Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives.

Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom® Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom® Citrus Genotyping Arrays for Citrus and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of Citrus and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both Citrus and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, "PolyHighResolution" (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available.

One-year pulmonary impairment after severe COVID-19: a prospective, multicenter follow-up study.

BACKGROUND: Long-term pulmonary sequelae following hospitalization for SARS-CoV-2 pneumonia is largely unclear. The aim of this study was to identify and characterise pulmonary sequelae caused by SARS-CoV-2 pneumonia at 12-month from discharge. METHODS: In this multicentre, prospective, observational study, patients hospitalised for SARS-CoV-2 pneumonia and without prior diagnosis of structural lung diseases were stratified by maximum ventilatory support ("oxygen only", "continuous positive airway pressure (CPAP)" and "invasive mechanical ventilation (IMV)") and followed up at 12 months from discharge. Pulmonary function tests and diffusion capacity for carbon monoxide (DLCO), 6 min walking test, high resolution CT (HRCT) scan, and modified Medical Research Council (mMRC) dyspnea scale were collected. RESULTS: Out of 287 patients hospitalized with SARS-CoV-2 pneumonia and followed up at 1 year, DLCO impairment, mainly of mild entity and improved with respect to the 6-month follow-up, was observed more frequently in the "oxygen only" and "IMV" group (53% and 49% of patients, respectively), compared to 29% in the "CPAP" group. Abnormalities at chest HRCT were found in 46%, 65% and 80% of cases in the "oxygen only", "CPAP" and "IMV" group, respectively. Non-fibrotic interstitial lung abnormalities, in particular reticulations and ground-glass attenuation, were the main finding, while honeycombing was found only in 1% of cases. Older patients and those requiring IMV were at higher risk of developing radiological pulmonary sequelae. Dyspnea evaluated through mMRC scale was reported by 35% of patients with no differences between groups, compared to 29% at 6-month follow-up. CONCLUSION: DLCO alteration and non-fibrotic interstitial lung abnormalities are common after 1 year from hospitalization due to SARS-CoV-2 pneumonia, particularly in older patients requiring higher ventilatory support. Studies with longer follow-ups are needed.

The hidden interplay between sex and COVID-19 mortality: the role of cardiovascular calcification.

Recent clinical and demographical studies on COVID-19 patients have demonstrated that men experience worse outcomes than women. However, in most cases, the data were not stratified according to gender, limiting the understanding of the real impact of gender on outcomes. This study aimed to evaluate the disaggregated in-hospital outcomes and explore the possible interactions between gender and cardiovascular calcifications. Data was derived from the sCORE-COVID-19 registry, an Italian multicentre registry that enrolled COVID-19 patients who had undergone a chest computer tomography scan on admission. A total of 1683 hospitalized patients (mean age 67±14 years) were included. Men had a higher prevalence of cardiovascular comorbidities, a higher pneumonia extension, more coronary calcifications (63% vs.50.9%, p<0.001), and a higher coronary calcium score (391±847 vs. 171±479 mm3, p<0.001). Men experienced a significantly higher mortality rate (24.4% vs. 17%, p=0.001), but the death event tended to occur earlier in women (15±7 vs. 8±7 days, p= 0.07). Non-survivors had a higher coronary, thoracic aorta, and aortic valve calcium score. Female sex, a known independent predictor of a favorable outcome in SARS-CoV2 infection, was not protective in women with a coronary calcification volume greater than 100 mm3. There were significant differences in cardiovascular comorbidities and vascular calcifications between men and women with SARS-CoV2 pneumonia. The differences in outcomes can be at least partially explained by the different cardiovascular profiles. However, women with poor outcomes had the same coronary calcific burden as men. The presumed favorable female sex bias in COVID-19 must therefore be reviewed in the context of comorbidities, especially cardiovascular ones.

COVID-19: high-resolution computed tomography findings in the first 64 patients admitted to the Hospital of Cremona, the epicentre of the pandemic in Europe.

PURPOSE: In December 2019, a new coronavirus (SARS-CoV-2) was identified as being responsible for the pulmonary infection called COVID-19. On 21 February 2020, the first autochthonous case of COVID-19 was detected in Italy. Our goal is to report the most common chest computed tomography (CT) findings identified in 64 patients, in the initial phase of COVID-19. METHODS: Sixty-four chest high-resolution computed tomography (HRCT) examinations performed at the Radiology Unit of the Hospital of Cremona, from 22 to 29 February 2020, of 64 patients during first week of hospitalization for COVID-19 were retrospectively evaluated. All cases were confirmed by real-time RT-PCR for SARS-CoV-2. Image analysis was independently conducted by 2 radiologists with 10 years and 1 year of experience in chest imaging. The inter-observer agreement was obtained by applying a Cohen's κ test. RESULTS: The average age of patients was 67.1 years (± 12.2); men 42 (66%). HRCT was performed on the 5th (± 1.5) day of hospitalization. More frequently, the initial CT changes of the lung show more or less extensive areas of ground-glass, as single pattern or with parenchymal consolidations. Coronavirus lung involvement appears very frequently multi-lobar, bilateral, and it concerns both subpleural and central regions. An excellent agreement (κ: 0.88-1, CI: 0.79-1.01, p < 0.05) concerning CT findings between the 2 operators was reached. CONCLUSIONS: Our data suggest that detection of the most frequent pulmonary CT-scan changes, in the early stages of COVID-19, can be performed, with excellent agreement, among readers with different experience, and consequently attribute their exact diagnostic value, in an appropriate clinical and environmental exposure setting.

Incidence and characterization of acute pulmonary embolism in patients with SARS-CoV-2 pneumonia: A multicenter Italian experience.

BACKGROUND AND AIMS: Several studies reported a high incidence of pulmonary embolism (PE) among patients with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, but detailed data about clinical characteristics, risk factors of these patients and prognostic role of PE are still lacking. We aim to evaluate the occurrence of pulmonary embolism among patients with SARS-CoV-2 infection, and to describe their risk factors, clinical characteristics, and in-hospital clinical outcomes. METHODS: This is a multicenter Italian study including 333 consecutive SARS-CoV-2 patients admitted to seven hospitals from February 22 to May 15, 2020. All the patients underwent computed tomography pulmonary angiography (CTPA) for PE detection. In particular, CTPA was performed in case of inadequate response to high-flow oxygen therapy (Fi02≥0.4 to maintain Sp02≥92%), elevated D-dimer (>0.5µg/mL), or echocardiographic signs of right ventricular dysfunction. Clinical, laboratory and radiological data were also analyzed. RESULTS: Among 333 patients with laboratory confirmed SARS-CoV-2 pneumonia and undergoing CTPA, PE was detected in 109 (33%) cases. At CTPA, subsegmental, segmental, lobar and central thrombi were detected in 31 (29%), 50 (46%), 20 (18%) and 8 (7%) cases, respectively. In-hospital death occurred in 29 (27%) patients in the PE-group and in 47 (21%) patients in the non-PE group (p = 0.25). Patients in PE-group had a low rate of traditional risk factors and deep vein thrombosis was detected in 29% of patients undergoing compression ultrasonography. In 71% of cases with documented PE, the thrombotic lesions were located in the correspondence of parenchymal consolidation areas. CONCLUSIONS: Despite a low rate of risk factors for venous thromboembolism, PE is present in about 1 out 3 patients with SARS-CoV-2 pneumonia undergoing CTPA for inadequate response to oxygen therapy, elevated D-dimer level, or echocardiographic signs of right ventricular dysfunction. In most of the cases, the thromboses were located distally in the pulmonary tree and were mainly confined within pneumonia areas.

Chest CT-derived pulmonary artery enlargement at the admission predicts overall survival in COVID-19 patients: insight from 1461 consecutive patients in Italy.

OBJECTIVES: Enlarged main pulmonary artery diameter (MPAD) resulted to be associated with pulmonary hypertension and mortality in a non-COVID-19 setting. The aim was to investigate and validate the association between MPAD enlargement and overall survival in COVID-19 patients. METHODS: This is a cohort study on 1469 consecutive COVID-19 patients submitted to chest CT within 72 h from admission in seven tertiary level hospitals in Northern Italy, between March 1 and April 20, 2020. Derivation cohort (n = 761) included patients from the first three participating hospitals; validation cohort (n = 633) included patients from the remaining hospitals. CT images were centrally analyzed in a core-lab blinded to clinical data. The prognostic value of MPAD on overall survival was evaluated at adjusted and multivariable Cox's regression analysis on the derivation cohort. The final multivariable model was tested on the validation cohort. RESULTS: In the derivation cohort, the median age was 69 (IQR, 58-77) years and 537 (70.6%) were males. In the validation cohort, the median age was 69 (IQR, 59-77) years with 421 (66.5%) males. Enlarged MPAD (≥ 31 mm) was a predictor of mortality at adjusted (hazard ratio, HR [95%CI]: 1.741 [1.253-2.418], p < 0.001) and multivariable regression analysis (HR [95%CI]: 1.592 [1.154-2.196], p = 0.005), together with male gender, old age, high creatinine, low well-aerated lung volume, and high pneumonia extension (c-index [95%CI] = 0.826 [0.796-0.851]). Model discrimination was confirmed on the validation cohort (c-index [95%CI] = 0.789 [0.758-0.823]), also using CT measurements from a second reader (c-index [95%CI] = 0.790 [0.753;0.825]). CONCLUSION: Enlarged MPAD (≥ 31 mm) at admitting chest CT is an independent predictor of mortality in COVID-19. KEY POINTS: • Enlargement of main pulmonary artery diameter at chest CT performed within 72 h from the admission was associated with a higher rate of in-hospital mortality in COVID-19 patients. • Enlargement of main pulmonary artery diameter (≥ 31 mm) was an independent predictor of death in COVID-19 patients at adjusted and multivariable regression analysis. • The combined evaluation of clinical findings, lung CT features, and main pulmonary artery diameter may be useful for risk stratification in COVID-19 patients.

Spontaneous pneumomediastinum in COVID-19 pneumonia.

Spontaneous pneumomediastinum is a benign entity but can worsen the underlying condition with which it is associated. We evaluated the incidence and the clinical relevance of spontaneous pneumomediastinum in a consecutive series of 102 patients with COVID-19 pneumonia. Six cases of pneumomediastinum were identified by high-resolution chest CT-scan. Three patients required early intubation, and one of them died, while in in the remaining subjects the clinical course was benign. The presence of pneumomediastinum required some changes in the management of mechanical ventilation. In conclusion, spontaneous pneumomediastinum is a possible complication of severe COVID-19 pneumonia that can affect patient management and clinical outcomes.

Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes.

Compared with genomic data of individual markers, haplotype data provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational and experimental phasing methods have been developed for analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility of this valuable genetic resource. Gamete cells, the natural packaging of haploid complements, are ideal materials for phasing entire chromosomes because the majority of the haplotypic allele combinations has been preserved. Therefore, compared with the current diploid-based phasing methods, using haploid genomic data of single gametes may substantially reduce the complexity in inferring the donor's chromosomal haplotypes. In this study, we developed the first easy-to-use R package, Hapi, for inferring chromosome-length haplotypes of individual diploid genomes with only a few gametes. Hapi outperformed other phasing methods when analyzing both simulated and real single gamete cell sequencing data sets. The results also suggested that chromosome-scale haplotypes may be inferred by using as few as three gametes, which has pushed the boundary to its possible limit. The single gamete cell sequencing technology allied with the cost-effective Hapi method will make large-scale haplotype-based genetic studies feasible and affordable, promoting the use of haplotype data in a wide range of research.

Congenital absence of pericardium: two cases and a comprehensive review of the literature.

Congenital absence of pericardium (CAP) is a rare condition, generally asymptomatic or paucisymptomatic, nevertheless sporadic cases complicated by sudden death are described. CAP can be diagnosed by CT and MRI. It is classified as total or partial, and partial defects are divided into left defects and right defects. Interestingly, several articles highlight the correlation between CAP and some anatomical lung abnormalities, such as presence of lung parenchyma between the main pulmonary artery and ascending aorta, lung parenchyma between the base of the heart and left hemidiaphragm, and lung parenchyma between the proximal ascending aorta and right pulmonary artery.

Monophasic Synovial Sarcoma of Prostatic Fascia: Case Report and Literature Review.

Synovial sarcoma (SS) primarily occurs in the para-articular soft tissue of the lower extremities in young adults and it is extremely rare in the prostatic region. We report a case of a 46-year-old man who presented with urinary retention. Pelvic ultrasound (US) examination, computed tomography (CT), and magnetic resonance imaging (MRI) demonstrated an 8.5 cm mass that appeared to originate in the prostatic fascia of the right lobe. Preoperative prostatic ultrasound transrectal needle biopsy revealed mesenchymal neoplastic tissue. Patient underwent surgery. The final pathologic findings were consistent with the diagnosis of monophasic synovial sarcoma.

When a thymic carcinoma "becomes" a GIST.

Thymic carcinoma (TC) is a rare intrathoracic malignancy that it can be invasive and refractory to conventional treatment. Comprehensive genomic analysis evidenced a molecularly distinct subset of thymic carcinoma with high prevalence of c-kit mutation, which may behave as a gastrointestinal stromal tumor (GIST). Here, we present a case report of TC with c-Kit mutation, who has relapsed after exposure to multiple lines of combination chemotherapy, but he has shown an impressive and long lasting response to sunitinib after imatinib failure.

Intra-observer and interobserver reliability of the 'Pico' computed tomography method for quantification of glenoid bone defect in anterior shoulder instability.

OBJECTIVE: To evaluate the intra-observer and interobserver reliability of the 'Pico' computed tomography (CT) method of quantifying glenoid bone defects in anterior glenohumeral instability. MATERIALS AND METHODS: Forty patients with unilateral anterior shoulder instability underwent CT scanning of both shoulders. Images were processed in multiplanar reconstruction (MPR) to provide an en face view of the glenoid. In accordance with the Pico method, a circle was drawn on the inferior part of the healthy glenoid and transferred to the injured glenoid. The surface of the missing part of the circle was measured, and the size of the glenoid bone defect was expressed as a percentage of the entire circle. Each measurement was performed three times by one observer and once by a second observer. Intra-observer and interobserver reliability were analyzed using intraclass correlation coefficients (ICCs), 95% confidence intervals (CIs), and standard errors of measurement (SEMs). RESULTS: Analysis of intra-observer reliability showed ICC values of 0.94 (95% CI = 0.89-0.96; SEM = 1.1%) for single measurement, and 0.98 (95% CI = 0.96-0.99; SEM = 1.0%) for average measurement. Analysis of interobserver reliability showed ICC values of 0.90 (95% CI = 0.82-0.95; SEM = 1.0%) for single measurement, and 0.95 (95% CI = 0.90-0.97; SEM = 1.0%) for average measurement. CONCLUSION: Measurement of glenoid bone defect in anterior shoulder instability can be assessed with the Pico method, based on en face images of the glenoid processed in MPR, with a very good intra-observer and interobserver reliability.

Prensagem uniaxial de cerâmica dental / Uniaxial pressing of dental ceramic

Foi desenvolvido um novo processamento de cerâmica dental, por meio de uma etapa de prensagem uniaxial, com objetivo de aumentar a tenacidade à fratura do material cerâmico, quando utilizado em prótese dental toda cerâmica, padronizar e simplificar as etapas de conformaçäo e condensaçäo no seu procedimento de execuçäo. Está apoiado no uso de um líquido aditivo ligante, substituindo a água do processo convencional. Foi comprovado um aumento significativo de tenacidade à fratura do produto cerâmico prensado, quando comparado com os produtos cerâmicos obtidos pelo processo convencional

Estudo de uma liga alternativa de prata-paládio para uso odontológico / Study of the alternative alloy of silver-paladium for dental purpose

Os autores elaboraram um estudo comparativo, entre uma liga de ouro convencional e uma seminobre alternativa de prata-paládio, com 7 por cento de ouro na sua composiçäo. Após todos os testes e critérios pré-estabelecidos, foi observado que no emprego desta liga alternativa, se comportou de modo seguro no que tange às suas propriedades físico-químicas e biológicas, quando no uso odontológico. Assim sendo, acreditamos que esta pesquisa tenha contribuído de maneira relevante para o conhecimento profundo de novos ensaios no campo integrado metalurgia-odontologia