Miracle-dz/UniFAR-FTUs huggingface dataset:
Validating accelerometry-derived proxies of energy expenditure using the doubly labelled water method in the smallest penguin species

ABSTRACT Understanding energy use is central to understanding an animal's physiological and behavioural ecology. However, directly measuring energy expenditure in free-ranging animals is inherently difficult. The doubly labelled water (DLW) method is widely used to investigate energy expenditure in a range of taxa. Although reliable, DLW data collection and analysis is both financially costly and time consuming. Dynamic body acceleration (e.g. VeDBA) calculated from animal-borne accelerometers has been used to determine behavioural patterns, and is increasingly being used as a proxy for energy expenditure. Still its performance as a proxy for energy expenditure in free-ranging animals is not well established and requires validation against established methods. In the present study, the relationship between VeDBA and the at-sea metabolic rate calculated from DLW was investigated in little penguins (Eudyptula minor) using three approaches. Both in a simple correlation and activity-specific approaches were shown to be good predictors of at-sea metabolic rate. The third approach using activity-specific energy expenditure values obtained from literature did not accurately calculate the energy expended by individuals. However, all three approaches were significantly strengthened by the addition of mean horizontal travel speed. These results provide validation for the use of accelerometry as a proxy for energy expenditure and show how energy expenditure may be influenced by both individual behaviour and environmental conditions.
Psoriatic arthritis screening: A systematic literature review and experts’ recommendations

Objective To analyze the performance of psoriatic arthritis (PsA) screening tools, examine their implementation in daily practice, and reach a consensus about the best screening tool for implementation in daily practice in different medical settings. Methods A systematic literature review (SLR), structured telephone interviews to hospitals, and a multidisciplinary nominal group meeting were all conducted. The SLR employed sensitive search strategies using Medline, Embase, and the Cochrane Library up to January 2020. Two reviewers independently selected articles that reported data on PsA screening tools and that included sufficient data to at least calculate the sensitivity and specificity of those tools (e.g., questionnaires, algorithms, specific questions, and biomarkers). The hospital interviews collected data regarding the process of suspected PsA diagnosis and referral to rheumatology, the implementation of PsA screening tools, and barriers and facilitators to implementation of those tools. In the nominal group meeting, a multidisciplinary team of experts discussed all these data and subsequently recommended a screening tool for implementation. Results The SLR included 41 moderate-quality studies that analyzed 14 PsA screening tools, most of which were questionnaire-based tools. All of these studies reported a moderate-good performance but presented different characteristics regarding the time to completion or the number and type of items or questions. The implementation of screening tools was low (30.5%). The experts ultimately recommended regular use of a PsA screening tool, preferably the PURE-4 questionnaire. Conclusions The implementation of PsA screening tools like the PURE-4 questionnaire in daily practice likely improves the prognosis of PsA patients.
A Newly Identified Prophage Gene, ymfM, Causes SOS-Inducible Filamentation in Escherichia coli

Filamentation is an important biological mechanism that aids in the survival, pathogenesis, and antibiotic resistance of bacteria within different environments, including pathogenic bacteria such as uropathogenic Escherichia coli. Here, we have identified a bacteriophage-encoded cell division inhibitor which contributes to the filamentation that occurs during the SOS response. ABSTRACT Rod-shaped bacteria such as Escherichia coli can regulate cell division in response to stress, leading to filamentation, a process where cell growth and DNA replication continue in the absence of division, resulting in elongated cells. The classic example of stress is DNA damage, which results in the activation of the SOS response. While the inhibition of cell division during SOS has traditionally been attributed to SulA in E. coli, a previous report suggests that the e14 prophage may also encode an SOS-inducible cell division inhibitor, previously named SfiC. However, the exact gene responsible for this division inhibition has remained unknown for over 35 years. A recent high-throughput overexpression screen in E. coli identified the e14 prophage gene, ymfM, as a potential cell division inhibitor. In this study, we show that the inducible expression of ymfM from a plasmid causes filamentation. We show that this expression of ymfM results in the inhibition of Z ring formation and is independent of the well-characterized inhibitors of FtsZ ring assembly in E. coli, SulA, SlmA, and MinC. We confirm that ymfM is the gene responsible for the SfiC phenotype, as it contributes to the filamentation observed during the SOS response. This function is independent of SulA, highlighting that multiple alternative division inhibition pathways exist during the SOS response. Our data also highlight that our current understanding of cell division regulation during the SOS response is incomplete and raises many questions regarding how many inhibitors there actually are and their purpose for the survival of the organism. IMPORTANCE Filamentation is an important biological mechanism that aids in the survival, pathogenesis, and antibiotic resistance of bacteria within different environments, including pathogenic bacteria such as uropathogenic Escherichia coli. Here, we have identified a bacteriophage-encoded cell division inhibitor which contributes to the filamentation that occurs during the SOS response. Our work highlights that there are multiple pathways that inhibit cell division during stress. Identifying and characterizing these pathways are critical steps in understanding survival tactics of bacteria, which become important when combating the development of bacterial resistance to antibiotics and their pathogenicity.
Network-Related Changes in Neurotransmitters and Seizure Propagation During Rodent Epileptogenesis

Objective To test the hypothesis that glutamate and GABA are linked to the formation of epilepsy networks and the triggering of spontaneous seizures, we examined seizure initiation/propagation characteristics and neurotransmitter levels during epileptogenesis in a translationally relevant rodent model of mesial temporal lobe epilepsy. Methods The glutamine synthetase (GS) inhibitor methionine sulfoximine was infused into one of the hippocampi in laboratory rats to create a seizure focus. Long-term video-intracranial EEG recordings and brain microdialysis combined with mass spectrometry were used to examine seizure initiation, seizure propagation, and extracellular brain levels of glutamate and GABA. Results All seizures (n = 78 seizures, n = 3 rats) appeared first in the GS-inhibited hippocampus of all animals, followed by propagation to the contralateral hippocampus. Propagation time decreased significantly from 11.65 seconds early in epileptogenesis (weeks 1–2) to 6.82 seconds late in epileptogenesis (weeks 3–4, paired t test, p = 0.025). Baseline extracellular glutamate levels were 11.6-fold higher in the hippocampus of seizure propagation (7.3 µM) vs the hippocampus of seizure onset (0.63 µM, analysis of variance/Fisher least significant difference, p = 0.01), even though the concentrations of the major glutamate transporter proteins excitatory amino acid transporter subtypes 1 and 2 and xCT were unchanged between the brain regions. Finally, extracellular GABA in the seizure focus decreased significantly from baseline several hours before a spontaneous seizure (paired t test/false discovery rate). Conclusion The changes in glutamate and GABA suggest novel and potentially important roles of the amino acids in epilepsy network formation and in the initiation and propagation of spontaneous seizures.
Bioaccumulation and toxic effects of copper on growth and oxygen consumption by the postlarvae of Penaeus indicus

The aim of this study was to assess the toxic impact of copper on postlarvae (PL) of the penaeid shrimp Penaeus indicus. Tolerance, growth, oxygen consumption and metal accumulation were investigated in these PL on exposure to copper. Tolerance studies were conducted for 96 h to assess the tolerance limits of P. indicus PL exposed to different concentrations of copper using static renewal bioassay tests. Using the Probit method, the regression equation was calculated as Y=0.4899+2.3562 X, with a correlation coefficient of 0.9707. The 96 h LC50 was 0.8204 ppm. The effect of sublethal (one-fifth of 96 h LC50) copper on PL for short- and long-term exposures revealed a significant (p<0.05) decrease in the rate of oxygen consumption, metabolic rate, mean length, wet and dry weight of the exposed PL over their respective controls which can be attributed to a gradual and time-dependent accumulation of the metal, as noticed in the exposed PL through accumulation studies. Overall, the data suggest that on chronic exposure even sublethal concentrations of copper can reduce the metabolic rate and growth in P. indicus PL. This is perhaps the first attempt to use the wild P. indicus PL as a bioindicator of copper toxicity.
Computational modeling of malignant ascites reveals CCL5–SDC4 interaction in the immune microenvironment of ovarian cancer

Fluid accumulation in the abdominal cavity is commonly found in advanced‐stage ovarian cancer patients, which creates a specialized tumor microenvironment for cancer progression. Using single‐cell RNA sequencing (scRNA‐seq) of ascites cells from five patients with ovarian cancer, we identified seven cell types, including heterogeneous macrophages and ovarian cancer cells. We resolved a distinct polarization state of macrophages by MacSpectrum analysis and observed subtype‐specific enrichment of pathways associated with their functions. The communication between immune and cancer cells was predicted through a putative ligand–receptor pair analysis using NicheNet. We found that CCL5, a chemotactic ligand, is enriched in immune cells (T cells and NK cells) and mediates ovarian cancer cell survival in the ascites, possibly through SDC4. Moreover, SDC4 expression correlated with poor overall survival in ovarian cancer patients. Our study highlights the potential role of T cells and NK cells in long‐term survival patients with ovarian cancer, indicating SDC4 as a potential prognostic marker in ovarian cancer patients.
Genetic association analysis of the cardiovascular biomarker: N-terminal fragment of pro-B-type natriuretic peptide (NT-proBNP)

Background NT-proBNP is a biomarker of cardiovascular disease (CVD). Little is known about the heritability and genetic variants associated with NT-proBNP. Therefore, we estimated the heritability of and examined genetic associations of SNPs in the BNP gene region with circulating NT-proBNP and prevalent CVD in 4,331 participants from the Long Life Family Study (LLFS). Methods and results Genotypes of 10 SNPs from the NPPB and NPPA regions that encode BNP and A-type natriuretic peptide, respectively, were tested for association with NT-proBNP and prevalent cardiovascular disease and risk factors. We performed analyses using the Sequential Oligogenic Linkage Analysis (SOLAR) program to account for family relatedness, and adjusted all models for age, sex, and field center. The mean age of the LLFS was 69.8 years (range 24–110) with 55.4% females. NT-proBNP was significantly heritable (h2 = 0.21; P = 4x10-14), and the minor alleles of rs632793 (p<0.001) and rs41300100 (p = 0.05) were independently associated with higher serum NT-proBNP levels. Additionally, the minor allele of rs632793 was significantly and consistently associated with lower prevalent CVD, including blood pressures, independent of NT-proBNP level (all P<0.05). Results for prevalent CVD, but not NT-proBNP levels, showed significant interaction by familial generation. Conclusion In this family-based study of subjects with exceptional longevity, we identified several allelic variants in the BNP gene region associated with NT-pro-BNP levels and prevalent CVD.
Acute hypobaric hypoxia and cardiac energetic response in prepubertal rats: Role of nitric oxide

What is the central question of this study? In adult rat hearts, exposure to hypobaric hypoxia increases tolerance to hypoxia–reoxygenation, termed endogenous cardioprotection. The mechanism involves the nitric oxide system and modulation of mitochondrial oxygen consumption. What is the cardiac energetic response in prepubertal rats exposed to hypobaric hypoxia? What is the main finding and its importance? Prepubertal rats, unlike adult rats, did not increase tolerance to hypoxia–reoxygenation in response acute exposure to hypobaric hypoxia, which impaired cardiac contractile economy. This finding could be related to a failure to increase nitric oxide synthase expression, hence modulation of mitochondrial oxygen consumption and ATP production.
Objective Evidence of Gastro-Esophageal Reflux Disease is Rare in Patients with Autoimmune Gastritis.

BACKGROUND AND AIMS Patients with autoimmune atrophic gastritis (AAG) often complain of acid reflux symptoms, despite the evidence of hypo-achlorhydria. Rome IV criteria are used to define functional esophageal disorders. Our aim was to characterize gastroesophageal reflux disease (GERD) phenotypes in patients with AAG. METHODS Between 2017-2018, 172 AAG patients were evaluated at Gastro-Oncology outpatient clinic of University of Padua. Of them, 38 patients with reflux symptoms underwent high-resolution manometry (HRM) and multichannel intraluminal impedance-pH monitoring (MII-pH). Seventy-six AAG consecutive patients asymptomatic for gastroesophageal reflux were selected as age and gender matched controls. Serum biomarkers (pepsinogens, gastrin-17 and Helicobacter pylori antibodies), upper endoscopy, histology and clinical data were compared. RESULTS Out of 38/172 (22%) AAG patients with reflux symptoms, 2/38 had a GERD diagnosis based on abnormal esophageal acid exposure and 6/38 had a major motility disorder (i.e. outflow obstruction). Among the 30/38 patients with normal endoscopic findings, 9/30 had reflux hypersensitivity, 19 functional heartburn, 1 functional globus, 1 functional chest pain according to the Rome IV criteria. Antral atrophy, advanced corpus atrophy and OLGA stage were more frequent in controls than in reflux patients (p=0.01, p=0.031, p=0.01, respectively). No differences were found for serum biomarkers and symptom presentation. Most of the patients received proton pump inhibitors (PPIs) treatment (87%), with a minority (34%) reporting clinical benefit. CONCLUSIONS Reflux symptoms are relatively common in AAG patients, but a firm diagnosis of GERD is rare (5%), whereas most of the patients have a functional disorder. PPI treatment is mostly clinical ineffective and should not be largely indicated.
Influence of Dissolved Organic Carbon and Suspension Viscosity on Membrane Fouling in Submerged Membrane Bioreactor

Abstract This paper deals with the membrane fouling in membrane bioreactor (MBR). Based on the experimental data obtained in the MBR pilot plant study, the influence of F/M ratio on the irreversible and reversible fouling was discussed in the wide range of MLSS concentration. In the case of lower MLSS concentration (2,000–3,000 mg/L), irreversible fouling rate of membrane increased with increasing F/M ratio because of the accumulation of DOC in the mixed liquor. It seems that soluble microbial products with the similar size of the membrane pore will be most responsible for the irreversible fouling. In the case of higher MLSS concentration (8,000–12,000 mg/L), reversible fouling rate of membrane increased with increasing F/M ratio because of the increased suspension viscosity caused by the increased activated sludge size or volume even in the same MLSS concentration.
THE ROLE OF RELATIVE RESPONSE FACTOR IN RELATED SUBSTANCES METHOD DEVELOPMENT BY HIGH PERFORMANCE LIQUID CHROMATOGRAPHY (HPLC)

A study was conducted on Relative Response Factor by changing the High Performance Liquid Chromatography (HPLC) chromatographic method conditions like different HPLC columns, Flow rate, pH, Temperature, Buffer concentration, Detector wavelength, different Detectors (Ultraviolet & Photo Diode Array Detectors) and different Solvent grades and observed the variations in established RRF. The authors have studied the impact on RRF by changing the Robustness parameters and HPLC columns and all the results were compared. The comparision study has shown that any slight variations in method conditions, the impact is observed on established RRF values.
Improving the sensitivity of cluster‐based statistics for functional magnetic resonance imaging data

Because of the high dimensionality of neuroimaging data, identifying a statistical test that is both valid and maximally sensitive is an important challenge. Here, we present a combination of two approaches for functional magnetic resonance imaging (fMRI) data analysis that together result in substantial improvements of the sensitivity of cluster‐based statistics. The first approach is to create novel cluster definitions that optimize sensitivity to plausible effect patterns. The second is to adopt a new approach to combine test statistics with different sensitivity profiles, which we call the min(p) method. These innovations are made possible by using the randomization inference framework. In this article, we report on a set of simulations and analyses of real task fMRI data that demonstrate (a) that the proposed methods control the false‐alarm rate, (b) that the sensitivity profiles of cluster‐based test statistics vary depending on the cluster defining thresholds and cluster definitions, and (c) that the min(p) method for combining these test statistics results in a drastic increase of sensitivity (up to fivefold), compared to existing fMRI analysis methods. This increase in sensitivity is not at the expense of the spatial specificity of the inference.
Impacts of n‐acetyl cysteine on gibberellic acid‐induced testicular dysfunction through regulation of inflammatory cytokines, steroid and antioxidant activity

In agriculture, gibberellic acid (GA3) is commonly used with extreme dangers for public health. The current research evaluates the improving effects of n‐acetyl cysteine (NAC, 150 mg/kg bw) co‐administered with GA3 (55 mg/kg bw) mediated testicular injury. Twenty‐four male albino rats were split into 4 groups: Negative control (CNT), NAC group, positive GA3 group and protective group, co‐administered NAC plus GA3. On day 21, rats were anesthetised then euthanised by decapitation. Blood samples were collected; testicular samples were taken for semen analysis, serum chemistry, RNA extraction, histological and antioxidants markers examination. Our results revealed a significant decline p < . 05 of catalase level and total antioxidant capacity. There was a substantial rise of MDA concentration in GA3‐treated rats along with a considerable decrease of the antioxidant markers (SOD, GSH) and serum male reproductive hormones. In GA3‐treated rats, an overexpression of the inflammatory cytokines (TNF‐α, IL‐1β) and anti‐inflammatory cytokine IL‐10 with boost mRNA expression of nuclear factor‐kappa (NFkB) were confirmed. There was downregulation of steroidogenesis genes and decrease in sperm quality and concentration with an increase in sperm abnormalities, all were reported in GA3‐treated rats. NAC treatment significantly increased the antioxidant state, testicular function beside structural germ cell and seminiferous tubules histology accompanied by upsurge of steroidogenic mRNA expressions (P450scc and 3β‐HSD) and downregulated the pro‐inflammatory cytokines mRNA expression (TNF‐α, IL‐1β). These results confirm the antioxidant capability of NAC and afford robust evidence about the ameliorative effect of the NAC to attenuate the testicular injury induced by GA3 through modulation of the antioxidant defence system, steroidogenic and pro‐inflammatory cytokines mRNA expression.
Impact of Sugar Tax on Sugar-sweetened Beverage Consumption among Saudi Schoolchildren.

PURPOSE In 2017, Saudi Arabia introduced a 120% tax on energy drinks and a 50% tax on soft drinks. The impact of this policy on the consumption of sugar-sweetened beverages (SSB) among schoolchildren is not known in this country. The present study evaluated the impact of the excise tax on SSB consumption in the tri-city metropolitan area of Dammam-Khobar-Dhahran, Eastern Province, Saudi Arabia. MATERIALS AND METHODS A repeated cross-sectional design was used to examine the difference between pre- and post-tax SSBs consumption among schoolchildren (12-14 years old) in Dammam-Khobar-Dhahran cities. A beverage-consumption frequency questionnaire was completed by 453 participants before the tax implementation and 334 participants after the tax implementation. The tax on soft drinks was increased by 50% and on energy drinks by 120%. Pre-tax data were collected in May 2017 and post-tax data in April 2018. RESULTS The proportion of participants who consumed energy drinks was 46.1% (95% CI: 42-51) before tax implementation, decreasing to 38.4% (95% CI: 33-44) after tax implementation, a reduction of nearly 8%. 92.5% (95% CI: 90-95) of the participants consumed soft drinks before tax implementation and 94.6% (95% CI: 92-97) did so after tax implementation, an increase of about 2%. CONCLUSIONS The study showed no statistically significant impact of tax implementation on the consumption of energy drinks and soft drinks in this sample of children.
Knowledge, attitude, and practice toward Zika virus among staff of comprehensive health services centers affiliated with Tehran University of Medical Sciences in 2020

Assessment of knowledge, attitude, and practice of healthcare providers regarding Zika virus, provides information on their ability to prevent its transmission, and emphasizes the necessity of implementing educational programs if their knowledge, attitude, and practice are low. Therefore, the present study aimed to investigate the knowledge, attitude, and practice of the staff of comprehensive health services centers affiliated with Tehran University of Medical Sciences regarding Zika Virus.
Evaluation of functional muscle anatomy scalability in the canine hind limb

In contrast to other mammals, the large variation in dog sizes is not accompanied by any significant genetic re‐organization. In order to study the relationship between body mass, limb length and the functional anatomical muscle parameters of the canine hind limb, a large dataset comprising of muscle masses, optimal muscle fibre lengths and physiological cross‐sectional area's (PCSA) were acquired for twenty‐five muscles in ten dogs of sizes varying between 20 kg and 52 kg. The potential of body mass and limb length for reliably scaling individual muscle masses, optimal muscle fibre lengths and PCSA's were examined. For the majority of the muscles of the canine hind limb, neither body mass nor limb length were reliable scaling parameter for either muscle masses, PCSA's and optimal fibre length. These results indicate the need of a breed‐specific approach to musculoskeletal modelling in future canine musculoskeletal research.