Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth and gut health in chickens on diets varying in fatty acid composition and selenium content

Abstract Chicken feed composition is essential to chicken health and meat composition. Fatty acids of the n-6 and n-3 families and selenium are of high importance to inflammatory processes. The effect of varying chicken dietary compositions in saturated and unsaturated oil sources with varying n-6 and n-3 levels combined with two levels of organic selenium on chicken growth, gizzard and gut health was studied. Wheat-based chicken diets supplemented with either 0.1 mg Se/kg feed or 1.0 mg Se/kg feed in combinations with rendered fat, soybean oil, rapeseed oil, linseed oil, palm oil, and red palm oil were used. Altering the fatty acid profile and selenium level did not significantly affect gizzard or gut health in broiler chickens, but increased early growth in chickens was seen for the red palm oil, linseed oil, and high selenium groups. Increased selenium levels lead to fewer incidences of loose digesta and higher gizzard weights.
Response of hepatic MFO activity and plasma sex steroids to secondary treatment of bleached kraft pulp mill effluent and mill shutdown

The discharge of bleached kraft mill effluent (BKME) into Jackfish Bay, Lake Superior, Canada, has been associated with a number of changes in the physiology and whole organism responses of four fish species. Current studies have been following physiological indicators of BKME impact for evidence of improvement after the installation of a secondary treatment system. Secondary treatment has not been successful in eliminating BKME impacts on hepatic mixed-function oxygenase (MFO) activity in white sucker (Catostomus commersoni) because fish collected from Jackfish Bay after initiation of secondary treatment exhibited similar MFO activity as recorded in samples collected during two previous years. Hepatic MFO activity was also induced in long-nose sucker (Catostomus catostomus), lake whitefish (Coregonus clupeaformis), and lake trout (Salvelinus namaycush) after secondary treatment. However, samples collected two weeks after a planned mill maintenance shutdown showed no MFO induction in long-nose sucker, reduced MFO activity in white sucker, and a reduced impact zone for MFO induction in lake whitefish. A reduction in circulating levels of gonadal sex steroids has also been recorded in fish exposed to primary-treated BKME in Jackfish Bay. In contrast, neither secondary treatment nor mill shutdown was sucessful in eliminating impacts of BKME exposur on levels of testosterone and 17β-estradiol in female white sucker and long-nose sucker. The short duration of MFO induction after shutdown and the peristence of steroid reductions suggest that (a) secondary treatment has not been successful in removing “MFO-active” compounds from BKME, (b) induction is not related to sediment contamination with persistent compounds, (c) the inducing agents are rapidly cleared by fish, and (d) effects on steroids may not be directly related to MFO induction.
Exclusion of Vibrio spp. by an antagonistic marine actinomycete Streptomyces rubrolavendulae M56

A marine actinomycete Streptomyces rubrolavendulae M56 isolated from the sediments of Bay of Bengal and displaying biogranulation property was used for the study. The strain showed antagonistic property against vibrios, the opportunistic pathogens in aquaculture. The efficacy of the biogranules of actinomycete M56 in competitive exclusion of Vibrio spp. was tested both in vitro and in vivo. Streptomyces rubrolavendulae M56 biogranules could significantly exclude the pathogenic Vibrio spp. in co-culture experiments (in vitro). In vivo exclusion of Vibrio spp. in a Penaeus monodon postlarval rearing system was evaluated by treatment of the rearing water with biogranules of S. rubrolavendulae M56. The experiments proved that S. rubrolavendulae M56 biogranules could reduce the pathogenic Vibrio spp. , while maintaining total heterotrophic bacterial count. Therefore, the actinomycete biogranules (M56) can be used as a promising alternative to antibiotics in the shrimp larval production system which is often affected by vibriosis.
Genotype–phenotype associations in a large PRPH2‐related retinopathy cohort

Molecular variant interpretation lacks disease gene‐specific cohorts for determining variant enrichment in disease versus healthy populations. To address the molecular etiology of retinal degeneration, specifically the PRPH2‐related retinopathies, we reviewed genotype and phenotype information obtained from 187 eyeGENE® participants from 161 families. Clinical details were provided by referring clinicians participating in the eyeGENE® Network. The cohort was sequenced for variants in PRPH2. Variant complementary DNA clusters and cohort frequency were compared to variants in public databases to help us to determine pathogenicity by current American College of Medical Genetics and Genomics/Association for Molecular Pathology interpretation criteria. The most frequent variant was c.828+3A>T, which affected 28 families (17.4%), and 25 of 79 (31.64%) variants were novel. The majority of missense variants clustered in the D2 intracellular loop of the peripherin‐2 protein, constituting a hotspot. Disease enrichment was noted for 23 (29.1%) of the variants. Hotspot and disease‐enrichment evidence modified variant classification for 16.5% of variants. The missense allele p.Arg172Trp was associated with a younger age of onset. To the best of our knowledge, this is the largest patient cohort review of PRPH2‐related retinopathy. Large disease gene‐specific cohorts permit gene modeling for hotspot and disease‐enrichment analysis, providing novel variant classification evidence, including for novel missense variants.
ALTERATIONS OF CYCLIC NUCLEOTIDE‐RELATED ENZYMES AND ATPase DURING UNILATERAL ISCHEMIA AND RECIRCULATION IN GERBIL CEREBRAL CORTEX

Abstract— Several enzyme activities were determined in gerbil cerebral cortex during unilateral ischemia or in the post‐ischemic period following 1 h of ischemia. Adenylate cyclase and Na + ‐K + ‐activated ATPase showed essentially the same pattern. Neither enzyme changed during ischemia but the activities decreased on recirculation to 40–60% of right side control by 5 h. The ATPase had returned to control level by 20h; the adenylate cyclase by 7 days of recirculation. Particulate cyclic AMP‐dependent protein kinase in the ischemic left hemisphere decreased throughout the 6h of ischemia. It remained depressed in the first 5 h of the post‐ischemic period but returned to control by 20 h. The soluble protein kinase activity, the soluble cyclic AMP and cyclic GMP phosphodiesterase and the Mg2+ dependent ATPase did not change significantly during the ischemic or post‐ischemic periods. The results suggest that ischemia and/or recirculation may affect cellular membranes and membrane‐bound enzymes, in particular. Furthermore, the results imply that despite apparent metabolite recovery during the post‐ischemic period, enzymatic changes are occurring that may be important for both the quality of recovery and the response to further ischemic insult.
Gastrointestinal bacteria in Rohu, Labeo rohita (Actinopterygii: Cypriniformes: Cyprinidae): scanning electron microscopy and bacteriological study.

The gut microbiota of marine and freshwater fish has been widely investigated during the last two decades (Cahill 1990, Ringø et al. 1995, Hansen and Olafsen 1999, Ringø and Birkbeck 1999, Ghosh et al. 2002a, Saha et al. 2006). It is a consensus view that dense bacterial population levels occurs in the gastrointestinal (GI) tract of fish (Austin 2002), and the gut microbiota can be defined as either autochthonous (indigenous) or allochtonous (transient) depending upon its ability to adhere and colonize the mucus layer in the digestive tract (Ringø and Birkbeck 1999, Ringø et al. 2003, 2007). Previous studies have isolated different bacteria species from the gut of one of the Indian major carps—rohu, Labeo rohita (Hamilton, 1822) and it has been suggested that the gut microbiota might be beneficial in the nutrition of the fish (Ghosh et al. 2002a, Kar and Ghosh 2008, Ray et al. 2010). Furthermore, attempts have also been made to use beneficial gut bacilli originally isolated from rohu as the probiotics for the fish (Ghosh et al. 2002b, 2003). One of the major criteria for selecting a probiotic strain is its ability to adhere and ACTA ICHTHYOLOGICA ET PISCATORIA (2010) 40 (2): 129–135 DOI: 10.3750/AIP2010.40. 2.05
Rare loss-of-function mutations of PTGIR are enriched in fibromuscular dysplasia

Abstract Aims Fibromuscular dysplasia (FMD) and spontaneous coronary artery dissection (SCAD) are related, non-atherosclerotic arterial diseases mainly affecting middle-aged women. Little is known about their physiopathological mechanisms. We aimed to identify rare genetic causes to elucidate molecular mechanisms implicated in FMD and SCAD. Methods and results We analysed 29 exomes that included familial and sporadic FMD. We identified one rare loss-of-function variant (LoF) (frequencygnomAD = 0.000075) shared by two FMD sisters in the prostaglandin I2 receptor gene (PTGIR), a key player in vascular remodelling. Follow-up was conducted by targeted or Sanger sequencing (1071 FMD and 363 SCAD patients) or lookups in exome (264 FMD) or genome sequences (480 SCAD), all independent and unrelated. It revealed four additional LoF allele carriers, in addition to several rare missense variants, among FMD patients, and two LoF allele carriers among SCAD patients, including one carrying a rare splicing mutation (c.768 + 1C>G). We used burden test to test for enrichment in patients compared to gnomAD controls, which detected a putative enrichment in FMD (PTRAPD = 8 × 10−4), but not a significant enrichment (PTRAPD = 0.12) in SCAD. The biological effects of variants on human prostaclycin receptor (hIP) signalling and protein expression were characterized using transient overexpression in human cells. We confirmed the LoFs (Q163X and P17RfsX6) and one missense (L67P), identified in one FMD and one SCAD patient, to severely impair hIP function in vitro. Conclusions Our study shows that rare genetic mutations in PTGIR are enriched among FMD patients and found in SCAD patients, suggesting a role for prostacyclin signalling in non-atherosclerotic stenosis and dissection.
Cigarette Smoking during Pregnancy: Effects on Antioxidant Enzymes, Metallothionein and Trace Elements in Mother-Newborn Pairs

The effect of maternal smoking as a source of exposure to toxic metals Cd and Pb on superoxide dismutase (SOD) and glutathione peroxidase (GPx) activity, metallothionein (MT), Cd, Pb, Cu, Fe, Mn, Se and Zn concentrations were assessed in maternal and umbilical cord blood and placenta in 74 healthy mother-newborn pairs after term delivery. Sparse discriminant analysis (SDA) was used to identify elements with the strongest impact on the SOD, GPx and MT in the measured compartments, which was then quantified by multiple regression analysis. SOD activity was lower in maternal and cord plasma, and higher in the placenta of smokers compared to non-smokers, whereas GPx activity and MT concentration did not differ between the groups. Although active smoking during pregnancy contributed to higher maternal Cd and Pb concentrations, its contribution to the variability of SOD, GPx or MT after control for other elements identified by SDA was not significant. However, an impaired balance in the antioxidant defence observed in the conditions of relatively low-to-moderate exposure levels to Cd and Pb could contribute to an increased susceptibility of offspring to oxidative stress and risk of disease development later in life. Further study on a larger number of subjects will help to better understand complex interactions between exposure to toxic elements and oxidative stress related to maternal cigarette smoking.
Increased glucocorticoid concentrations in early life cause mitochondrial inefficiency and short telomeres

ABSTRACT Telomeres are DNA structures that protect chromosome ends. However, telomeres shorten during cell replication and at critically low lengths can reduce cell replicative potential, induce cell senescence and decrease fitness. Stress exposure, which elevates glucocorticoid hormone concentrations, can exacerbate telomere attrition. This phenomenon has been attributed to increased oxidative stress generated by glucocorticoids (‘oxidative stress hypothesis’). We recently suggested that glucocorticoids could increase telomere attrition during stressful periods by reducing the resources available for telomere maintenance through changes in the metabolic machinery (‘metabolic telomere attrition hypothesis’). Here, we tested whether experimental increases in glucocorticoid levels affected telomere length and mitochondrial function in wild great tit (Parus major) nestlings during the energy-demanding early growth period. We monitored resulting corticosterone (Cort) concentrations in plasma and red blood cells, telomere lengths and mitochondrial metabolism (metabolic rate, proton leak, oxidative phosphorylation, maximal mitochondrial capacity and mitochondrial inefficiency). We assessed oxidative damage caused by reactive oxygen species (ROS) metabolites as well as the total non-enzymatic antioxidant protection in plasma. Compared with control nestlings, Cort-nestlings had higher baseline corticosterone, shorter telomeres and higher mitochondrial metabolic rate. Importantly, Cort-nestlings showed increased mitochondrial proton leak, leading to a decreased ATP production efficiency. Treatment groups did not differ in oxidative damage or antioxidants. Hence, glucocorticoid-induced telomere attrition is associated with changes in mitochondrial metabolism, but not with ROS production. These findings support the hypothesis that shortening of telomere length during stressful periods is mediated by glucocorticoids through metabolic rearrangements. Summary: Experimental simulation of natural stressful developmental conditions reveals that glucocorticoid hormones induce telomere shortening by decreasing mitochondrial efficiency without altering oxidative stress, suggesting that telomeres are costly to maintain.
Saving the Diabetic Foot During the COVID-19 Pandemic: A Tale of Two Cities

Of all the late complications of diabetes, those involving the foot have traditionally required more face-to-face patient visits to clinics to treat wounds by debridement, offloading, and many other treatment modalities. The advent of the coronavirus disease 2019 (COVID-19) pandemic has resulted not only in the closing of most outpatient clinics for face-to-face consultations but also in the inability to perform most laboratory and imaging investigations. This has resulted in a paradigm shift in the delivery of care for those with diabetic foot ulcers. The approaches to this challenge in two centers with an interest in diabetic foot disease, including virtual consultations using physician-to-patient and physician–to–home nurse telemedicine as well as home podiatry visits, are described in this review and are illustrated by several case vignettes. The outcomes from these two centers suggest that we may be witnessing new possibilities in models of care for the diabetic foot.
Child school injury in Lebanon: A study to assess injury incidence, severity and risk factors

Background School-based injuries represent a sizeable portion of child injuries. This study investigated the rates of school-based injuries in Lebanon, examining injury mechanisms, outcomes and associated risk factors. Methods Data were prospectively collected by intern school nurses at 11 private schools for the 2018–2019 academic year. Descriptive and inferential analyses were performed. Chi-square comparisons were conducted to determine the significance of any differences in injury rates between boys and girls for each category of school. Results 4,619 injury cases were collected. The yearly rate for school injuries was 419.1 per 1,000 children for the year 2018–2019. Boys demonstrated a significantly higher injury rate for all mechanisms of injuries, with the exception of being injured while walking, injured in the gym/sports areas, and other areas outside the playground and classroom. Elementary school children had the highest rate of injuries, nearly 2.4 times higher than kindergarten, 2.8 times higher than middle school, and 14.5 times higher than high school. Injuries to the face, upper extremities, and lower extremities were nearly 3 times more common than injuries to other areas of the body. Bumps/hits and bruises were most common—almost 3 times more likely than all other injury types. Injuries were mainly minor or moderate in severity—severe injuries were about 10 times less likely. Most injuries were unintentional, with rates nearly 5 times higher than those with unclear intent and 12 times higher than intentional injuries. Conclusions School injuries represent a relatively common problem. Compliance with playground safety standards coupled with the implementation of injury prevention strategies and active supervision at schools can curtail child injuries and ensure a safe and injury-free school environment.
Antioxidant, Anti-Inflammatory, and Microbial-Modulating Activities of Essential Oils: Implications in Colonic Pathophysiology

Essential oils (EOs) are a complex mixture of hydrophobic and volatile compounds synthesized from aromatic plants, most of them commonly used in the human diet. In recent years, many studies have analyzed their antimicrobial, antioxidant, anti-inflammatory, immunomodulatory and anticancer properties in vitro and on experimentally induced animal models of colitis and colorectal cancer. However, there are still few clinical studies aimed to understand their role in the modulation of the intestinal pathophysiology. Many EOs and some of their molecules have demonstrated their efficacy in inhibiting bacterial, fungi and virus replication and in modulating the inflammatory and oxidative processes that take place in experimental colitis. In addition to this, their antitumor activity against colorectal cancer models makes them extremely interesting compounds for the modulation of the pathophysiology of the large bowel. The characterization of these EOs is made difficult by their complexity and by the different compositions present in the same oil having different geographical origins. This review tries to shift the focus from the EOs to their individual compounds, to expand their possible applications in modulating colon pathophysiology.
Metric dental diversity of Ryukyu Islanders: a comparative study among Ryukyu and other Asian populations

Mesiodistal and buccolingual crown diameters were examined to describe and compare patterns of metric dental variation in five modern samples from the Ryukyu Island chain (Miyako, Ishigaki, Tokunoshima, and two samples from Okinawa Island). Principal component analysis applied to two separate datasets, raw measurement and standardized (C-score) data, for 32 Asian and Pacific samples, including the five Ryukyu Islander series, produced an overall size factor and three shape factors (relative size of mesiodistal diameters versus buccolingual diameters and two kinds of front-back polarity). Ryukyu Islanders have similar crown dimensions as those of the predominant eastern Asian groups, characterized by mesodont dentition. In terms of shape factors, Ryukyu Islanders are distinctive among eastern Asian population groups on the one hand, and show diversity among themselves on the other hand. The inter-regional variation of Ryukyu Island groups estimated by Fst falls within the range of 4–6% of the total variance, which is greater than those of Arctic population samples (Aleuts and Eskimos). The average within-group variance of the Ryukyu Island series measured by the R-matrix method (intra-regional variation) is compatible with those of East and Northeast Asians, Micronesians, and Polynesians. These findings suggest that differential patterns of long-term gene flow from an outside source, geographical isolation, and genetic drift in each island of the Ryukyu Island chain has produced the morphological diversification of modern Ryukyu Islanders.
Cost-Effectiveness of Hepatocellular Carcinoma Surveillance: An Assessment of Benefits and Harms.

OBJECTIVES The value of hepatocellular carcinoma (HCC) surveillance is defined by the balance of benefits, i.e., early tumor detection, and potential harms, related to false positive and indeterminate results. Although physical harms can be observed in 15%-20% of patients with cirrhosis undergoing HCC surveillance, previous cost-effectiveness analyses have not incorporated costs of harms. We aimed to evaluate the cost-effectiveness of HCC surveillance including both benefits and harms. DESIGN We constructed a Markov model to compare surveillance strategies of ultrasound (US) alone, US and alpha fetoprotein (AFP), and no surveillance in 1 million simulated patients with compensated cirrhosis. Harms included imaging and biopsy in patients undergoing surveillance for HCC. Model inputs were based on literature review, and costs were derived from the Medicare fee schedule, with all costs inflated to 2018 dollars. The primary outcome was the incremental cost-effectiveness ratio per incremental quality-adjusted life-year. RESULTS In the base case analysis, US with AFP was the dominant strategy over both US alone and no surveillance. In a probabilistic sensitivity analysis, US with AFP was the most cost-effective strategy in 80.1% of simulations at a willingness-to-pay threshold of $100,000 per quality-adjusted life-year. In our threshold analyses, an HCC incidence >0.4% per year and surveillance adherence >19.5% biannually were necessary for US with AFP to be cost-effective compared with no surveillance. DISCUSSION Accounting for both surveillance-related benefits and harms, US and AFP is more cost-effective for HCC surveillance than US alone or no surveillance in patients with compensated cirrhosis.
The impact of a yoga-based physical therapy group for individuals with traumatic brain injury: results from a pilot study

ABSTRACT Objective To compare the impacts of yoga-based physical therapy versus a seated rest within the context of standard rehabilitation practice on sleep, heart rate variability (HRV), anxiety, and fatigue during acute traumatic brain injury (TBI) rehabilitation. Methods Eleven individuals participated in this crossover study involving the following interventions in a randomized order: group yoga-based physical therapy (YPT), conventional physical therapy (CPT), and group seated rest in a relaxing environment (SR). HRV and self-reported anxiety and fatigue were measured immediately before and after each group, and sleep after each condition and at baseline. Data was analyzed using generalized linear mixed models with repeated measures. Results The interaction between time and treatment was statistically significant (p = .0203). For the SR treatment, wake after sleep onset (WASO) rate was reduced from 14.99 to 10.60 (IRR = 0.71; p = .006). Time and treatment were not found to be statistically significantly associated with any of the secondary outcomes. Conclusion Yoga-based physical therapy is feasible and safe in the inpatient rehabilitation setting following TBI. Sleep quality improved following the addition of a one-hour seated rest in a relaxing environment to a standard rehabilitation daily schedule, suggesting that structured rest time may be beneficial to sleep hygiene during inpatient rehabilitation following TBI. ClinicalTrials.Gov Registration Number: NCT03701594