Ancient DNA research has developed rapidly over the past few decades due to the improvement in PCR and next-generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from the raw sequencing data. This is often difficult due to the degradation of ancient DNA and high levels of contamination, especially homologous contamination. In this study, we collected whole genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from the homologous contaminations, we attempted to recover reads based on the ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing the homologous contaminations to a very low proportion. Overall, these recommendations for ancient DNA mapping and separation of endogenous DNA in this study could facilitate future studies of ancient DNA.
A 59-year-old male with a history of unstable angina was diagnosed with a myocardial bridge of the left anterior descending artery (LAD) and apical variant hypertrophic cardiomyopathy (AHCM). He underwent unroofing of the myocardial bridge and a left ventricular apical myectomy. Intraoperatively, epicardial ultrasound was used to identify the myocardial bridge with systolic compression of the LAD and confirm resolution of this compression postoperatively. Furthermore, epicardial ultrasound was used for guiding the degree of apical resection of the decompressed heart. This novel use of intraoperative epicardial ultrasound can help guide surgeons preoperatively and confirm results immediately after an operation.
The brain is the most cholesterol rich organ in the body containing about 25% of the body’s free cholesterol. Cholesterol cannot pass the blood brain barrier and be imported or exported directly, instead it is synthesised in situ and metabolised to oxysterols, oxidised forms of cholesterol, which can pass the blood brain barrier. 24S-Hydroxycholesterol is the dominant oxysterol in brain after parturition but during development a myriad of other oxysterols are produced which persist as minor oxysterols after birth. During both development and in later life, oxysterols and other sterols interact with a variety of different receptors, including nuclear receptors e.g. liver X receptors; membrane bound G protein-coupled receptors e.g. smoothened; the endoplasmic reticulum resident proteins e.g. INSIG (insulin induced gene), or the cholesterol sensing protein SCAP (SREBP cleavage activating protein); and the ligand-gated ion channel N-methyl-D-aspartate receptors found in nerve cells. In this review we summaries the different oxysterols (neuro-oxysterol) and sterols (neuro-sterols) found in the central nervous system whose biological activity is transmitted via these different classes of protein receptors.
Predicting the behavior of overland flow with analytical solutions to the kinematic wave equation is appealing due to its relative ease of implementation. Such simple solutions, however, have largely been constrained to applications on simple planar hillslopes. This study presents analytical solutions to the kinematic wave equation for hillslopes with modest topographic curvature that causes divergence or convergence of runoff flowpaths. The solution averages flow depths along changing hillslope contours whose lengths vary according hillslope width function, and results in a one-dimensional approximation to the two-dimensional flow field. The solutions are tested against both two-dimensional numerical solutions to the kinematic wave equation (in ParFlow) and against experiments that use rainfall simulation on machined hillslopes with defined curvature properties. Excellent agreement between numerical, experimental and analytical solutions is found in all cases. The solutions show that curvature drives large changes in maximum flow rate qmax and time of concentration tc, predictions frequently used in engineering hydrologic design and analysis.
Introduction Erectile Dysfunction (ED) is common in older age and in diabetes (DM). Phosphodiesterase type 5-inhibitors (PDE5-is) are the first-line for ED. We investigated how type of diabetes and age of males affects the PDE5-i use in the primary care setting. Methods 2018-19 general practice level quantity of all PDE5-i agents were taken from the GP Prescribing Data set in England. The variation in outcomes across practices was examined across one year, and for the same practice against the previous year. Results We included 5,761 larger practices supporting 25.8million men of whom 4.2million≥65 years old. Of these, 1.4million had T2DM, with 0.8million of these>65. 137,000 people had T1DM. 28.8million tablets of PDE5-i were prescribed within the 12 months (2018-19) period in 3.7million prescriptions (7.7 tablets/prescription), at total costs of £15.8million (£0.55/tablet). The NHS ED limit of 1 tablet/user/week suggests that 540,000 males are being prescribed a PDE5-i at a cost of £29/year each. With approximately 30,000 GPs practising, this is equivalent to one GP providing 2.5 prescriptions/week to overall 18 males. There was a 3x variation between the highest decile of practices (2.6 tablets/male/year) and lowest decile (0.96 tablets/male/year). The statistical model captured 14% of this variation and showed T1DM males were the largest users, while men age<65 with T2DM were being prescribed 4 times as much as non-DM. Those T2DM>65 were prescribed 80% of the non-DM amount. Conclusion There is wide variation in use of PDE5-is. With only 14% variance capture, other factors including wide variation in patient awareness, prescribing rules of local health providers, and recognition of the importance of male sexual health by GP prescribers might have significant impact.
1. Trees are characterised by the large number of seeds they produce. Although most of those seeds will never germinate, plenty will. Of those which germinate, many die young, and eventually only a minute fraction will grow to adult stage and reproduce. Is this just a random process? Do variations in germination and survival at very young stages rely on variations in adaptations to microgeographic heterogeneity? and do these processes matter at all in determining tree species distribution and abundance? 2. We have studied these questions with the Neotropical Symphonia syngameon. In the Guiana shield, Symphonia are represented by at least two sympatric taxa or ecotypes, Symphonia globulifera found almost exclusively in bottomlands, and a yet undescribed more generalist taxon/ecotype, Symphonia sp1. A reciprocal transplantation experiment (510 seeds, 16 conditions) was set-up and followed over the course of 6 years to evaluate the survival and performance of individuals from different ecotypes and provenances. 3. Germination, survival, growth, and herbivory showed signs of local adaptation, with some combinations of ecotypes and provenances growing faster and surviving better in their own habitat or provenance region. S. globulifera was strongly penalised when planted outside its home habitat but showed the fastest growth rates when planted in its home habitat, suggesting it’s a specialist of a high-risk high-gain strategy. Conversely, S. sp1 behaved as a generalist, performing well in a variety of environments. 4. Synthesis: The differential performance of seeds and seedlings in the different habitats matches the known distribution of both ecotypes, indicating that environmental filtering at the very early stages can be a key determinant of tree species distributions, even at the microgeographic level and among very closely related taxa. Furthermore, such differential performance also contributes to explain, in part, the maintenance of the different ecotypes in the Symphonia syngameon living in intimate sympatry despite occasional gene flow.
Pericardial cysts are considered rare incidental findings, which are generally asymptomatic in nature. Occasionally, patients may represent with chest discomfort, dyspnea or palpitations. Pericarditis related to a ruptured pericardial cyst has not been previously reported in the literature. Here, we report the case of a 62-year-old male who developed acute pericarditis as a result of a ruptured enlarging pericardial cyst.
There is an urgent need for targeted and effective COVID-19 treatment. A number of medications, including hydroxychloroquine, remdesivir, lopinavir-ritonavir, fapiravir, and tocilizumab, have been identified as potential treatments for COVID-19. Bringing these repurposed medications to the public for COVID-19 will require robust and high-quality clinical trials. This article reviews translational science principles and strategies for conducting clinical trials in a pandemic and evaluates recent trials for each drug candidate. We hope that this knowledge will help focus efforts during this crisis and lead to the expedited development and approval of COVID-19 therapy.
The SARS-CoV-2, the causative agent of COVID-19, has been established to gain access to the human cell via the ACE2 receptor similar to its familial coronavirus SARS-CoV which led to the outbreak in 2003. A concern with the newer 2019 coronavirus is its 10-20-fold higher affinity to the ACE2 receptor that of SARS-CoV, aiding its effective human-to-human transmission which has led to this pandemic. ACE2 receptor expression is thought to be upregulated in use with ACE inhibitors. As ACE inhibitors are known to be a used extensively in the treatment of hypertension it was a concern regarding the risk of using these medications alongside a SARS-COV-2 infection. ACE inhibitors are also used in the treatment regime of other common conditions including diabetes and Cardiovascular disease (CVD). It is worth noting that ACE2 expression has found to be upregulated by the use of thiazolidinediones and ibuprofen too. Consequently, the increased expression of ACE2 would facilitate infection with COVID-19. Therefore, it would hypothesise that diabetes and hypertension treatment with ACE2-stimulating drugs would increase the risk of developing severe and fatal COVID-19.
Initiation of statin treatment is suggested to increase the international normalised ratio (INR) among warfarin users. However, available data is limited and conflicting. We conducted a register-based cohort study to evaluate the drug-drug interaction between warfarin and statins. By linking data on INR measurements and filled prescriptions, we identified warfarin users 2000-2015 initiating simvastatin (n=1,363), atorvastatin (n=165), or rosuvastatin (n=23). Simvastatin initiation led to an increase in mean INR from 2.40 to 2.71, with INRs peaking after 4 weeks, corresponding to a mean change of 0.32 (95%CI 0.25-0.38). High-dose and low-dose simvastatin led to comparable changes (mean change 0.33 vs 0.29). Initiation of atorvastatin and rosuvastatin lead to INR increases of 0.27 (95%CI 0.12-0.42) and 0.30 (95%CI -0.09-0.69). In conclusion, initiation of simvastatin, atorvastatin, or rosuvastatin among warfarin users led to a minor increase in INR. The magnitude of this change is for most patients likely of limited clinical relevance.
Biofilms commonly develop in flowing aqueous environments, where the flow causes the biofilm to deform. Because biofilm deformation affects the flow regime, and because biofilms behave as complex heterogeneous viscoelastic materials, few models are able to predict biofilm deformation. In this study, a phase field continuum model coupled with the Oldroyd-B constitutive equation was developed and used to simulate biofilm deformation. The accuracy of the model was evaluated using two types of biofilms: a synthetic biofilm, made from alginate mixed with bacterial cells, and a Pseudomonas aeruginosa biofilm. Shear rheometry was used to experimentally determine the mechanical parameters for each biofilm, as inputs for the model. Biofilm deformation under fluid flow was monitored experimentally using optical coherence tomography. The fit between the experimental and modeling geometries after fluid-driven deformation was very good, with relative errors of 12.8% for synthetic biofilm and 22.2% for homogenized P. aeruginosa biofilm. This is the first demonstration of the effectiveness of a viscoelastic phase field biofilm model. This model provides an important tool for predicting biofilm viscoelastic deformation. It also can benefit the design and control of biofilms in engineering systems.
Human olfactory mucosa cells (hOMCs) have potential as a regenerative therapy for spinal cord injury. In our earlier work we derived the PA5 cells, a polyclonal population that retains functional attributes of primary OMCs. Microcarrier suspension culture is an alternative to planar 2D culture to produce cells in quantities that can meet the needs of clinical development. This study aimed to screen the effects of 10 microcarriers on PA5 hOMCs yield and phenotype. Studies performed in well plates led to a 2.9-fold higher cell yield on Plastic compared to Plastic Plus microcarriers with upregulation of neuronal markers β-III tubulin and nestin for both conditions. Microcarrier suspension culture resulted in concentrations of 1.4x105 cells/mL and 4.9x104 cells/mL for Plastic and Plastic Plus, respectively, after 7 days. p75NTR transcript was significantly upregulated for PA5 hOMCs grown on Plastic Plus compared to Plastic. Furthermore, co-culture of PA5 hOMCs grown on Plastic Plus with a neuronal cell line (NG108-15) led to increased neurite outgrowth. This study presents the successful expansion of PA5 cells using microcarrier suspension culture and it reveals competing effects of microcarriers on cell expansion versus functional attributes, showing that designing scalable bioprocesses should not only be driven by cell yields.
The focal adhesion kinase (FAK) and the proline-rich tyrosine kinase 2-beta (PYK2) are implicated in cancer progression and metastasis and represent promising biomarkers and targets for cancer therapy. FAK and PYK2 are recruited to Focal Adhesions (Fas) via interactions between their Focal Adhesion Targeting (FAT) domains and conserved segments (LD motifs) on the proteins Paxillin, Leupaxin and Hic-5. A promising new approach for the inhibition of FAK and PYK2 targets interactions of the FAK domains with proteins that promote localization at Focal Adhesions. Advances toward this goal include the development of surface plasmon resonance, HSQC-NMR and fluorescence polarization assays for the identification of fragments or compounds interfering with the FAK-Paxillin interaction. We have recently validated this strategy, showing that Paxillin mimicking polypeptides with 2-3 LD motifs displace FAK from FAs and block kinase-dependent and independent functions of FAK, including downstream integrin signalling and FA localization of the protein p130Cas. In the present work we study by all-atom molecular dynamics simulations the recognition of peptides with the Paxillin and Leupaxin LD motifs by the FAK-FAT and PYK2-FAT domains. Our simulations and free-energy analysis interpret experimental data on binding of Paxillin and Leupaxin LD motifs at FAK-FAT and PYK2-FAT binding sites, and assess the roles of consensus LD regions and flanking residues. Our results can assist in the design of effective inhibitory peptides of the FAK-FAT:Paxillin and PYK2-FAT:Leupaxin complexes and the construction of pharmacophore models for the discovery of potential small-molecule inhibitors of the FAK-FAT and PYK2-FAT focal adhesion based functions.
Background: Despite improved survival and morbidity after durable left ventricular assist device (dLVAD), outcomes for cardiogenic shock patients are suboptimal. Temporary mechanical circulatory support (tMCS) can permit optimization prior to dLVAD. Excellent outcomes have been observed using minimally-invasive dLVAD implantation. However, some feel tMCS contraindicates this approach. To evaluate whether left thoracotomy/hemisternotomy (LTHS) dLVAD placement is safe in this setting, we compared patients who did and did not require tMCS. Methods: Outcomes for patients receiving dLVADs via LTHS were compared among those bridged with ECMO, IABP, or no tMCS. We evaluated demographics, comorbidities, laboratory and hemodynamic data, and intra- and postoperative outcomes. Results: Eighty-three patients underwent LTHS dLVAD placement. Fifty did not require tMCS, while 22 (26%) required IABP, and 11 (13%) ECMO. Non-tMCS patients were primarily INTERMACS 3 (56%), while IABP recipients were mainly INTERMACS 2 (45%). All ECMO patients were INTERMACS 1. Patients with tMCS had worse end-organ function. Operative outcomes were similar except more concomitant procedures and red-cell transfusions in ECMO patients. ICU and hospital length of stay and inotrope duration were also similar. There were no differences in bleeding, stroke, and infection rates. Three- and twelve-month survival were: No tMCS: 94%, 86%; IABP: 100%, 88%; ECMO: 81%, 81% (p=0.45). Conclusions: Patients with cardiogenic shock can safely undergo LTHS dLVAD implantation after stabilization with ECMO or IABP. Outcomes and complications in these patients were comparable to a less severely ill cohort without tMCS.
Background Post-Cardiotomy ECMO (PC-ECMO) represents a unique subset of critically ill patients, with a paucity of data regarding long-term survival, and characteristics correlated with short and long-term outcomes. We present a retrospective cohort PC patients supported with ECMO at a single institution, with outcomes at 1 and 3-year follow-up. Methods Data was collected retrospectively for all patients requiring ECMO within 72 hours of index cardiac operation, excluding assist devices and heart transplantation. Operative data, frozen mediastinum status, cannulation site, postoperative hemorrhage, and timing of cannulation (immediate versus delayed) were all collected and examined. Primary outcomes were ability to wean from ECMO, hospital survival, and long-term survival. Results 33 patients required PC ECMO, representing a total of 179 days of ECMO support. Overall survival data were: ability to wean 61%, hospital survival 55%, one month survival 45%. The estimated 12 and 36 month survival for all PC ECMO patients was 40% and 33% respectively. Twelve and 36 month survival for all hospital survivors was 66% and 60% respectively. Operative times, type of operation performed, open chest status, reoperation for hemorrhage and cannulation location (central/peripheral) were all compared. There were no statistically significant relationships of these variables short or long-term survival. Conclusions Overall 12 month survival for PC-ECMO patients was 40%, and was 33% at 36 months. For hospital survivors, 1 year survival was 66%, and was 60% at 36 months. These data support PC-ECMO as a reasonable salvage strategy, with mid-term survival comparable to other surgically treated diseases.
Isoflavonoid is one of the groups of flavonoids that play pivotal roles in the survival of land plants. Chalcone synthase (CHS), the first enzyme of the isoflavonoid biosynthetic pathway, catalyzes the formation of a common isoflavonoid precursor. We have previously reported that an isozyme of soybean CHS (termed GmCHS1) is a key component of the isoflavonoid metabolon, a protein complex to enhance efficiency of isoflavonoid production. Here, we determined the crystal structure of GmCHS1 as a first step of understanding the metabolon structure, as well as to better understand the catalytic mechanism of GmCHS1.