Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of droplet digital PCR assays to quantify genes involved in nitrification and denitrification, comparison to quantitative real-time PCR and validation of assays in vineyard soil.

Quantifying genes in soil is important to relate the abundance of soil bacteria to biogeochemical cycles. Quantitative real-time PCR is widely used for quantification, but its use with environmental samples is limited by poor reaction efficiencies or by PCR inhibition through co-purified soil substances. Droplet digital PCR (ddPCR) is a technology for absolute, sensitive quantification of genes. This study optimized eight ddPCR assays to quantify total bacteria and archaea, nitrification (bacterial and archaeal amoA) and denitrification (nirS, nirK, nosZI, nosZII) genes involved in the generation or reduction of the greenhouse gas nitrous oxide. Detection and quantification thresholds were compared to quantitative real-time PCR and were equal to, or improved, in ddPCR. To validate the assays using environmental samples, soil DNA was isolated from two vineyards in the Okanagan valley in British Columbia, Canada over the 2017 growing season. Soil properties related to the observed gene abundances were determined. Total bacteria, nirK and nosZII increased with time and the soil C/N ratio and NH4+-N concentration affected total archaea and archaeal amoA negatively. The results, compared to other studies, showed that ddPCR is a valid alternative to qPCR to quantify genes involved in nitrification or denitrification.
The Authors’ reply: instantaneous pressure-flow relationships in aortic stenosis

The Authors’ reply We thank Professor Otto and Dr Bermejo for their interest and astute comments regarding our study.1 The echo frame for determining left ventricular volume at peak aortic velocity is estimated by the measuring the total number of frames from the R wave to the end systole and multiplying this by the fraction of time from the R wave to the peak aortic velocity and from the R wave to the end systole. In the initial report of EF1 in aortic stenosis (AS),2 the intraobserver and interobserver coefficients of variation were 6.7% and 9.8%. We acknowledge that EF1 …
Toll‐like receptor 2 mediates the immune response of the bovine oviductal ampulla to sperm binding

We previously reported that sperm binding to cultured bovine oviduct epithelial cells induces an anti‐inflammatory immune response. Now we have developed a differentiated explant model to focus on the oviductal ampulla, where fertilization occurs, and to study the effect of sperm capacitation on the immune response. We used heparin to stimulate bovine sperm capacitation. Fluorescence imaging showed that 5,5ʹ,6,6ʹ‐tetrachloro‐1,1ʹ,3,3ʹ‐tetraethylbenzimidazolyl‐carbocyanine iodide‐labeled sperm pretreated with (Hep(+)) or without (Hep(−)) heparin rapidly attached to the explant ciliated epithelium in similar numbers. However, only Hep(+) sperm upregulated explant messenger RNA (mRNA) transcription of TLR2, IL8, TGFB1, and PGES, without changes in TNFA and IL‐10 expression, while Hep(−) sperm only upregulated PGES. The responses were primarily anti‐inflammatory, with a greater response produced by Hep(+) sperm, which also produced a substantial increase in TLR2 protein expression in the epithelium. The addition of TLR1/2 (toll‐like receptor 1/2) antagonist to the Hep(+) and (Hep(−)) sperm‐explant coincubations reduced sperm attachment to the epithelium and inhibited TLR2 protein expression and some of the Hep(+) sperm‐induced mRNA transcription. Our observations suggest that the ampullar epithelium immunologically reacts more strongly to sperm that have undergone heparin stimulation of capacitation. This anti‐inflammatory response could serve to protect capacitated sperm as they approach the oocyte in the ampulla.
Artificially induced pneumothorax with a Veress needle for cryoablation of renal cell carcinoma

Abstract Thermal ablative techniques are used increasingly to treat renal cell carcinoma (RCC). Percutaneous cryoablation of tumors at the upper pole of the kidney may result in pulmonary damage due to the intervening lung parenchyma. We treated two patients with RCC in the upper pole of the kidney by inducing pneumothorax with a pneumoperitoneum needle before proceeding to percutaneous cryoablation. The procedures, performed under computed tomography (CT) fluoroscopy guidance, resulted in complete tumor necrosis. There was no pulmonary damage.
Cannabis Use and Prospective Long-Term Association with Anxiety: A Systematic Review and Meta-Analysis of Longitudinal Studies: Usage du cannabis et association prospective à long terme avec l’anxiété: une revue systématique et une méta-analyse d’études longitudinales

Objectives: Cannabis use is proposed as a risk factor for psychosis and is associated with depressive disorders. However, the relationship between recreational cannabis use and its longitudinal implications on anxiety conditions is less studied. The aim of this investigation is to systematically evaluate published literature and perform a meta-analysis of the data. Methods: A systematic search was performed of MEDLINE, Embase, and PsychINFO from inception to May 31, 2020, in addition to a hand search. Longitudinal studies that evaluated the relationship of cannabis use and development of anxiety were included. Where applicable, adjusted odds ratios (ORs) were extracted, pooled, and evaluated using random-effects meta-analysis. Results: After screening of unique abstracts (n = 6835), the final evaluation included 24 studies, of which 10 reported ORs that were analyzed quantitatively. Cannabis use was significantly associated with increased odds of developing any anxiety conditions (OR = 1.25; 95% CI, 1.01 to 1.54). Cannabis use was not significantly associated with developing generalized anxiety disorder, panic disorder, or social anxiety disorder. Review of studies not reporting OR revealed mixed results but are suggestive of a link between cannabis use and increased rates/severity of anxiety. Conclusions: Published evidence suggests that cannabis use is likely associated with increased risk of anxiety in the long term but variability of study designs precludes declaration of a causal relationship. Awareness of this association is of relevance for both clinical practice and mental health policy implementation.
Two Novel Pathogenic Variants Confirm RMND1 Causative Role in Perrault Syndrome with Renal Involvement

RMND1 (required for meiotic nuclear division 1 homolog) pathogenic variants are known to cause combined oxidative phosphorylation deficiency (COXPD11), a severe multisystem disorder. In one patient, a homozygous RMND1 pathogenic variant, with an established role in COXPD11, was associated with a Perrault-like syndrome. We performed a thorough clinical investigation and applied a targeted multigene hearing loss panel to reveal the cause of hearing loss, ovarian dysfunction (two cardinal features of Perrault syndrome) and chronic kidney disease in two adult female siblings. Two compound heterozygous missense variants, c.583G>A (p.Gly195Arg) and c.818A>C (p.Tyr273Ser), not previously associated with disease, were identified in RMND1 in both patients, and their segregation with disease was confirmed in family members. The patients have no neurological or intellectual impairment, and nephrological evaluation predicts a benign course of kidney disease. Our study presents the mildest, so far reported, RMND1-related phenotype and delivers the first independent confirmation that RMND1 is causally involved in the development of Perrault syndrome with renal involvement. This highlights the importance of including RMND1 to the list of Perrault syndrome causative factors and provides new insight into the clinical manifestation of RMND1 deficiency.
Home mechanical ventilation: back to basics

Over recent decades, the use of home mechanical ventilation (HMV) has steadily increased worldwide, with varying prevalence in different countries. The key indication for HMV is chronic respiratory failure with alveolar hypoventilation (e.g., neuromuscular and chest wall disease, obstructive airway diseases, and obesity-related respiratory failure). Most modern home ventilators are pressure-targeted and have sophisticated modes, alarms, and graphics, thereby facilitating optimization of the ventilator settings. However, different ventilators have different algorithms for tidal volume estimation and leak compensation, and there are also several different circuit configurations. Hence, a basic understanding of the fundamentals of HMV is of paramount importance to healthcare workers taking care of patients with HMV. When choosing a home ventilator, they should take into account many factors, including the current condition and prognosis of the primary disease, the patient’s daily performance status, time (hr/day) needed for ventilator support, family support, and financial costs. In this review, to help readers understand the basic concepts of HMV use, we describe the indications for HMV and the factors that influence successful delivery, including interface, circuits, ventilator accessories, and the ventilator itself.
THE FERTILITY POTENTIAL IS IMPAIRED IN BOYS WITH BILATERAL ASCENDING TESTES.

AIM Ascending testes has been documented to be descended in scrotum within the first year of life and then re-ascended. The aim of the study was to investigate to what extend the fertility potential was impaired in boys with such testes compared to the fertility potential of boys with late referral congenital cryptorchidism. METHODS From 2011-2018, 153 consecutive boys had bilateral orchidopexy performed between 2 and 7 (median 3.9) years of age. Sixty-seven boys were diagnosed with bilateral ascended testes and 86 boys with late referral bilateral congenital cryptorchidism. We assessed serum levels of inhibin B and gonadotropins and the histological parameters; number of germ cells per tubule cross-section (G/T) and number of Ad spermatogonia per tubule cross-section (AdS/T). All values were compared to our normal material. RESULTS Mean G/T of boys with ascended testes were not significantly higher than that of boys with congenital cryptorchidism (median 0.50 (range 0-2.29) versus 0.37 (0-2.57), p=0.11). 60% (40/67) of boys with ascending testes had mean G/T below normal range (versus 66%, p=0.40). Biopsies absent of Ad spermatogonia were noted in 31% (21/67) and 34% (29/86) of boys with ascending testes or congenital cryptorchidism, respectively (p=0.76). Serum levels of inhibin B and gonadotropins did not differ between the two groups. CONCLUSION The fertility potential of boys with bilateral ascended testes was impaired to almost the same level as that of boys with bilateral congenital cryptorchidism and should therefore be surgically corrected as soon as the diagnosis of ascended testes is settled.
Repurposing of FDA-Approved Toremifene to Treat COVID-19 by Blocking the Spike Glycoprotein and NSP14 of SARS-CoV-2

The global pandemic of Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to the death of more than 675,000 worldwide and over 150,000 in the United States alone. However, there are currently no approved effective pharmacotherapies for COVID-19. Here, we combine homology modeling, molecular docking, molecular dynamics simulation, and binding affinity calculations to determine potential targets for toremifene, a selective estrogen receptor modulator which we have previously identified as a SARS-CoV-2 inhibitor. Our results indicate the possibility of inhibition of the spike glycoprotein by toremifene, responsible for aiding in fusion of the viral membrane with the cell membrane, via a perturbation to the fusion core. An interaction between the dimethylamine end of toremifene and residues Q954 and N955 in heptad repeat 1 (HR1) perturbs the structure, causing a shift from what is normally a long, helical region to short helices connected by unstructured regions. Additionally, we found a strong interaction between toremifene and the methyltransferase nonstructural protein (NSP) 14, which could be inhibitory to viral replication via its active site. These results suggest potential structural mechanisms for toremifene by blocking the spike protein and NSP14 of SARS-CoV-2, offering a drug candidate for COVID-19.
New Eco-Materials Derived from Waste for Emerging Pollutants Adsorption: The Case of Diclofenac

This work proposes new eco-materials for the adsorption of diclofenac (DCF). The large consumption of this nonsteroidal anti-inflammatory drug combined with the inefficiency of wastewater treatment plants (WWTPs) leads to its presence in aquatic environments as an emerging pollutant. The adsorption technique is widely used for pharmaceutical removal. Moreover, due to the large effect of commercial adsorbents, in the frame of the Azure Chemistry approach, new sustainable materials are mandatory for removal as emerging pollutants. The work proposes three adsorbents that were obtained from different stabilization methods of fly ash derived from an incinerator plant; the stabilization techniques involved the use of various industrial by-products such as bottom ash, flue gas desulphurization residues, coal fly ash, and silica fume. The best performance, although less than activated carbon, was obtained by COSMOS (COlloidal Silica Medium to Obtain Safe inert: the case of incinerator fly ash), with a removal efficacy of approximately 76% with 15 g/L of material. Several advantages are expected not only from the DCF removal but also from an economic perspective (the newly obtained adsorbents are eco-materials, so they are cheaper in comparison to conventional adsorbents) and in terms of sustainability (no toxic reagents and no heating treatment are involved). This work highlights the adsorption performance of the new eco-materials and their potential use in WWTPs.
Implementing Precision Psychiatry: A Systematic Review of Individualized Prediction Models for Clinical Practice

Abstract Background The impact of precision psychiatry for clinical practice has not been systematically appraised. This study aims to provide a comprehensive review of validated prediction models to estimate the individual risk of being affected with a condition (diagnostic), developing outcomes (prognostic), or responding to treatments (predictive) in mental disorders. Methods PRISMA/RIGHT/CHARMS-compliant systematic review of the Web of Science, Cochrane Central Register of Reviews, and Ovid/PsycINFO databases from inception until July 21, 2019 (PROSPERO CRD42019155713) to identify diagnostic/prognostic/predictive prediction studies that reported individualized estimates in psychiatry and that were internally or externally validated or implemented. Random effect meta-regression analyses addressed the impact of several factors on the accuracy of prediction models. Findings Literature search identified 584 prediction modeling studies, of which 89 were included. 10.4% of the total studies included prediction models internally validated (n = 61), 4.6% models externally validated (n = 27), and 0.2% (n = 1) models considered for implementation. Across validated prediction modeling studies (n = 88), 18.2% were diagnostic, 68.2% prognostic, and 13.6% predictive. The most frequently investigated condition was psychosis (36.4%), and the most frequently employed predictors clinical (69.5%). Unimodal compared to multimodal models (β = .29, P = .03) and diagnostic compared to prognostic (β = .84, p < .0001) and predictive (β = .87, P = .002) models were associated with increased accuracy. Interpretation To date, several validated prediction models are available to support the diagnosis and prognosis of psychiatric conditions, in particular, psychosis, or to predict treatment response. Advancements of knowledge are limited by the lack of implementation research in real-world clinical practice. A new generation of implementation research is required to address this translational gap.
Biological and Genetic Heterogeneity in Trypanosoma dionisii Isolates from Hematophagous and Insectivorous Bats

This study describes the morphological, biochemical, and molecular differences among Trypanosoma dionisii isolates from hemocultures of hematophagous (Desmodus rotundus; n = 2) and insectivorous (Lonchorhina aurita; n = 1) bats from the Atlantic Rainforest of Rio de Janeiro, Brazil. Fusiform epimastigotes from the hematophagous isolates were elongated, whereas those of the insectivorous isolate were stumpy, reflected in statistically evident differences in the cell body and flagellum lengths. In the hemocultures, a higher percentage of trypomastigote forms (60%) was observed in the hematophagous bat isolates than that in the isolate from the insectivorous bat (4%), which demonstrated globular morphology. Three molecular DNA regions were analyzed: V7V8 (18S rDNA), glycosomal glyceraldehyde 3-phosphate dehydrogenase gene, and mitochondrial cytochrome b gene. The samples were also subjected to multilocus enzyme electrophoresis and random amplified polymorphic DNA analysis. All isolates were identified as T. dionisii by phylogenetic analysis. These sequences were clustered into two separate subgroups with high bootstrap values according to the feeding habits of the bats from which the parasites were isolated. However, other T. dionisii samples from bats with different feeding habits were found in the same branch. These results support the separation of the three isolates into two subgroups, demonstrating that different subpopulations of T. dionisii circulate among bats.
Autophagy Inhibits Grass Carp Reovirus (GCRV) Replication and Protects Ctenopharyngodon idella Kidney (CIK) Cells from Excessive Inflammatory Responses after GCRV Infection

Autophagy is an essential and highly conserved process in mammals, which is critical to maintaining physiological homeostasis, including cell growth, development, repair, and survival. However, the understanding of autophagy in fish virus replication is limited. In this study, we found that grass carp reovirus (GCRV) infection stimulated autophagy in the spleen of grass carp (Ctenopharyngodon idella). Moreover, both Western blot (WB) analysis and fluorescent tracer tests showed that GCRV infection induced the enhancement of autophagy activation in Ctenopharyngodon idella kidney (CIK) cells. Autophagy inducer rapamycin and autophagy inhibitor 3-MA pretreatment can inhibit and promote the proliferation of GCRV, respectively. In addition, grass carp autophagy-related gene 5 (CiATG5)-induced autophagy, as well as rapamycin, showed effects on GCRV replication in CIK cells. Transcriptome analysis revealed that the total number of differentially expressed genes (DEGs) in CiATG5 overexpression groups was less than that of the control during GCRV infection. Enrichment analysis showed that CiATG5 overexpression induced the enhancement of autophagy, lysosome, phagosome, and apoptosis in the early stage of GCRV infection, which led to the clearance of viruses. In the late stage, steroid biosynthesis, DNA replication, terpenoid backbone biosynthesis, and carbon metabolism were upregulated, which contributed to cell survival. Moreover, signaling pathways involved in the immune response and cell death were downregulated in CiATG5 overexpression groups. Further study showed that CiATG5 repressed the expression of inflammatory response genes, including cytokines and type I interferons. Taken together, the results demonstrate that autophagy represses virus replication and attenuates acute inflammatory responses to protect cells.
A meta‐analysis of microRNA networks regulated by melatonin in cancer: Portrait of potential candidates for breast cancer treatment

Melatonin is a ubiquitous molecule with a broad spectrum of functions including widespread anti‐cancer activities. Identifying how melatonin intervenes in complex molecular signaling at the gene level is essential to guide proper therapies. Using meta‐analysis approach, herein we examined the role of melatonin in regulating the expression of 46 microRNAs (miRNAs) and their target genes in breast, oral, gastric, colorectal, and prostate cancers, and glioblastoma. The deregulated miRNA‐associated target genes revealed their involvement in the regulation of cellular proliferation, differentiation, apoptosis, senescence, and autophagy. Melatonin changes the expression of miRNA‐associated genes in breast, gastric, and oral cancers. These genes are associated with cellular senescence, the hedgehog signaling pathway, cell proliferation, p53 signaling, and the hippo signaling pathway. Conversely, colorectal and prostate cancers as well as glioblastoma and oral carcinoma present a clear pattern of less pronounced changes in the expression of miRNA‐associated genes. Most notably, colorectal cancer displayed a unique molecular change in response to melatonin. Considering breast cancer network complexity, we compared the genes found during the meta‐analysis with RNA‐Seq data from breast cancer‐bearing mice treated with melatonin. Mechanistically, melatonin upregulated genes associated with immune responses and apoptotic processes, whereas it downregulated genes involved in cellular aggressiveness/metastasis (eg, mitosis, telomerase activity, and angiogenesis). We further characterized the expression profile of our gene subsets with human breast cancer and found eight upregulated genes and 16 downregulated genes that were appositively correlated with melatonin. Our results pose a multi‐dimension network of tumor‐associated genes regulated by miRNAs potentially targeted by melatonin.
Measurable Cytokine Concentrations in Pig Seminal Plasma Are Modified by Semen Handling and Storage

Sample handling and storing are critical steps for the reliable measurement of circulating biomolecules in biological fluids. This study evaluates how cytokine measurements in pig seminal plasma (SP) vary depending on semen handling and SP storage. Thirteen cytokines (GM-CSF, IFNγ, IL-1α, IL-1β, IL-1ra, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-18 and TNFα) were measured using Luminex xMAP® technology in individual seminal plasma (SP) samples (n = 62) from healthy breeding boars. Three separate experiments explored the delay (2 h and 24 h) in SP collection after ejaculation (Experiment 1) and SP storage, either short-term (5 °C, −20 °C and −80 °C for 72 h, Experiment 2) or long-term (at −20 °C and −80 °C for two months, Experiment 3), before analysis. Levels in fresh SP-samples were used as baseline control values. Delays in SP harvesting of up to 24 h did not substantially impact SP cytokine measurements. Some cytokines showed instability in stored SP samples, mainly in long-term storage. Ideally, cytokines in pig SP should be measured in fresh samples harvested within 24 h after ejaculation. If storage of SP is imperative, storage conditions should be adjusted for each cytokine.