PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies.

PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous genes, as well as to their corresponding phylogeny-based orthology and paralogy relationships. In addition, PhylomeDB trees and alignments can be downloaded for further processing to detect and date gene duplication events, infer past events of inter-species hybridization and horizontal gene transfer, as well as to uncover footprints of selection, introgression, gene conversion, or other relevant evolutionary processes in the genes and organisms of interest. Here, we describe the latest evolution of PhylomeDB (version 5). This new version includes a newly implemented web interface and several new functionalities such as optimized searching procedures, the possibility to create user-defined phylome collections, and a fully redesigned data structure. This release also represents a significant core data expansion, with the database providing access to 534 phylomes, comprising over 8 million trees, and homology relationships for genes in over 6000 species. This makes PhylomeDB the largest and most comprehensive public repository of gene phylogenies. PhylomeDB is available at http://www.phylomedb.org.

Platelet-rich Plasma for the Treatment of Erectile Dysfunction: A Prospective, Randomized, Double-blind, Placebo-controlled Clinical Trial.

PURPOSE: We assessed the safety and efficacy of 2 injections of platelet-rich plasma for treating mild to moderate erectile dysfunction by conducting a prospective, randomized, double-blind, placebo-controlled clinical trial. MATERIALS AND METHODS: Men with mild to moderate erectile dysfunction (International Index of Erectile Function scores 11-25) were randomized to receive either 2 injections of platelet-rich plasma or placebo separated by 1 month. Primary outcome was percentage of men meeting minimum clinically important difference at 1 month after the second injection. Secondary outcomes were change in International Index of Erectile Function at 1, 3, and 6 months, and changes in penile vascular parameters and adverse events at 6 months. RESULTS: We randomized 61 men: 28 into platelet-rich plasma and 33 into placebo. There was no difference between groups in percentage of men meeting minimum clinically important difference at 1 month: 14 (58.3%) in platelet-rich plasma vs 15 (53.6%) in placebo (P = .730). Mean International Index of Erectile Function-Erectile Function domain changed from 17.4 (95% CI 15.8-19.0) to 21 (17.9-24.0) at 1 month in men receiving platelet-rich plasma, vs 18.6 (17.3-19.8) to 21.6 (19.1-24.1) in the placebo group; however, there was no significant difference between groups (P = .756). There were no major adverse events and only 1 minor adverse event in each group. There were no changes in penile Doppler parameters from baseline to 6 months. CONCLUSIONS: The results of our prospective, double-blind, randomized, placebo-controlled clinical trial suggest that 2 injections of intracavernosal platelet-rich plasma separated by 1 month in men with mild to moderate erectile dysfunction is safe, but we found no difference in efficacy between platelet-rich plasma and placebo.

Assessing the energy trap of industrial agriculture in North America and Europe: 82 balances from 1830 to 2012.

Early energy analyses of agriculture revealed that behind higher labor and land productivity of industrial farming, there was a decrease in energy returns on energy (EROI) invested, in comparison to more traditional organic agricultural systems. Studies on recent trends show that efficiency gains in production and use of inputs have again somewhat improved energy returns. However, most of these agricultural energy studies have focused only on external inputs at the crop level, concealing the important role of internal biomass flows that livestock and forestry recirculate within agroecosystems. Here, we synthesize the results of 82 farm systems in North America and Europe from 1830 to 2012 that for the first time show the changing energy profiles of agroecosystems, including livestock and forestry, with a multi-EROI approach that accounts for the energy returns on external inputs, on internal biomass reuses, and on all inputs invested. With this historical circular bioeconomic approach, we found a general trend towards much lower external returns, little or no increases in internal returns, and almost no improvement in total returns. This "energy trap" was driven by shifts towards a growing dependence of crop production on fossil-fueled external inputs, much more intensive livestock production based on feed grains, less forestry, and a structural disintegration of agroecosystem components by increasingly linear industrial farm managements. We conclude that overcoming the energy trap requires nature-based solutions to reduce current dependence on fossil-fueled external industrial inputs and increase the circularity and complexity of agroecosystems to provide healthier diets with less animal products. Supplementary Information: The online version contains supplementary material available at 10.1007/s13593-023-00925-5.

Platelet Rich Plasma (PRP) Growth Factor Concentration Varies in Men With Erectile Dysfunction.

BACKGROUND: Platelet Rich Plasma (PRP) is a novel therapy rich in growth factors and cytokines used to target the underlying causes of erectile dysfunction (ED). It is not known, however, if the composition of growth factors in PRP varies between men. AIM: To evaluate PRP growth factor variability among men with ED. METHODS: Whole blood was collected from 8 participants with at least a 6-month history of ED. Seven men with Peyronie's disease and 1 healthy male (without sexual dysfunction) were used as the control group. PRP was extracted from whole blood using the Arthrex Angel system. A Human Growth Factor Antibody Array for 41 proteins was performed using 3 participants and the healthy control. Using all 16 samples, quantitative detection of factors from the array that were decreased by 1.5-fold were validated with western blot. OUTCOMES: From the growth factor array, 2 growth factors-granulocyte-macrophage colony stimulating factor and transforming growth factor-ß were identified as having a 1.5-fold decrease between the participants and the control. Vascular endothelial growth factor (VEGF) was selected because androgens can upregulate VEGF production. Other than a weak negative correlation between VEGF expression and age, we found no correlation between growth factor expression for granulocyte-macrophage colony stimulating factor or transforming growth factor-ß and age, body mass index, or comorbidities. CLINICAL TRANSLATION: PRP growth factor concentration appears to vary among men with ED. PRP treatment for ED may need to be personalized for patients, depending on individual growth factor concentration. STRENGTHS AND LIMITATIONS: This study demonstrates the variability in PRP growth factors among men with ED. This is an important finding in the investigation of PRP as a restorative treatment option for men with ED. Our study, however, was limited by a small sample size. CONCLUSION: PRP growth factors vary among men with ED. Khodamoradi K, Dullea A, Golan R, et al. Platelet Rich Plasma (PRP) Growth Factor Concentration Varies in Men With Erectile Dysfunction. J Sex Med 2022;19:1488-1493.

MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life.

Inferring homology relationships across genes in different species is a central task in comparative genomics. Therefore, a large number of resources and methods have been developed over the years. Some public databases include phylogenetic trees of homologous gene families which can be used to further differentiate homology relationships into orthology and paralogy. MetaPhOrs is a web server that integrates phylogenetic information from different sources to provide orthology and paralogy relationships based on a common phylogeny-based predictive algorithm and associated with a consistency-based confidence score. Here we describe the latest version of the web server which includes major new implementations and provides orthology and paralogy relationships derived from ∼8.2 million gene family trees-from 13 different source repositories across ∼4000 species with sequenced genomes. MetaPhOrs server is freely available, without registration, at http://orthology.phylomedb.org/.

Peyronie's disease in a patient after COVID-19 infection: A case report.

Coronavirus disease 2019 (COVID-19) is an emerging infectious disease caused by a novel coronavirus (SARS-CoV-2), which demonstrates the ability to invade endothelial cells and cause systemic inflammation. Many possible long-term sequelae of COVID-19 remain unidentified. We describe a case of a man who developed Peyronie's disease after a resolved COVID-19 infection. Erectile dysfunction was confirmed by the International Index of Erectile Function-15(IIEF) and Sexual Health Inventory for Men(SHIM) scores. A diagnosis was Peyronie's disease was confirmed on ultrasound. Furthermore, he was found to have low endothelial progenitor cells colony-forming units and low brachial artery flow-mediated vasodilation, both of that are indicative of endothelial dysfunction. This case suggests Peyronie's disease should be considered as a possible sequela of COVID-19 infection and providers should inquire about a history of COVID-19 infection in patients presenting with Peyronie's disease.

Effect of Natesto on Reproductive Hormones, Semen Parameters and Hypogonadal Symptoms: A Single Center, Open Label, Single Arm Trial.

PURPOSE: To evaluate the effect of short-acting 4.5% nasal testosterone gel (Natesto) on serum testosterone, gonadotropins, total motile sperm count, health related quality of life and sexual function. MATERIALS AND METHODS: This was a single institution, open label, single arm trial conducted between November 2017 and September 2019 at the University of Miami. Men 18 to 55 years old diagnosed with symptomatic hypogonadism (total testosterone less than 300 ng/dl on 2 occasions) were included. Men with azoospermia, vasectomy or a total motile sperm count less than 5 million were excluded. Enrolled patients were treated with Natesto, a short-acting nasal testosterone (125 µl per nostril, 11.0 mg testosterone per dose, TID) for 6 months. RESULTS: In total, 60 men were enrolled in the study. Of these, 44 and 33 patients were evaluated for testosterone at 3 and 6 months, respectively. A total of 31 patients (90.9%) reached a normal testosterone level (greater than 300 ng/dl) at 6 months. Follicle stimulating hormone and luteinizing hormone levels were maintained within the normal range in 81.8% and 72.7% of patients at 6 months, respectively. Total motile sperm count was maintained with total motile sperm count greater than 5 million over the treatment period in 88.4% of men at 3 months and 93.9% at 6 months. There were statistically significant improvements on International Index of Erectile Function sexual desire and overall satisfaction domains at 6 months. CONCLUSIONS: Natesto appears to increase testosterone while maintaining semen parameters in a majority of men. Natesto has the potential to be a safe and effective treatment for men with functional hypogonadism who wish to preserve semen parameters. Long-term studies beyond 6 months are needed before we can safely prescribe nasal testosterone gel for men interested in fertility.

Type 3 cytokines in liver fibrosis and liver cancer.

The type 3 cytokines IL-17 and IL-22 play a crucial, well synchronized physiological role in wound healing and repairing tissue damage due to infections or injury at barrier surfaces. These cytokines act on epithelial cells to induce secretion of early immune mediators, recruitment of inflammatory cells to the site of injury, and to trigger tissue repair mechanisms. However, if the damage persists or if these cytokines are dysregulated, then they contribute to a number of inflammatory pathologies, autoimmune conditions and cancer. The liver is a multifunctional organ that plays an essential role in metabolism, detoxification, and immune surveillance. It is also exposed to a variety of pathogens, toxins and injuries. Over the past decade, IL-17 and IL-22 have been implicated in various aspects of liver inflammation. IL-17 is upregulated in chronic liver injury and associated with liver disease progression. In contrast, IL-22 was shown to be hepatoprotective during acute liver injury but exhibited inflammatory effects in other models. Furthermore, IL-22 and IL-17 are both associated with poor prognosis in liver cancer. Finally, the regulatory mechanisms governing the physiological versus the pathological role of these two cytokines during acute and chronic liver injury remain poorly understood. In this review, we will summarize the current state of knowledge about IL-17 and IL-22 in wound healing during acute and chronic liver injury, their contribution to pathogenesis, their regulation, and their role in the transition from advanced liver disease to liver cancer.

Obesity and its cardiovascular effects.

Obesity is described in terms of body fat percentage or body mass index (BMI), despite the fact that these measures do not give full insight about the body fat distribution. It is presently a consistently growing universal challenge since it has tripled in the last 10 years, killing approximately 28 million people each year. In this review, we aim to clarify the different results of obesity on the working and physiology of the cardiovascular system and to reveal changes in the obesity "paradox"-a variety of cardiovascular outcomes in typical/overweight people. Central fat build-up in ordinary/overweight populaces has been related to expanded occurrences of myocardial infarction, heart failure, or all-cause mortality when contrasted with the obese populace. These discoveries are additionally clarified as the abundance and prolonged vulnerability to free fatty acids (FFAs) in obesity. This has been believed to cause the myocardial substrate to move from glucose to FFAs digestion, which causes lipid gathering in cardiomyocytes, spilling over to other lean tissues, and prompting a general atherogenic impact. This cardiomyocyte lipid aggregation has been demonstrated to cause insulin resistance and cardiovascular hypertrophy, and to lessen the heart functions in general. There is a proof backing the fact that fat tissue is not only an energy reservoir, it also coordinates hormones and proinflammatory cytokines and deals with the energy transition of the body by putting away abundant lipids in diverse tissues.

Influence of HLA on clinical and analytical features of pediatric celiac disease.

BACKGROUND: Celiac disease (CD) is triggered by gluten and related prolamines in genetically susceptible individuals. We aimed to investigate the influence of HLA-DQ genotypes in clinical, serological and histological features related to CD. METHODS: A retrospective observational study was performed including 463 Spanish patients with biopsy-proven CD. Clinical, serological, histological and HLA-DQ genetic data were collected from each participant. The presence of a family history of CD was also considered. Bivariate (chi-square tests or the Fisher's exact test) and multivariate (logistic regression after adjusting for age and sex) analyses were performed to assess the association between clinical and laboratory parameters with HLA-DQ. RESULTS: A predominance of females (62%), classical clinical presentation (86%) and positive anti-transglutaminase 2/endomysium antibodies (99%) was observed in our sample, with a mean age at onset of 2.6 ± 0.1 years. Five percent of our patients were first-degree relatives of subjects with CD, with HLA-DQ genetics showing increased homozygosity of HLA-DQ2.5 (p = 0.03) and HLA-DQ8 (p = 0.09). In the non-CD family history group, an association between delayed disease onset and HLA-DQ8 carriage was observed (p < 0.001), besides an influence of HLA-DQB1*02 gene dosage on clinical presentation and severity of histological damage (after adjusting for age and sex, p = 0.05 and p = 0.02, respectively) and a trend towards presence of specific antibodies (p = 0.09). These associations could not be evaluated properly in the group of patients with affected first-degree relatives due to the small sample size. CONCLUSIONS: HLA-DQ genotypic frequencies differ slightly between CD patients depending on their family history of CD. In patients lacking CD first-degree relatives, carriage of HLA-DQ2.5 with double dose of HLA-DQB1*02 seems to be associated with classical clinical presentation and more severe histological damage.

Methane Emissions from Artificial Waterbodies Dominate the Carbon Footprint of Irrigation: A Study of Transitions in the Food-Energy-Water-Climate Nexus (Spain, 1900-2014).

Irrigation in the Mediterranean region has been used for millennia and has greatly expanded with industrialization. Irrigation is critical for climate change adaptation, but it is also an important source of greenhouse gas emissions. This study analyzes the carbon (C) footprint of irrigation in Spain, covering the complete historical process of mechanization. A 21-fold total, 6-fold area-based, and 4-fold product-based increase in the carbon footprint was observed during the 20th century, despite an increase in water use efficiency. CH4 emissions from waterbodies, which had not previously been considered in the C footprint of irrigation systems, dominated the emission budget during most of the analyzed period. Technologies to save water and tap new water resources greatly increased energy and infrastructure demand, while improvements in power generation efficiency had a limited influence on irrigation emissions. Electricity production from irrigation dams may contribute to climate change mitigation, but the amount produced in relation to that consumed in irrigation has greatly declined. High uncertainty in CH4 emission estimates from waterbodies stresses a need for more spatially resolved data and an improved empirical knowledge of the links between water quality, water level fluctuations, and emissions at the regional scale.

HLA-DQ distribution and risk assessment of celiac disease in a Spanish center.

AIMS: celiac disease is a multisystem immune-mediated disease triggered by gluten in genetically susceptible individuals. The HLA-DQ2 and/or HLA-DQ8 heterodimers are encoded by the main genetic predisposing factors and their presence is required for the development of the immunological response that leads to the disease. However, the HLA-conferred risk can differ within different countries. The aim of the study was to analyze the risk of Spanish children to develop celiac disease according to their HLA-DQ genotype. METHODS: a retrospective observational case-control study was performed using a sample of 475 celiac patients and 628 controls. RESULTS: children carrying the HLA-DQ2.5 had the highest disease risk, especially those with two HLA-DQB1*02 alleles. A similar high risk was observed in HLA-DQ8 homozygous individuals. A risk conferred by HLA-DQ8 in heterozygosity and HLA-DQ2.2 was also found and two patients with celiac disease carried the HLA-DQ7.5 haplotype as the only HLA risk factor. CONCLUSIONS: there are four genetic risk categories according to the HLA-DQ genotype. The HLA-DQ7.5 genotype does not confer risk but should not be used to rule out celiac disease when a high suspicion of the disease exists. These findings could be relevant to determine when to perform serological screening in asymptomatic subjects at risk of celiac disease.

Use of XRD and SEM/EDX to predict age and sex from fire-affected dental remains.

In fire scenarios, the application and accuracy of traditional odontological methods are often limited. Crystalline studies and elemental profiling have been evaluated for their applicability in determining biological profiles (age and sex) from human dentition, particularly fire- and heat-affected dental remains. Thirty-seven teeth were paired according to tooth type and donor age/sex for the analysis of crown and root surfaces pre- and post-incineration using X-ray diffraction (XRD) and scanning electron microscopy (SEM/EDX). In unburned crowns, carbon (C) content showed a positive correlation with age, whereas phosphorus (P) and calcium (Ca) contents showed a negative correlation with age. In unburned roots, C, P and Ca contents also showed significant changes that were opposite of those observed in the crowns. In relation to sex, females exhibited a higher C ratio than males, whereas males showed significantly higher levels of oxygen (O), P and Ca in unburned roots. Incineration resulted in an increase in the crystallite size that correlated with increasing temperature. No differences in hydroxyapatite (HA) crystallite size were found between age groups; however, unburned teeth from females exhibited a larger crystallite size than did those from males. The challenges of using XRD with a 3D sample were overcome to allow analysis of whole teeth in a nondestructive manner. Further studies may be useful in helping predict the temperature of a fire.

Efficacy of a point-of-care test based on deamidated gliadin peptides for the detection of celiac disease in pediatric patients.

OBJECTIVE: The objective of the study was to assess the effectiveness of a point-of-care test (POCT) based on deamidated gliadin peptides (DGP) compared to the European Society for Paediatric Gastroenterology Hepatology and Nutrition (ESPGHAN) criteria diagnosis in the early detection of celiac disease (CD) in pediatric patients. METHODS: One hundred children (≤ 18 years) with suspected CD were selected, including siblings of celiac children that underwent gastroscopy for other gastrointestinal conditions. Patients with severe disease, following a gluten-free diet (GFD), with gastrointestinal bleeding, coagulopathy and infections in the last month were excluded. All children were evaluated with a POCT that detects immunoglobulin A (IgA) and immunoglobulin G (IgG) antibodies to DGP and total IgA. The POCT results were compared to CD diagnosis according to current ESPGHAN criteria. This involved the detection of IgA tissue transglutaminase (tTG) antibodies, the results of an intestinal biopsy and genetic testing. RESULTS: The prevalence of CD found in the present study was 48% (95% confidence interval in parenthesis 37.9-58.2%). The results of the POCT were concordant with the CD diagnosis made according to ESPGHAN criteria: 95.8% (85.7-99.4%) sensitivity, 98.1% (89.7-99.7%) specificity, 97.9% (88.7-99.6%) positive predictive value and 96.2% (87.0-99.4%) negative predictive value. Positive and negative likelihood ratios were 49.8 (7.2-347.5) and 0.04 (0.01-0.17), respectively. The POCT showed a 100% diagnostic accuracy in children younger than ten years of age. In total, three discordant results were found. CONCLUSION: Due to the high diagnostic accuracy in the pediatric population, the POCT can be considered as an effective tool for the early diagnosis of CD, especially in patients younger than ten years of age.

An international observational study suggests that artificial intelligence for clinical decision support optimizes anemia management in hemodialysis patients.

Managing anemia in hemodialysis patients can be challenging because of competing therapeutic targets and individual variability. Because therapy recommendations provided by a decision support system can benefit both patients and doctors, we evaluated the impact of an artificial intelligence decision support system, the Anemia Control Model (ACM), on anemia outcomes. Based on patient profiles, the ACM was built to recommend suitable erythropoietic-stimulating agent doses. Our retrospective study consisted of a 12-month control phase (standard anemia care), followed by a 12-month observation phase (ACM-guided care) encompassing 752 patients undergoing hemodialysis therapy in 3 NephroCare clinics located in separate countries. The percentage of hemoglobin values on target, the median darbepoetin dose, and individual hemoglobin fluctuation (estimated from the intrapatient hemoglobin standard deviation) were deemed primary outcomes. In the observation phase, median darbepoetin consumption significantly decreased from 0.63 to 0.46 µg/kg/month, whereas on-target hemoglobin values significantly increased from 70.6% to 76.6%, reaching 83.2% when the ACM suggestions were implemented. Moreover, ACM introduction led to a significant decrease in hemoglobin fluctuation (intrapatient standard deviation decreased from 0.95 g/dl to 0.83 g/dl). Thus, ACM support helped improve anemia outcomes of hemodialysis patients, minimizing erythropoietic-stimulating agent use with the potential to reduce the cost of treatment.

Hemodialysis patients receiving a greater Kt dose than recommended have reduced mortality and hospitalization risk.

Achieving an adequate dialysis dose is one of the key goals for dialysis treatments. Here we assessed whether patients receiving the current cleared plasma volume (Kt), individualized for body surface area per recommendations, had improved survival and reduced hospitalizations at 2 years of follow-up. Additionally, we assessed whether patients receiving a greater dose gained more benefit. This prospective, observational, multicenter study included 6129 patients in 65 Fresenius Medical Care Spanish facilities. Patients were classified monthly into 1 of 10 risk groups based on the difference between achieved and target Kt. Patient groups with a more negative relationship were significantly older with a higher percentage of diabetes mellitus and catheter access. Treatment dialysis time, effective blood flow, and percentage of on-line hemodiafiltration were significantly higher in groups with a higher dose. The mortality risk profile showed a progressive increase when achieved minus target Kt became more negative but was significantly lower in the group with 1 to 3 L clearance above target Kt and in groups with greater increases above target Kt. Additionally, hospitalization risk appeared significantly reduced in groups receiving 9 L or more above the minimum target. Thus, prescribing an additional 3 L or more above the minimum Kt dose could potentially reduce mortality risk, and 9 L or more reduce hospitalization risk. As such, future prospective studies are required to confirm these dose effect findings.

Small-Caliber Lead Failure After Generator Exchange.

INTRODUCTION AND OBJECTIVES: The Sprint Fidelis defibrillator lead (Medtronic) was recalled in 2007 due to an increased risk of failure. The generator exchange (GE) procedure has been associated with the development of Fidelis lead dysfunction. The aim of this study was to compare the rate of dysfunction between Sprint Fidelis and other defibrillator leads during the first year after GE. METHODS: A multicenter retrospective study involving patients from the UMBRELLA database who underwent GE with previous normal lead function and minimum follow-up of 1 year after the procedure was performed. The incidence of lead dysfunction was determined via remote monitoring and defined as pacing impedance > 1,500 ohm, high-voltage impedance > 100 ohm, R wave sensing under 2 mV, or the presence of VT/VF episodes classified as noise. RESULTS: A total of 531 patients were included (114 Fidelis). In the first year after GE, the total incidence of lead dysfunction was 3.6%. No significant differences were found between Fidelis and the others in survival analysis (3.5% vs. 3.6%, respectively, log-rank 0.002, P = 0.962). CONCLUSIONS: According to our results, the preventive removal/replacement of the Sprint Fidelis leads with normal function until GE is not a recommended practice since the rate of dysfunction after the procedure in this subgroup is no different compared with other defibrillator leads.

Ring-Closing and Cross-Metathesis with Artificial Metalloenzymes Created by Covalent Active Site-Directed Hybridization of a Lipase.

A series of Grubbs-type catalysts that contain lipase-inhibiting phosphoester functionalities have been synthesized and reacted with the lipase cutinase, which leads to artificial metalloenzymes for olefin metathesis. The resulting hybrids comprise the organometallic fragment that is covalently bound to the active amino acid residue of the enzyme host in an orthogonal orientation. Differences in reactivity as well as accessibility of the active site by the functionalized inhibitor became evident through variation of the anchoring motif and substituents on the N-heterocyclic carbene ligand. Such observations led to the design of a hybrid that is active in the ring-closing metathesis and the cross-metathesis of N,N-diallyl-p-toluenesulfonamide and allylbenzene, respectively, the latter being the first example of its kind in the field of artificial metalloenzymes.