. To conduct this study, we used a questionnaire with 40 questions and surveyed 208 farmers in Jhunjhunu district, Rajasthan. We analyzed the data using SPSS. Here are the key findings: About 58.3% of the farmers have some awareness of antibiotics, and 49.5% are aware of antimicrobial resistance (AMR). Notably, as the level of education increases, so does awareness of antibiotics. Unfortunately, 63.9% of the farmers are not aware of the withdrawal time, and 64% have no idea about the presence of antibiotic residues during this period. Around 75% of farmers vaccinate their animals, but approximately 56.9% of individuals have never undergone an antibiotic sensitivity test (ABST) for milk. Around 48.6% of farmers are unaware of government testing centers. Several factors hinder farmers from implementing proper animal management practices, such as the high fees of veterinarians. When their animals become sick, their first choice is home remedies, followed by using old prescriptions. Additionally, 63.9% stop treatment once the animal looks better. A significant portion (83.8%) of farmers rely on local pharmacists for medicine. It has been determined that there is no significant correlation between education, experience, age, and the level of awareness concerning withdrawal periods, the existence of government antibiotic sensitivity test (ABST) centers, and entities responsible for sending samples for ABST. In our qualitative analysis, focus groups identified significant barriers to following best farm practices and spreading awareness about AMR. These findings suggest that addressing AMR in livestock requires a comprehensive approach. This should include targeted education and awareness programs for farmers, as well as improved access to veterinary services.