The UCSC Genome Browser has been an important tool for genomics and clinical genetics since the sequence of the human genome was first released in 2000. As it has grown in scope to display more types of data it has also grown more complicated. The data, which are dispersed at many locations worldwide, are collected into one view on the Browser, where the graphical interface presents the data in one location. This supports the expertise of the researcher to interpret variants in the genome. Because the analysis of Single Nucleotide Variants (SNVs) and Copy Number Variants (CNVs) require interpretation of data at very different genomic scales, different data resources are required. We present here several Recommended Track Sets designed to facilitate the interpretation of variants in the clinic, offering quick access to datasets relevant to the appropriate scale.

Pembrolizumab is more widespread use clinically with Pembrolizumab being recommended as a first-line therapy for advanced NSCLC. At the same time, some new adverse reactions have also been discovered, including hyperpigmentation. We hereby present a 77-year-old Chinese female with primary bronchial lung cancer. Genetic testing showed negative for EGFR and ALK. Immunohistochemical analysis showed tumor proportion score (TPS) of PD-L1 was 80% on tumor cells. Then the patient received pembrolizumab 200mg every three weeks, as the first-line therapy. Two courses after initiation pembrolizumab, hyperpigmentation appeared on her face and back of the hand. The right middle lobe mass and mediastinal lymph node metastasis progressed after nine courses after initiation of pembrolizumab, and the patient’s entire face turned black. It potentially indicates that cutaneous adverse events of hyperpigmentation, might be a negative predictor of response to pembrolizumab in metastatic lung adenocarcinoma patients.

Aims: To assess the impact of cytochrome P450 (CYP) 2C19 polymorphisms on the clinical efficacy and safety of voriconazole. Methods: We systematically searched PubMed, EMBASE, CENTRAL, ClinicalTrials.gov, and three Chinese databases from their inception to March 18, 2021 using a predefined search algorithm to identify relevant studies. Studies that reported voriconazole-treated patients and information on CYP2C19 polymorphisms were included. The efficacy outcome was success rate. The safety outcomes included overall adverse events, hepatotoxicity and neurotoxicity. Results: A total of 20 studies were included. Intermediate metabolizers (IMs) and Poor metabolizers (PMs) were associated with increased success rates compared with normal metabolizers (NMs) (risk ratio (RR): 1.18, 95% confidence interval (CI): 1.03~1.34, I2=0%, p=0.02; RR: 1.28, 95%CI: 1.06~1.54, I2=0%, p=0.01). PMs were at increased risk of overall adverse events in comparison with NMs and IMs (RR: 2.18, 95%CI: 1.35~3.53, I2=0%, p=0.001; RR: 1.80, 95% CI: 1.23~2.64, I2=0%, p=0.003). PMs demonstrated a trend towards an increased incidence of hepatotoxicity when compared with NMs (RR: 1.60, 95%CI: 0.94~2.74, I2=27%, p=0.08), although there was no statistically significant difference. In addition, there was no significant association between CYP2C19 polymorphisms and neurotoxicity. Conclusions: IMs and PMs were at a significant higher success rate in comparison with NMs. PMs were significantly associated with an increased incidence of all adverse events compared with NMs and IMs. Researches are expected to further confirm these findings. Additionally, the relationship between hepatotoxicity and CYP2C19 polymorphisms deservers clinical attention.

The relationship between intrinsic, closure-free threshold stress intensity and near-tip residual stress, characterizes the effect of load magnitude as well as load history on near-threshold fatigue crack growth rates. It serves as a reference against which precise closure data can be extracted from growth rates to calibrate analytical estimates. These possibilities were subjected to rigorous experimental verification involving threshold and near-threshold fatigue response under overloads, underloads with load-shedding on a steel prone to oxide debris formation. The study reveals why conventional load shedding practice to characterize threshold stress intensity is prone to yield unconservative and misleading results.

Background and Objective: Ectopic beats originating from the pulmonary vein (PV) trigger atrial fibrillation (AF). The purpose of this study was to clarify the electrophysiological determinant of AF initiation from the PVs. Methods: Pacing studies were performed with a single extra stimulus mimicking an ectopic beat in the left superior pulmonary veins (LSPVs) in 62 patients undergoing AF ablation. Inducibility of AF, effective refractory period (ERP) and conduction properties within the PVs were analyzed. Results: A single extra stimulus in LSPV induced AF in 20 patients (32% of all patients) at the mean coupling interval (CI) of 172 ms. A CI-dependent anisotropic conduction at the AF onset was visualized in a 3D-mapping. Onset of AF was site-specific with reproducibility in each individual. Mean ERP in LSPV in the AF inducible group was shorter than that in the AF non-inducible group (182 ± 55 ms vs 254 ± 51 ms, P<0.0001). LSPV ERP dispersion was greater in the AF inducible group than in the AF non-inducible group (45 ± 28 ms vs 27 ± 19 ms, P<0.01). Circumferential intra-PV conduction time (IPVCT) exhibited decremental properties in response to shortening of CI, and the prolongation of IPVCT in the AF inducible site was greater than that in the AF non-inducible site (P<0.05) in each individual. Conclusions: Location and coupling interval of an ectopic excitation ultimately determine the initiation of AF from the PVs. ERP dispersion and circumferential conduction delay may lead to anisotropic conduction and reentry within the PVs that initiate AF.

Background. Scar-related atrial tachycardias (ATs) are very challenging and no comparative studies have been conducted between the up-to-date systems, namely the new Confidense HD coloring mapping module (HD) and the new Rhythmia (RM) mapping system. Objectives. Our study sought to compare both strategies in terms of: (1) diagnosis and immediate treatment success: (2) procedure parameters in AT presenting patients. Methods and Results. Overall, 38 patients (68±9 years old) were randomized (HD=20, RM=18). The AT mechanisms did not differ between the groups: macro/small loop reentrant mechanisms were more common in both groups (12/20 [60%] versus 10/18 [56%], P=0.9), with the remaining diagnosed as multiloop (5/20 [25%] versus 4/18 [22%]; p=0.9); focal (1/20 [5%] versus 2/18 [11%], P=0.9), and localized reentrant (2/20 [10%] versus 2/18 [11%]). The procedure parameters were as follows: tachycardia cycle length (275±30 vs. 280±50; p=0.7); number of activation maps per patient (2±1 vs 2±1; p=0.9); procedure time (138±90 vs. 139±90 min; p=0.98); X-ray time exposure (20±11 vs. 24±18 min; p=0.42); RF application time (39±36 vs. 25±28 min; p=0.21); and mean number of circuits per patient (1.8±1 vs. 1.6±0.9; 0.6). Acute success was obtained in 15/20 pts (75%) of the HD group and 14/18 (78%) of the RM group (p=0.9). The procedure failed in 2 patients with the HD coloring and they were converted to the RM group without success. No crossover was carried out in the RM group. Conclusions. This randomized study demonstrates that HD coloring and Rhythmia systems exhibit a similar efficacy in achieving acute AT termination.

Background Increasing numbers of patients surviving malignant bone tumors around the knee joint have led to an increasing importance to investigate long-term results. This study assessed the long-term results of rotationplasty after resection of malignant bone tumors regarding functional outcome and quality of life to allow better comparison with other treatment options in bone cancer treatment. Procedure 60 participants who underwent rotationplasty due to bone cancer took part in this multicentric questionnaire-based study. The long-term functional outcome was measured by the Musculoskeletal tumor society score (MSTS) and the Tegner activity level scale. The health-related quality of life (HRQL) was assessed by using the Short Form Health Survey (SF-36). Results Patients treated with rotationplasty (median follow-up of 22 years, range 10-47 years) regained a high level of activity (median MSTS score of 24). Even a return to high level sports was possible (mean Tegner activity level scale of 4). Duration of follow-up did not influence the functional outcome. HRQL scores were comparable to the general German population. Concerns of psychological problems due to the unusual appearance of the rotated foot have not been confirmed. Conclusion Rotationplasty can be a good alternative to endoprosthetic replacement or amputation, either as primary surgery or as a salvage procedure. Especially for growing children and very active patients rotationplasty should be considered.

The low expression strength and fixed induction initiation have always been the main obstacle for applying the bacterial quorum sensing (QS) system to protein production. As a typical QS system in Bacillus subtilis, ComQXPA activates the promoter PsrfA using ComX and ComA as the auto-inducer and promoter activator, respectively. This study developed a series of novel auto-induction expression systems in B. subtilis WB600 based on ComQXPA using super-folder green fluorescent protein as the reporter. First, the -35 region of PsrfA was replaced by the corresponding conserved sequence of σA-dependent promoters, yielding P1 with an 85% enhanced expression strength. Second, by conducting a semi-rational design within the spacer between -35 and -15 regions of in P1, we generated the ComQXPA promoter PS1E, the expression strength of which is 8.22-fold higher than that of PsrfA. Based on PS1E, we finally obtained three types of auto-induction expression systems with the induction initiations ranging from 1.5 h to 9.5 h by optimizing the combination of the promoters for ComX and ComA. By using the auto-induction expression systems, the yield of Bacillus deramificans pullulanase in B. subtilis reached 80.2 U/mL, 0.36-fold higher than the strongest constitutive promoter P566. With the diversity in dynamic features, the novel auto-induction expression systems provide great potential for improving protein expression and metabolite production in B. subtilis.

Aim: Metamizole (dipyrone) is a prodrug not detectable in serum or urine after oral ingestion. The primary metabolite is 4-methylaminoantipyrine (4-MAA), which can be N-demethylated to 4-aminoantipyrine (4-AA) or oxidized to 4-formylaminoantipyrine (4-FAA) by cytochrome P450 (CYP)-dependent reactions. Our aim was to identify the CYPs involved. Methods: We investigated the metabolism of 4-MAA in vitro using CYP expressing supersomes and the pharmacokinetics of metamizole in the presence of CYP inhibitors in healthy volunteers. Results: The experiments in supersomes revealed CYP1A2 as the major CYP for 4-MAA N-demethylation and 4-FAA formation. CYP2C19 and CYP2D6 contributed to N-demethylation but not to FAA formation. In the subsequent clinical study, we investigated the influence of ciprofloxacin (strong CYP1A2 inhibitor), fluconazole (strong CYP2C19 inhibitor) and the combination ciprofloxacin/fluconazole on the pharmacokinetics of a single dose of metamizole in n=12 healthy volunteers in a randomized, placebo-controlled, double-blind study. Both ciprofloxacin and fluconazole inhibited the metabolism of 4-MAA, confirming the in vitro results. Ciprofloxacin, fluconazole and ciprofloxacin/fluconazole increased the AUC0-12h of 4-MAA by 51%, 17% and 92%, respectively. Ciprofloxacin, fluconazole and ciprofloxacin/fluconazole decreased the AUC0-12h of 4-AA by 27%, 12% and 24%, respectively, and of 4-FAA by 33%, 9% and 51%, respectively. Ciprofloxacin, fluconazole and ciprofloxacin/fluconazole increased the half-life of 4-MAA from 3.22 h (placebo) to 3.91, 3.69 and 6.07 h, respectively. Conclusion: CYP1A2 is the major CYP for the conversion of 4-MAA to 4-AA and 4-FAA. CYP1A2 inhibition increases the 4-MAA exposure by a factor of approximately 1.5, which could be relevant for dose-dependent adverse reactions.

Objective The Model for End- Stage Liver Disease (MELD) score is a composite number of physiologic parameters and likely has non-linear effects on operative outcomes. . We use machine learning to evaluate the relationship between MELD score and outcomes of cardiac surgery. Methods All STS indexed elective cardiac surgical procedures at our institution between 2011 and 2018 were included. MELD score was retrospectively calculated. Logistic regression models and an imbalanced random forest classifier was created on operative mortality using 30 preoperative characteristics. Cox regression models and random forest survival models were created for long-term survival. Variable importance analysis (VIMP) was conducted to rank variables by predictive power. Linear and machine learned models were compared with their receiver operating characteristic (ROC) and Brier score respectively. Results The patient population included 3,872 individuals. Operative mortality was 1.7% and 5-year survival was 82.1%. MELD score was the 4th largest positive predictor on VIMP analysis for both operative long-term survival and the strongest negative predictor for operative mortality. The logistic model ROC area was 0.762, compared to the random forest classifier ROC of 0.674. The Brier score of the random forest survival model was larger (worse) than the cox regression starting at 2 years and continuing throughout the study period. Conclusions MELD score and other continuous variables had high degrees of non-linearity to mortality. This is demonstrated by the fact that MELD score was not significant in the cox multivariable regression but was strongly important in the random forest survival model.

Here we present a unique case of Harlequin syndrome without Horner syndrome after contralateral Th3 intradural tumor resection. Harlequin sign in our case presented probably to resection of sympathetic nerves while removing meningioma. Syndrome is rare in neurosurgical procedure, but we think that surgeons must be aware of it.

Using Computer Models to Identify Synthetic Quorum Sensing Inducers for S. aureus BacteriaBy: Anokh AmbadipudiWord Count: 4630

Introduction Type 2 diabetes mellitus (T2DM) frequently associates with increasing multi-morbidity/treatment complexity. Some headway has been made to identify genetic and non-genetic risk factors for T2DM. However longitudinal clinical histories of individuals both before and after diagnosis of T2DM are likely to provide additional insight into both diabetes aetiology/further complex trajectory of multi-morbidity. Methods This study utilised diabetes patients/controls enrolled in the DARE (Diabetes Alliance for Research in England) study where pre- and post-T2DM diagnosis longitudinal data was available for trajectory analysis. Longitudinal data of 281 individuals (T2DM n=237 vs matched non-T2DM controls n=44) were extracted, checked for errors and logical inconsistencies and then subjected to Trajectory Analysis over a period of up to 70 years based on calculations of the proportions of most prominent clinical conditions for each year. Results For individuals who eventually had a diagnosis of T2DM made, a number of clinical phenotypes were seen to increase consistently in the years leading up to diagnosis of T2DM. Of these documented phenotypes, the most striking were diagnosed hypertension (more than in the control group) and asthma. This trajectory over time was much less dramatic in the matched control group. Immediately prior to T2DM diagnosis a greater indication of ischaemic heart disease proportions was observed. Post-T2DM diagnosis, the proportions of T2DM patients exhibiting hypertension and infection continued to climb rapidly before plateauing. Ischaemic heart disease continued to increase in this group as well as retinopathy, impaired renal function and heart failure. Conclusion These observations provide an intriguing and novel insight into the onset and natural progression of T2DM. They suggest an early phase of potentially-related disease activity well before any clinical diagnosis of diabetes is made. Further studies on a larger cohort of DARE patients are underway to explore the utility of establishing predictive risk scores.

Abstract Aim: To investigate the health care utilization and drug consumption of patients with fibromyalgia (FM). Materials and Methods: This is a cross-sectional study using the Clalit Health Care database. Clalit is the largest HMO in Israel, serving more than 4.4 million enrollees. We identified FM patients and age and sex-matched controls. Indicators of healthcare utilization and drug consumption were extracted and analyzed for both groups. Results: The study included 14,296 FM patients and 71,324 controls. The mean age was 56 years, with a female predominance of 92%. The mean number of visits across of all healthcare services (hospitalizations, emergency department visit, general practitioner clinic visits, rheumatology clinic visits and pain clinic visits) and the mean difference (MD) were significantly higher for FM patients compared to controls (MD 0.66, p<0.001; MD 0.23, p<0.001; MD 7.49, p<0.001; MD 0.31, p<0.001; MD 0.13, p<0.001), respectively. Drug use was significantly and consistently higher among FM patients compared to controls; NSAIDs (non-steroidal anti-inflammatory drugs) OR 2.56, P<0.001; Opioids OR 4.23, P<0.001; TCA (tricyclic antidepressants) OR 8.21, P<0.001; Gabapentinoids OR 6.31, P<0.001; SSRI (selective serotonin reuptake inhibitors) OR 2.07, P<0.001; SNRI (serotonin-norepinephrine reuptake inhibitor) OR 7.43, P<0.001. Conclusion: Healthcare utilization and drug use are substantially higher among patients with fibromyalgia compared to controls

Aldosterone binds to the mineralocorticoid receptor (MR), a transcription factor of the nuclear receptor family, present in the kidney and in various other non-epithelial cells including the heart and the vasculature (Cannavo et al., 2018). Indeed, extra-renal pathophysiological effects of this hormone have been characterized, extending its actions to the cardiovascular (CV) system (Messaoudi et al., 2012). A growing body of clinical and pre-clinical evidence suggests that MR activation plays an important pathophysiological role in CV remodeling by promoting cardiac hypertrophy, fibrosis, arterial stiffness, as well as in inflammation and oxidative stress (Bauersachs et al., 2015). The following review article outlines the role of MR in CV disease with a focus on myocardial remodeling and heart failure (HF) including clinical trials as well as cellular and animal studies.

Genetic monitoring using non-invasive samples provides a complement or alternative to traditional population monitoring methods. However, Next Generation Sequencing approaches to monitoring typically require high quality DNA and the use of non-invasive samples (e.g. scat) is often challenged by poor DNA quality and contamination by non-target species. One promising solution is a highly multiplexed sequencing approach called Genotyping-in-thousands by sequencing (GT-seq), which can enable cost-efficient genomics-based monitoring for populations based on non-invasively collected samples. Here, we develop and validate a GT-seq panel of 324 single nucleotide polymorphisms (SNPs) optimized for genotyping of polar bears based on DNA from non-invasively collected fecal samples. We demonstrate 1) successful GT-seq genotyping of DNA from a range of sample sources, including successful genotyping of 85.7% of non-invasively collected fecal samples determined to contain polar bear DNA, and 2) that we can reliably differentiate individuals, ascertain sex, assess relatedness, and resolve population structure of Canadian polar bear subpopulations based on a GT-seq panel of 324 SNPs. Our GT-seq data reveal similar spatial-genetic patterns as previous polar bear studies but at lesser cost per sample and using non-invasively collected samples, indicating the potential of this approach for population monitoring. This GT-seq panel provides the foundation for a non-invasive toolkit for polar bear monitoring and contribute to community-based programs – a framework which may serve as a model for wildlife management and contribute to conservation and policy for species worldwide.

Leptospirosis is a zoonotic neglected disease of worldwide public health concern. Leptospira species can infect a wide range of wild and domestic mammals and can lead to a spectrum of disease, including severe and fatal forms. Herein, we report for the first time a fatal Leptospira interrogans infection in a free-ranging nonhuman primate (NHP), a black-tufted marmoset. Icterus, pulmonary hemorrhage, interstitial nephritis and hepatocellular dissociation were the main findings raising the suspicion of leptospirosis. Diagnostic confirmation was based on specific immunohistochemical and PCR assays for Leptospira species. Immunolocalization of leptospiral antigens and identification of pathogenic species ( L. interrogans species) were important for better understanding the pathogenesis of disease. One Health related implications of free-ranging NHPs in anthropized areas and transmission dynamics of human and animal leptospirosis are discussed.

Objective: To establish the predicted value of lung function determined by impulse oscillometry (IOS) in children (4~17 years old) in China. Methods: A total of 6270 healthy children aged 4 to 17 in Shanghai were included. The Master Screen IOS pulmonary function device (Jaeger Co, Germany) was used to detect the respiratory total impedance (Zrs), response frequency (Fres), viscosity resistance (Rrs) and elastic resistance (Xrs) at various oscillation frequencies, and the indexes above were analyzed. The stepwise multivariate regression was used to establish the regression equation of related parameters of IOS in different genders. Results The median age of 6270 children (3345 boys and 2925 girls) was 10 years, ranging from 4 to 17 years. The differences in the main IOS parameters between different age and height groups are statistically significant regardless of sex (P<0.05). The values of Z5, R5, R20, and Fres decreased with the increase of age and height, while X5 increased with the increase of age and height. The stepwise multivariate regression analysis showed that IOS parameters were related to height, age, and weight, and most IOS parameters were most closely related to height (the absolute value of regression coefficient was the largest). Conclusions: The study revealed the normal predicted value of pulmonary function by IOS in healthy children in China. In the evaluation of the results of the lung function measurements, the use of this predicted value equation is more in line with the characteristics of Chinese children than that of foreign countries. Key words: impulse oscillometry; respiratory function test; normal predicted value; child

Cover letter Pediatric Pulmonology Dear Editor, Enclosed is a manuscript to be considered in Pediatric Pulmonology that does not require an abstract , usually. This letter to the editor entitled “Ventilatory limitations are not associated with dyspnea on exertion or reduced aerobic fitness in pectus excavatum: a critical information that must be highlighted to prevent inappropriate interventions” comments the reports by Hardie and al. which tested the hypothesis that PEX deformities are associated with a pulmonary impairment during exercise and concluded that resting lung volume measurements were associated with the anatomic degree of PEX severity.

Title Page: MinicommentaryThis is a minicommentary on Reid et al. “How common are complications following polypropylene mesh, biological xenograft 3 and native tissue surgery for pelvic organ prolapse? A secondary analysis from the PROSPECT trial”.Title: Understanding Risk: a substitute for Information?Author : Swati Jha (MD, FRCOG)Consultant Gynaecologist and Honorary Senior Clinical Lecturer, Sheffield University. Subspecialist in UrogynaecologyInstitute : Department of Urogynaecology, Sheffield Teaching Hospitals NHS Foundation TrustAddress : Sheffield Teaching Hospitals, Level 4, Jessop Wing, Tree Root Walk, Sheffield. S10 2SFSwati.Jha1@nhs.net0044 (0)114 2268568Fax : 0114 2268165

ENT emergencies are heterogeneous and include infections, inflammatory and traumatic conditions. We observed what appeared to be a dramatic alteration in emergency presentations to our unit during the early phase of 1st COVID-19 Lockdown in 2020. Objective- This study compares pre COVID-19 presentations with 1st Lockdown presentations and examines the overall numbers; conditions encountered and draw conclusions which may influence future planning for ENT services. Setting-Records for emergency ENT presentations to a regional centre were examined for two comparable 61-day time periods. Design and Participants-Presentations for April and May 2019 (pre COVID-19) were compared to April and May 2020 (1st Lockdown). Records were compared with regards to overall numbers, demography, diagnosis and treatment. Admissions for COVID-19 related airway interventions and admissions/attendances for elective complications were excluded. Results and conclusion-In the pre COVID-19 group, 649 emergency presentations were recorded: 401 infection related cases, 90 epistaxis, and 158 non-infectious/traumatic cases. In the 1st Lockdown group, 254 emergency presentations were recorded: 121 infection related cases, 56 epistaxis and 77 non-infectious/ traumatic cases. Overall, there was a 61% reduction in emergency presentations during the 1st Lockdown. Infectious cases reduced by 70%, epistaxis reduced by 38% and non-infectious cases fell by 51%. All of these differences were statistically significant (p value <0.05). The infectious category showed the greatest reduction in presentations and within this category the greatest change was observed in Laryngeal infections (95%), facial cellulitis (84%) and Tonsil infections (73%).

We are reporting a case of Guillain- Barré syndrome seven days after the first dose of Pfizer-BioNTech COVID-19 Vaccine. As this vaccine is still under investigation, reporting possible rare side effects is essential. In this case, the temporal relationship was suggestive of a vaccine-induced cause.

Title Page: Minicommentary

Background and Purpose: Cellular Communication Network Factor 2 (CCN2) is a matricellular protein normally present in the vascular wall but overexpressed in several cardiovascular diseases. CCN2 has been proposed as a downstream mediator of profibrotic actions of Transforming Growth Factor (TGF)-β and Angiotensin II (Ang II). However, its direct role in cardiovascular diseases is not completely understood. Experimental Approach: To investigate the direct role of CCN2 under vascular pathological conditions, a conditionally deficient CCN2 (CCN2-KO) mouse was evaluated infused or not with Ang II. Key Results: In the absence of CCN2, Ang II infusion induced a rapid (within 48 hours) aortic aneurysm generation and increased aneurysm rupture with 80 % lethality at the endpoint. CCN2 deletion caused elastin layer disruption and increased metalloproteinase activity, which were aggravated by Ang II administration. Aortic RNA-seq studies and the subsequent Gene Ontology enriched analysis pointed out the aldosterone biosynthesis process as one of the most enriched terms in absence of CCN2. Pharmacological aldosterone pathway intervention in Ang II-infused CCN2-KO mice, by treatment with the mineralocorticoid receptor antagonist spironolactone, reduced aneurysm formation and mortality after Ang II infusion. Conclusion and Implications: CCN2 deletion induces a rapid aneurysm formation and rupture after Ang II infusion which is partially prevented by blocking the mineralocorticoid receptor. Our present data highlight, for the first time, the potential role of CCN2 as a vascular homeostatic factor and its relevance in the aldosterone synthesis, opening new avenues to future studies in aortic aneurysm treatment.