Sustained milk consumption after 2 years post-Milk Epicutaneous therapy for Eosinophilic EsophagitisJonathan M. Spergel, MD, PhD1,2; Amanda B. Muir, MD2,3; Chris A. Liacouras, MD2,3;Deirdre Burke1, CRA; Megan O. Lewis, MSN, RN, CPNP1; Terri Brown-Whitehorn, MD1,2, Antonella Cianferoni, MD, PhD1,21Division of Allergy and Immunology, The Children’s Hospital of Philadelphia, PA, USA, 2Department of Pediatrics, The Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA, USA, 3Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, PA, USAAuthor contribution:JMS-study design, writing manuscript, interpreting data; ABM-writing manuscript, study visits, data interpretation; CAL-writing manuscript, study design, interpreting data; DB-writing manuscript, regulatory coordinator, coordination and collection of data, study visits; MOL-writing manuscript, collection of data, study visits; TBW-writing manuscript, collection of data and study visits, AC-interpreting data, collection of data, study visits, regulatory itemsTo the Editor:Eosinophilic Esophagitis (EoE) is an allergic disease of the esophagus without any curative therapy. Typical symptoms of EoE are feeding difficulties, vomiting, abdominal pain and dysphagia and vary by age, with a diagnosis confirmed on esophageal biopsy with> 15 eosinophils/high power field (eos/hpf).1 The two treatment options for pediatric EoE2 are: 1) topical swallowed steroids, which is effective in inducing EoE remission in 50-90% of patients, depending on the dose, formulation and medication used; 2) dietary elimination of the causative allergen/s which is effective in 50-70% of patients with selective food elimination, and 95% with elemental diets3. Cow’s milk (CM) is the most common food allergen causing disease in up to 65% of patients.4 When either treatment is discontinued, inflammation and symptoms recur.3Epicutaneous immunotherapy (EPIT) is an investigational immunotherapy using low dose allergen exposure through the skin to induce desensitization. In the randomized controlled clinical trial,Study of Efficacy and Safety of Viaskin® Milk for CM-induced EoE (SMILEE Study) , 20 pediatric participants with CM-induced EoE were randomized to receive EPIT with Viaskin® Milk (n=15) or placebo (n=5)(details in appendix). After CM-induced EoE was confirmed, EPIT therapy was applied daily for 9 months during a CM-free period, followed by CM-containing diet for 2 months (Figure 1). At 11 months, subjects completed an upper endoscopy with biopsy to evaluate tissue eosinophilia as the primary endpoint. In the pre-defined per-protocol population (7 patients-Viaskin® Milk, 2 patients- placebo), Viaskin® Milk treated subjects had a lower number of eosinophils/high power field (eos/hpf) on biopsy (25.57 ± 31.19) compared to placebo (95 ± 63.64). After the blinded phase, 19 subjects were eligible to enroll in the open-label extension (additional 11 months of therapy) and had repeat endoscopy and biopsy. At the end of the open-label phase, 6/19 subjects had < 6 eos/hpf (32% response rate); 3/19 subjects had 7-14 eos/hpf for total response rate of 47%.5As part of routine clinical care, we continue to follow all 19 subjects who completed the open-label extension (currently 2 years after the end of Viaskin® Milk therapy) to understand whether CM continued in their diet without symptoms. Four of 5 subjects who had <6 eos/hpf after milk introduction were able to continue with approximately 2 servings of CM/day without any symptoms (Table 1). One of these patients had a clinically indicated endoscopy and biopsy that had 0 eosinophils. Two subjects, who had 6-14 eos/hpf during the study, continued to tolerate CM, including one subject who continued to have 6-14 eos/hpf on repeat endoscopy. In addition, 4 subjects who had significant symptoms ingesting CM and had > 15 eos/hpf during the initial SMILEE study were able to add CM back into their diet without having symptoms, as either baked CM (n=2) or regular CM with concomitant swallowed steroids therapy (n=2).The follow-up of this pilot study for the use of EPIT for milk-induced EoE suggests that the treatment effect can persist for 2 years after stopping therapy; six out of 7 patients in the responder and partial responder groups remain completely symptom-free while consuming an average of 2 servings/day of CM. In contrast to the current therapies of diet elimination or swallowed topical steroids where symptoms return when therapy is stopped, EPIT has demonstrated a persistent effectiveness. These findings align with EPIT’s proposed mechanism of action, by directly targeting and reprogramming the immune response to allergen.3 EPIT may induce true tolerance, as is observed in murine models, where Foxp3(+) CD25(+) CD4(+) T regulatory cells are induced and can transfer tolerance.6 Further longer-term studies are needed to examine this possibility and confirm these unique findings.Reference:1. Spergel JM, Dellon ES, Liacouras CA, et al. Summary of the updated international consensus diagnostic criteria for eosinophilic esophagitis: AGREE conference. Ann Allergy Asthma Immunol.2018;121:281-284.2. Spergel JM, Brown-Whitehorn TA, Muir A, Liacouras CA. Medical algorithm: Diagnosis and treatment of eosinophilic esophagitis in children. Allergy. 2020;75:1522-1524.3. Nhu QM, Aceves SS. Medical and dietary management of eosinophilic esophagitis. Ann Allergy Asthma Immunol.2018;121:156-161.4. Kagalwalla AF, Amsden K, Shah A, et al. Cow’s milk elimination: a novel dietary approach to treat eosinophilic esophagitis.J Pediatr Gastroenterol Nutr. 2012;55:711-716.5. Spergel JM, Elci OU, Muir AB, et al. Efficacy of Epicutaneous Immunotherapy in Children With Milk-Induced Eosinophilic Esophagitis. Clin Gastroenterol Hepatol. 2020;18:328-336 e327.6. Dioszeghy V, Mondoulet L, Dhelft V, et al. The regulatory T cells induction by epicutaneous immunotherapy is sustained and mediates long-term protection from eosinophilic disorders in peanut-sensitized mice. Clin Exp Allergy. 2014;44:867-881.Sincerely,Jonathan M. Spergel, MD, PhD1,2; Amanda B. Muir, MD2,3; Chris A. Liacouras, MD2,3;Deirdre Burke1, CRA; Megan O. Lewis, MSN, RN, CPNP1; Terri Brown-Whitehorn, MD1,2, Antonella Cianferoni, MD, PhD1,21Division of Allergy and Immunology, The Children’s Hospital of Philadelphia, PA, USA, 2Department of Pediatrics, The Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA, USA, 3Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, PA, USAFunding Sources: The Children’s Hospital of Philadelphia Eosinophilic Esophagitis Family FundAcknowledgements: JMS, CAL, TBW and MOL are consultants for DBV Technology.Correspondence: Jonathan M. Spergel MD, PhDThe Children’s Hospital of PhiladelphiaDivision of Allergy and ImmunologyWood Bldg 3352D3401 Civic Center Blvd,Philadelphia, PA 19104Email: spergel@email.chop.eduPhone: 1-215-590-2549Table 1

A 51 yo man presented with weakness and constitutional symptoms, found on labs to have EJ-antibody antisynthetase syndrome. Myopathy is usually a late manifestation of Antisynthetase syndrome and is steroid-responsive, however in our case it occurred earlier. It is important to consider Antisynthetase syndrome in patients presenting with inflammatory myopathy.

Aims: Hypophosphatemia is an increasingly recognized side-effect of ferric carboxymaltose (FCM) and possibly iron isomaltoside/ferric derisomaltose (IIM), which are used to treat iron deficiency. To determine frequency, severity, duration and risk factors of incident hypophosphatemia after treatment with FCM and IIM. Methods: A systematic literature search for articles indexed in EMBASE, PubMed and Web of Science in years 2005 to 2020 was carried out using the search terms ‘ferric carboxymaltose’ OR ‘iron isomaltoside’. Prospective clinical trials reporting outcomes on hypophosphatemia rate, mean nadir serum phosphate and/or change in mean serum phosphate from baseline were selected. Hypophosphatemia rate and severity were compared for studies on IIM vs. FCM after stratification for chronic kidney disease. Meta-regression analysis was used to investigate risk factors for hypophosphatemia. Results: Across the 42 clinical trials included in the meta-analysis, FCM induced a significantly higher incidence of hypophosphatemia than IIM (47%, 95% CI 36-58% vs. 4%, 95% CI 2-5%), and significantly greater mean decreases in serum phosphate (0.40 versus 0.06 mmol/L). Hypophosphatemia persisted at the end of the study periods (maximum 3 months) in up to 45% of patients treated with FCM. Meta-regression analysis identified low baseline serum ferritin and transferrin saturation, and normal kidney function as significant predictors of hypophosphatemia. Conclusion: FCM is associated with a high risk of hypophosphatemia, which does not resolve for at least 3 months in a large proportion of affected patients. More severe iron deficiency and normal kidney function are risk factors for hypophosphatemia.

Background and Purpose: It is well established that both smokers and patients with COPD are at a significantly heightened risk of cardiovascular disease (CVD), although the mechanisms underpinning the onset and progression of comorbid CVD are largely unknown. Here, we explored whether cigarette smoke (CS) exposure impairs vascular function in mice and given the well-known pathological role for oxidative stress in COPD, whether the antioxidant compound ebselen prevents CS-induced vascular dysfunction in mice. Experimental Approach: Male BALB/c mice were exposed to either room air (sham) or CS generated from 9 cigarettes per day, 5 days a week for 8 weeks. Mice were treated with ebselen (10mg/kg, oral gavage once daily) or vehicle (5% w/v CM cellulose in water) 1 h prior to the first CS exposure of the day. Upon sacrifice, bronchoalveolar lavage fluid (BALF) was collected to assess pulmonary inflammation and the thoracic aorta was excised to investigate vascular endothelial and smooth muscle dilator responses ex-vivo. Key Results: CS exposure caused a significant increase in lung inflammation which was reduced by ebselen. CS also caused significant endothelial dysfunction in the thoracic aorta which was attributed to a downregulation of eNOS expression and increased vascular oxidative stress. Ebselen abolished the aortic endothelial dysfunction seen in CS-exposed mice by reducing the oxidative burden and preserving eNOS expression. Conclusion and Implications: Targeting CS-induced oxidative stress with ebselen may provide a novel means for treating the life-threatening pulmonary and cardiovascular manifestations associated with cigarette smoking and COPD.

Molecular targeted drugs and immune checkpoint blockades are not indicated for all advanced non-small cell lung cancer (NSCLC) cases. For such patients, cytotoxic drugs are the main treatment, and the prognosis remains poor. We present a valuable case of advanced NSCLC that was potentially permanent cured by pemetrexed maintenance chemotherapy.

Background: To identify alarming symptoms that could potentially lead to severe form of COVID-19 pneumonia (i.e. novel coronavirus pneumonia: NCP), a disease that is now having pandemic spread. Methods: Articles from PubMed, Embase, Cochrane database and Google up to 24 February 2020 were systematically reviewed. 18 publications that had documented cases of COVID-19 pneumonia were identified. The relevant data were extracted, systematically reviewed and further evaluated using meta-analysis. We define severe COVID-19 pneumonia as the disease status that requires admission to the intensive care unit (ICU) and respiratory/circulatory support, which is in align with the guideline from the World Health Organization (WHO). Results: 14 studies including 1,424 patients were considered eligible and analyzed. Symptoms such as fever (89.2%), cough (67.2%), fatigue (43.6%) were quite common; but dizziness, hemoptysis, abdominal pain and conjunctival congestion/conjunctivitis were relatively rare. The incidence of dyspnea was significantly higher in patients with severe than non-severe COVID-19 pneumonia (42.7% vs.16.3%, p<0.0001). Similarly, fever and diarrhea were also drastically more common in patients with severe form (p=0.0374 and 0.0267). Further meta-analysis using three high-quality China-based studies confirmed such findings and showed that dyspnea, fever and diarrhea were 3.53 (OR: 3.53, 95%CI: 1.95-6.38), 1.70 (OR: 1.70, 95%CI: 1.01-2.87), and 1.80 (OR: 1.80, 95%CI: 1.06-3.03) folds higher respectively in patients with severe COVID-19 pneumonia. Conclusion: Dyspnea, fever and diarrhea are significantly more prevalent in patients with severe COVID-19 pneumonia, suggesting they are alarming symptoms that warrant close attention and timely management.

Background: Bacterial vaginosis is a frequent source of vaginal infection among reproductive-aged women. Astodrimer gel is a novel drug which demonstrated favorable outcomes for treatment of patients with bacterial vaginosis. Aim: We attempted to conduct a systematic review and meta-analysis of all randomized controlled trials (RCTs) which examined the efficacy and safety of astodrimer gel in patients with bacterial vaginosis. Methods: We searched four databases from inception to August 15th, 2020 using relevant keywords. We identified all RCTs which surveyed the efficacy and safety of astodrimer gel in treating patients with bacterial vaginosis. We appraised the quality of the included RCTs using the Cochrane risk of bias assessment tool. We pooled dichotomous outcomes as numbers and totals and reported them as risk ratios (RR) with 95% confidence intervals (95% CI) under random- or fixed-effects meta-analysis models depending on heterogeneity. Results: Three eligible studies comprising four independent RCTs and 1165 patients were identified (614 and 551 patients received astodrimer gel and placebo, respectively). For efficacy outcomes (n=320 astodrimer gel versus n=260 placebo), astodrimer gel was significantly superior to placebo for all pooled efficacy outcomes, including clinical cure rate (at 9-12 and 21-30 days), microbiological Nugent cure rate (at 9-12 and 21-30 days), patient self-reported absence of vaginal odor/discharge (at 9-12 and 21-30 days), resolution of Amsel criteria (at 9-12 days) and percentage of patients who received rescue therapy (during study). With respect to safety outcomes (n=614 astodrimer gel versus n=551 placebo), astodrimer gel demonstrated equal tolerability to placebo for all pooled safety endpoints, expect unfavorably for vulvovaginal candidiasis and treatment-related vulvovaginal candidiasis. Conclusions: Astodrimer gel is effective in treating bacterial vaginosis and corroborated by clinical (Amsel criteria) and microbiological (Nugent score) measurements as well as patient-reported symptoms. Moreover, astodrimer gel is largely safe and associated with marginal rate of vulvovaginal candidiasis.

Rasmussen's encephalitis is a rare chronic neurological disorder, characterized by unilateral inflammation of the cerebral cortex, drug-resistant epilepsy, progressive neurological and cognitive impairment. We report a case of a 17-year old male with persistent epilepsy, intellectual impairment, and cognitive deterioration.

Pericardial fat pad in transverse sinus adjacent to LAA is a rare condition that may resemble LAA thrombosis especially in suspected cases. More TEE angulations and 3D TEE can confirm the diagnosis.

Aim: We evaluated the COVID-19 threat in patients receiving intravesical BCG therapy which has immunotherapeutic effects and is of vital importance in most of the individuals with high-risk non-muscle-invasive bladder cancer (NMIBC) and investigated the need for postponement of this therapy. Methods: A total of 71 patients, who were diagnosed with high-risk NMIBC and on intravesical BCG treatment regularly (induction or maintenance), were enrolled in the study. The patients were classified into two groups depending on whether they were diagnosed with COVID-19 during the pandemic period or not. Results: Of 71 patients, 26 underwent a COVID-19 polymerase chain reaction test with clinical suspicion during the pandemic period. Of these 26 patients, 4 were diagnosed with COVID-19. Age of the patients, working status (working/retired), compliance with containment measures against the pandemic, number of BCG courses, adverse effects after BCG therapy, and systemic immune-inflammation index, which is an inflammation-related parameter, were not different between groups (p>0.05). Neutrophil/lymphocyte ratio was significantly higher in the COVID-19 positive group (p<0.05). COVID-19 positivity was higher in age groups 50-64 (6.6%) and 65-80 (5.8%) years than that in similar age groups of the normal population. Conclusion: Every effort should be made to administer intravesical BCG treatment in high-risk NMIBC patients even during the pandemic period. However, increased risk of COVID-19 transmission should be kept in mind and protective measures against COVID-19 for healthcare providers and patients before the procedure should be taken optimally. The procedure should be postponed in patients with lymphopenia in recent complete blood count.

Background: Coronavirus disease-19 (Covid-19) had an unprecendented effect on both nations and health systems. Time series modeling using Auto-Regressive Integrated Moving Averages (ARIMA) models have been used to forecast variables extensively in statistics and econometrics. Objectives: The aim is to predict the total number of Covid-19 cases in the United States of America using ARIMA models of time-series analysis. Methods: We used time series analysis to build an ARIMA model of the total number of cases from January 21, 2020 to August 7, 2020 and used the model to predict cases in the following 7 days, from August 8, 2020 to August 14, 2020. Hyndman and Khandakar algorithm was used to select components of ARIMA models. Percentage error was used to evaluate forecasting accuracy. Results: During the model building period, 4,883,646 cases were diagnosed and during 14 days of validation period additional 313,502 new cases were added. ARIMA model with (p,d,q) components of (5,2,1) was used for forecasting. The mean percentage error of forecast was 0.09% and forecast accuracy was high in the following week. Conclusion: ARIMA models can ve used to forecast the total number of cases of Covid-19 patients in the upcoming first week.

Background: IgA nephropathy (IgAN) advances from multiple pathogenic “hits” resulting in poorly O-galactosylated IgA1 glycoforms (Gd-IgA1), production of antibodies and glomerular deposition of immune complexes. A sequence of immune responses arising from plasma cells, T cells and antigen presenting cells (APCs), causes glomerular injury. Methods: This study was designed to phenotype subsets of B cells, monocytes and T cells in the peripheral circulation and their association with inflammatory cytokines and renal function in patients with IgAN, healthy controls (HC) and disease controls with autosomal dominant polycystic kidney disease (ADPKD). Results: We observed a significant decrease in the proportion of pre-switched B cells and plasmablasts, but an increase in long-lived plasma cells in the peripheral circulation of IgAN patients compared to HC. The proportion of non-classical monocytes was significantly higher in IgAN patients compared to both HC and ADPKD. We also report an association between sCD40L levels and the proportion of pre-switched B cells, as well as sCD40L and MCP-1 levels and albuminuria in IgAN patients. Conclusions: We applied an easy-access method to analyze subsets of immune cells as well as relevant inflammatory mediators in IgAN patients. Our data demonstrate an altered B cell profile that indicates a pathophysiological role of the B cell lineage and an increased proportion of non-classical monocytes that suggests their role in the disease process.

The early damage of asphalt pavement is closely related to the mechanical behavior of asphalt mixture. In order to study the mechanical response of asphalt mixture particles under vehicle load, a 2 DOF 1/4 vehicle model composed of mass block-spring-damper was constructed in this paper. Based on the discrete element theory, a three-dimensional discrete element model of asphalt pavement with random distribution of coarse aggregate was constructed according to material gradation and porosity. The dynamic load of vehicle on the road surface was solved by using road roughness as excitation. The constitutive relation between particles was described by parallel bond and linear bond. The microstructure parameters of each structure layer were obtained by trial and error method. The “fish” language program was written to realize vehicle load movement. Finally, the mechanical response and velocity of the pavement structure layer particles were solved. The results show that the vertical displacement of the pavement calculated by the discrete element method is less than 8.9% of that calculated by the finite element method, which indicates that the discrete element method is more feasible. The vertical compressive stress of the upper layer is 14.1% higher than that of the middle layer, 57.7% higher than that of the lower layer, and 80% higher than that of the base layer. The longitudinal compressive stress of the upper layer is 64.3% greater than that of the upper layer. The grain at the bottom of the middle layer is mainly subjected to tensile stress. The particles in the upper and middle layers mainly bear transverse compressive stress while the other structural layers bear transverse tensile stress. The transverse, longitudinal and vertical velocities of the upper layer particles vary dramatically during vehicle startup and braking. When the vehicle is running stably, the particle velocity of each structure layer is small. The lateral and vertical velocity curves of the particles are antisymmetric, while the longitudinal velocity curves of the particles are symmetric.

Background: Coronary artery disease is a major public health problem. Early diagnosis and treatment of coronary artery disease is crucial. There is a need for a practical, reliable and cost-effective non-invasive imaging tool. We aimed to evaluate the rest ischemia with speckle tracking echocardiography (STE) compare to the two methods in patients who were scheduled coronary angiography according to the stress tests. Methods: We included fifty patients with stable angina pectoris who were scheduled for conventional coronary angiography after the stress tests in our study. Speckle tracking echocardiography was performed just before coronary angiography. The association of 2 parameters with coronary artery disease was investigated and compared. Results: Among 50 patients recruited for the study, 38 of them had severe CAD (>50%), whereas 12 patients had non-significant CAD. Post systolic shortening (PSS) was significantly related with CAD (p<0.0001). The relationship of PLS with the area at risk was found to be statistically insignificant but global longitudinal strain (GLS) was significantly lower in patients with severe CAD (p=0.011) Conclusion: PSS may detect coronary ischemia in patients with stable coronary artery disease and it is more sensitive and specific in patients with stable CAD. PSS is a very useful, practical and easy applicable non invasive tool for the detection of severe coronary artery disease at rest.

Internal erosion is one of the most common causes of failure in hydraulic engineering structures, such as embankments and levees. It also plays a vital role in the geohazards (such as landslides and sinkhole developments) and more importantly, the earth landscape evolution, which has a broad environmental and ecosystem impacts. The groundwater seepage is multi-directional, and its multi-dimensional nature could affect the initiation and the progression of internal erosion. With a newly developed apparatus, we carry out nine internal erosion experiments under five different seepage directions. The results reveal that the critical hydraulic gradient increases as the seepage direction varies from the horizontal to the vertical. After a global erosion is triggered, preferential erosion paths distribute randomly from the bottom to the top of the specimen. If the seepage direction is not vertical, small preferential erosion paths merge into a large erosion corridor, in which the loss of fine particles is significant but negligible outside. Results of experiments manifest that the erosion is heterogeneous and three-dimensional, even in the unidirectional seepage flow. The particles are rapidly eroded at the early stage of the erosion, indicating a high erosion rate. With the erosion time increasing, the particle loss slows down and even ceases if the time is long enough. The erosion rate increases if the seepage direction approaches a vertical direction. Overall, the erosion rate approximately decreases with erosion time exponentially. We proposed exponential equations to illustrate the variation of the erosion rate in the erosion process.

Interactions with microbial symbionts have yielded great macroevolutionary innovations across the tree of life, like the origins of chloroplasts and the mitochondrial powerhouses of eukaryotic cells. There is also increasing evidence that host-associated microbiomes influence patterns of microevolutionary adaptation in plants and animals. Here we describe how microbes can facilitate adaptation in plants and how to test for and differentiate between the two main mechanisms by which microbes can produce adaptive responses in higher organisms: microbe-mediated local adaptation and microbe-mediated adaptive plasticity. Microbe-mediated local adaptation is when local plant genotypes have higher fitness than foreign genotypes because of a genotype-specific affiliation with locally important microbes. Microbe-mediated adaptive plasticity occurs when local plant phenotypes have higher fitness than foreign phenotypes as a result of interactions with locally important microbes. These microbial effects on adaptation can be difficult to differentiate from traditional modes of adaptation but may be prevalent. Ignoring microbial effects may lead to erroneous conclusions about the traits and mechanisms underlying adaptation, hindering management decisions in conservation, restoration, and agriculture.

Background: The house dust mite (HDM) is the most common cause of allergic diseases, and TLR4 acts as an overarching receptor for allergic responses. This study aimed to identify novel allergen binding to TLR4 in HDMs and unveil its unique role in allergic responses. Methods: Der p 38 was purified and characterized by LC-MS/MS-based peptide mapping. Biolayer interferometry and structure modeling unveiled TLR4-binding activity and the structure of recombinant Der p 38. The allergenicity of Der p 38 was confirmed by a skin prick test, and basophil activation and dot blot assays. Results: The skin prick test identified 24 out of 45 allergic subjects (53.3%) as Der p 38-positive subjects. Der p 38-augmented CD203c expression was noted in the basophils of Der p 38-positive allergic subjects. In animal experiments, Der p 38 administration induced the infiltration of neutrophils as well as eosinophils and exhibited clinical features similar to asthma via TLR4 activation. Persistent Der p 38 administration induced severe neutrophil inflammation. Der p 38 enhanced cytokine production in human bronchial epithelial cells, which inhibited apoptosis in neutrophils and eosinophils. The mechanisms involved LYN, PI3K, AKT, ERK, and NF-κB. Conclusions: These findings showed that Der p 38 is a bridge allergen between eosinophilic and neutrophilic inflammation, and contribute to understanding the TLR4-mediated complex pathogenesis of allergic diseases.

Chinese flowering cabbage (Brassica rapa var. parachinensis) is a popular and widely cultivated leaf vegetable crop in Asia. Here, we performed a high quality de novo assembly of the 384 Mb genome of 10 chromosomes of a typical cultivar of Chinese flowering cabbage with an integrated approach using PacBio, Illumina, and Hi-C technology. We modeled 47,598 protein-coding genes in this analysis and annotated 52% (205.9/384) of its genome as repetitive sequences including 17% in DNA elements and 22% in long terminal retrotransposons (LTRs). Phylogenetic analysis reveals the genome of the Chinese flowering cabbage has a closer evolutionary relationship with the AA diploid progenitor of the allotetraploid species, Brassica juncea. Comparative genomic analysis of Brassica species with different subgenome types (A, B and C) reveals that the pericentromeric regions on chromosome 5 and 6 of the AA genome have been significantly expanded compared to the orthologous genomic regions in the BB and CC genomes, largely drive by LTR-retrotransposon amplification. This lineage-specific expansion may play a role in the species divergence in the Brassica genus. Furthermore, we found that a large amount of structural variations (SVs) identified within B. rapa lines that could impact coding genes, suggesting the functional significance of SVs on Brassica genome evolution. Overall, our high-quality genome assembly of the Chinese flowering cabbage provides a valuable genetic resource for deciphering the genome evolution of Brassica species and it can potentially serve as the reference genome guiding the molecular breeding practice of B. rapa crops.

A decade ago, de novo transcriptome assembly evolved as a versatile and powerful approach to make evolutionary assumptions, analyze gene expression, and annotate novel transcripts, in particular, for non-model organisms lacking an appropriate reference genome. Various tools have been developed to generate a transcriptome assembly, and even more computational methods depend on the results of these tools for further downstream analyses. In this issue of Molecular Ecology Resources, Freedman et al. (2020) present a comprehensive analysis of errors in de novo transcriptome assemblies across public data sets and different assembly methods. They focus on two implicit assumptions that are often violated: First, the assembly presents an unbiased view of the transcriptome. Second, the expression estimates derived from the assembly are reasonable, albeit noisy, approximations of the relative frequency of expressed transcripts. They show that appropriate filtering can reduce this bias but can also lead to the loss of a reasonable number of highly expressed transcripts. Thus, to partly alleviate the noise in expression estimates, they propose a new normalization method called length-rescaled CPM. Remarkably, the authors found considerable distortions at the nucleotide level, which leads to an underestimation of diversity in transcriptome assemblies. The study by Freedman et al. clearly shows that we have not yet reached “high-quality” in the field of transcriptome assembly. Above all, it helps researchers be aware of these problems and filter and interpret their transcriptome assembly data appropriately and with caution.

Pan-allergens can contribute to severity and perpetuation of allergic diseases, as a result of leading to IgE-medicated poly-sensitization and cross-reactivity to human self-antigens. Cyclophilins are well-known pan-allergens of various groups of cross-reactive allergens. CyPs have been identified with five classic CyP isoforms (CyPA, B, C, D and E). In the present study, the physicochemical and immunologic characteristics of CyPs were predict by bioinformatics and immunoinformatics approaches. The results indicated that CyPA family possesses multiple identified allergens. CyPE showed closer evolutionary relationship and high sequence identity with allergenic CyPA and the structure and antigenicity of CyPE were conserved significantly compared with allergenic CyPA. To verify results of In silico analysis，CyPE from HMD were successfully constructed and purified. ELISA resuls indicated that 2/14 patient serum had positive reactions to CyPE. CyPE is low antigenicity but sufficient to induced significant airway inflammation in mouse models and IgE, IgG1, eosinophil infiltration, IL-4 and co-stimulatory molecules of CyPE were markedly lower levels than Der f 29. Structure and immunoinformatics analysis demonstrated that RNA-binding motif of CyPE may reduce the immunogenicity of CyPE and structure variation of B-cell epitopes is the reason why CyPB is no IgE activity. This work is of significance in the diagnosis and treatment of allergy.

In addition to known allergens, other proteins in pollen can aid the development of an immune response in allergic individuals. The contribution of the “unknown” protein allergens is apparent in phylogenetically related species where, despite of high homology of the lead allergens, the degree of allergenic potential can vary greatly. The aim of this study was to identify other potentially allergenic proteins in pollen of three common and highly related allergenic tree species: birch (Betula pendula), hazel (Corylus avellana) and alder (Alnus glutinosa). For that purpose, we carried out a comprehensive, comparative proteomic screening of the pollen from the three species. In order to maximize protein recovery and coverage, different protein extraction and isolation strategies during sample preparation were employed. As a result, we report 2500 - 3000 identified proteins per each of the pollen species. Identified proteins were further used for a number of annotation steps, providing insight into differential distribution of peptidases, peptidase inhibitors and other potential allergenic proteins across the three species. Moreover, we carried out functional enrichment analyses that, interestingly, corroborated high species similarity in spite of their relatively distinct protein profiles. We provide to our knowledge first insight into proteomes of two very important allergenic pollen types, hazel and alder, where not even transcriptomics data is available, and compared them to birch. Datasets from this study can be readily used as protein databases, and as such serve as basis for further functional studies.

Automatic pollen image identification using neural networks increases accuracy for hay fever forecasts

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The time-dependent density functional theory (TD-DFT) was used to calculate the vibronic absorption spectrum of berberine (BER) in an aqueous solution. The best agreement with the experimental spectrum gives the O3LYP functional. Functionals with long-range correction showed poor agreement with experiment. The molecular orbitals of BER involved in the electronic transition during light absorption in the visible spectral region have been obtained. The dipole moments and atomic charges of the ground and excited states of the BER molecule have been calculated. Maps of BER electron density and electrostatic potential have been drawn. A significant photoinduced electron transfer from the outer di-oxygen five-membered heterocycle to the center of the BER chromophore has been found. According to our calculations, vibronic coupling and Boltzmann distribution play a significant role in the absorption spectrum of BER.