Challenges in gene-oriented approaches for pangenome content discovery.

Given a group of genomes, represented as the sets of genes that belong to them, the discovery of the pangenomic content is based on the search of genetic homology among the genes for clustering them into families. Thus, pangenomic analyses investigate the membership of the families to the given genomes. This approach is referred to as the gene-oriented approach in contrast to other definitions of the problem that takes into account different genomic features. In the past years, several tools have been developed to discover and analyse pangenomic contents. Because of the hardness of the problem, each tool applies a different strategy for discovering the pangenomic content. This results in a differentiation of the performance of each tool that depends on the composition of the input genomes. This review reports the main analysis instruments provided by the current state of the art tools for the discovery of pangenomic contents. Moreover, unlike previous works, the presented study compares pangenomic tools from a methodological perspective, analysing the causes that lead a given methodology to outperform other tools. The analysis is performed by taking into account different bacterial populations, which are synthetically generated by changing evolutionary parameters. The benchmarks used to compare the pangenomic tools, in addition to the computational pipeline developed for this purpose, are available at https://github.com/InfOmics/pangenes-review. Contact: V. Bonnici, R. Giugno Supplementary information: Supplementary data are available at Briefings in Bioinformatics online.

CMR for myocardial iron overload quantification: calibration curve from the MIOT Network.

OBJECTIVES: R2* cardiac magnetic resonance (CMR) allows the non-invasive measurement of myocardial iron. We calibrated cardiac R2* values against myocardial tissue-measured iron concentration by using a segmental approach and we assessed the iron distribution. METHODS: Five hearts of thalassemia patients were donated after death/transplantation to the CoreLab of the Myocardial Iron Overload in Thalassemia Network. A multislice multiecho R2* approach was adopted. After CMR, used as guidance, the heart was cut in three short-axis slices and each slice was cut into different equiangular segments according to AHA segmentation and differentiated into endocardial and epicardial layers. Tissue iron concentration was measured by atomic absorption spectrometer technique. RESULTS: Fifty-five samples were used since only for two hearts all the 16 samples were analyzed. Mean iron concentration was 4.71 ± 4.67 mg/g dw. Segmental iron levels ranged from 0.24 to 13.78 mg/g dw. The coefficient of variability of iron for myocardial segments ranged from 8.08 to 24.54% (mean 13.49 ± 6.93%). Iron concentration was significantly higher in the epicardial than in the endocardial layer (5.99 ± 6.01 vs 4.84 ± 4.87 mg/g dw; p = 0.042). Four different circumferential regions (anterior, septal, inferior, and lateral) were defined. A circumferential heterogeneity was noted, with more iron in the anterior region, followed by the inferior region. The direct nonlinear fitting of R2* and [Fe] data led to the calibration curve: [Fe] = 0.0022 ∙ (R2*-ROI)1.462 (R-square = 0.956). CONCLUSIONS: Our data further validate R2* CMR using a segmental approach as a sensitive and early technique for quantifying iron distribution in the current clinical practice. KEY POINTS: • Calibration in humans for cardiovascular magnetic resonance R2* against myocardial iron concentration was provided. • A circumferential heterogeneity in cardiac iron distribution was detected: more iron was observed in the anterior region, followed by the inferior region. This finding corroborates the use of a segmental T2* CMR approach in the clinical practice to detect a heterogeneous iron distribution. • The comparison between the cardiac T2* values obtained with the region-based and the pixel-wise approaches showed a significant correlation and no significant difference but, in presence of significant iron load, the region-based approach resulted in significantly higher T2* values.

Can the TLR-4-mediated signaling pathway be "a key inflammatory promoter for sporadic TAA"?

Thoracic aorta shows with advancing age various changes and a progressive deterioration in structure and function. As a result, vascular remodeling (VR) and medial degeneration (MD) occur as pathological entities responsible principally for the sporadic TAA onset. Little is known about their genetic, molecular, and cellular mechanisms. Recent evidence is proposing the strong role of a chronic immune/inflammatory process in their evocation and progression. Thus, we evaluated the potential role of Toll like receptor- (TLR-) 4-mediated signaling pathway and its polymorphisms in sporadic TAA. Genetic, immunohistochemical, and biochemical analyses were assessed. Interestingly, the rs4986790 TLR4 polymorphism confers a higher susceptibility for sporadic TAA (OR = 14.4, P = 0.0008) and it represents, together with rs1799752 ACE, rs3918242 MMP-9, and rs2285053 MMP-2 SNPs, an independent sporadic TAA risk factor. In consistency with these data, a significant association was observed between their combined risk genotype and sporadic TAA. Cases bearing this risk genotype showed higher systemic inflammatory mediator levels, significant inflammatory/immune infiltrate, a typical MD phenotype, lower telomere length, and positive correlations with histopatological abnormalities, hypertension, smoking, and ageing. Thus, TLR4 pathway should seem to have a key role in sporadic TAA. It might represent a potential useful tool for preventing and monitoring sporadic TAA and developing personalized treatments.

Delayed Traumatic Rupture of the Spleen in a Patient with Mantle Cell Non-Hodgkin Lymphoma after an In-Hospital Fall: A Fatal Case.

Splenic rupture and hematoma are significant complications that can occur in patients with non-Hodgkin lymphoma (NHL). Understanding these associated complications is essential for optimal patient management and enhanced patient outcomes. Histopathological and immunohistochemical analyses are crucial in diagnosing NHL and assessing splenic involvement. In this study, a judicial autopsy had been requested by the Prosecutor's Office for a malpractice claim due to a fall in the hospital. In the Emergency Department, a 72-year-old man fell from a gurney and reported sustaining a wound to his forehead. No other symptoms were reported. A face and brain CT scan showed no abnormalities. Nine days after discharge, the patient presented with abdominal pain. An abdominal CT revealed splenic rupture and hemoperitoneum. The patient underwent open splenectomy but showed signs of hemodynamic shock and subsequently died. The evidence from the autopsy allowed us to diagnose mantle cell non-Hodgkin lymphoma with spleen involvement, previously unknown. Histopathological and immunohistochemical analyses were performed to assess the diagnosis of splenic rupture and estimate its timing. The findings strongly suggest that the splenic rupture was associated with the patient's fall and the pre-existing malignancy. This case highlights the importance of considering an underlying hematological malignancy when investigating delayed splenic rupture. An immunohistochemical study of spleen samples allowed the timing of splenic hematoma and rupture to be assessed, leading to the establishment of a causal relationship with trauma.

Oligo-antigenic diet in the treatment of chronic anal fissures. Evidence for a relationship between food hypersensitivity and anal fissures.

OBJECTIVES: Patients with chronic constipation due to food hypersensitivity (FH) had an elevated anal sphincter resting pressure. No studies have investigated a possible role of FH in anal fissures (AFs). We aimed to evaluate (1) the effectiveness of diet in curing AFs and to evaluate (2) the clinical effects of a double-blind placebo-controlled (DBPC) challenge, using cow's milk protein or wheat. METHODS: One hundred and sixty-one patients with AFs were randomized to receive a "true-elimination diet" or a "sham-elimination diet" for 8 weeks; both groups also received topical nifedipine and lidocaine. Sixty patients who were cured with the "true-elimination diet" underwent DBPC challenge in which cow's milk and wheat were used. RESULTS: At the end of the study, 69% of the "true-diet group" and 45% of the "sham-diet group" showed complete healing of AFs (P<0.0002). Thirteen of the 60 patients had AF recurrence during the 2-week cow's milk DBPC challenge and 7 patients had AF recurrence on wheat challenge. At the end of the challenge, anal sphincter resting pressure significantly increased in the patients who showed AF reappearance (P<0.0001), compared with the baseline values. The patients who reacted to the challenges had a significantly higher number of eosinophils in the lamina propria and intraepithelial lymphocytes than those who did not react to the challenges. CONCLUSIONS: An oligo-antigenic diet combined with medical treatment improved the rate of chronic AF healing. In more than 20% of the patients receiving medical and dietary treatment, AFs recurred on DBPC food challenge.

Juvenile sudden cardiac death due to congenital coronary ostial valve-like ridges: A case report and literature review.

Coronary artery anomalies are a heterogeneous group of congenital disorders affecting the coronary pattern with a characteristic (origin, number, number of hosts, course, etc.). They are rarely found in the population. We report the case of a 21-year-old male who died from sudden cardiac death caused by an isolated coronary ostial obstruction, secondary to a rare anomaly, the presence of a valve-like ridge consisting of a small fold in the Valsalva aortic sinus. The study provides a brief literature review on the pathophysiology, diagnosis, and clinical and medico-legal issues in coronary artery anomaly cases that may be helpful in forensic practice when dealing with sudden cardiac death in young people and highlights key points for further research and public health measures.

Useless and limits of Postmortem CT (PMCT) in a complex case of preterm infant murder.

The present case-report empathizes the usefulness of post-mortem computed tomography (PMCT) in the detection of live birth signs in a baby found dead, comparing the results with standard autoptic, histologic and immunohistochemical examinations. The report describes the case of a new-born who was thrown out on the footpath from a window of the fifth floor according to the investigative police, whilst the mother has hidden herself immediately after childbirth. PMCT showed diffusely aerated lung parenchyma with signs of severe lung distress, air in the airways with no fluid inside, and air in the upper gastro-intestinal tract, in absence any resuscitation manoeuvres performed on the baby at delivery. PMCT underlined multiple fractures of the skull with degeneration of cerebral parenchyma. All these findings were confirmed by conventional autopsy and histological and immunohistochemical examinations, clinching the usefulness of PMCT in differentiating live births from stillbirths.

Cardiovascular Implantable Electronic Device Infection and New Insights About Correlation Between Pro-inflammatory Markers and Heart Failure: A Systematic Literature Review and Meta-Analysis.

Introduction: Surgical approaches to treat patients with abnormal pro-inflammatory parameters remain controversial, and the debate on the correlation between hematological parameter alteration in cardiac implantable electronic device (CIED) infection and the increase in mortality continues. Methods: We performed a systematic review using the PubMed, Scopus, and Cochrane Library databases. Twenty-two articles from May 2007 to April 2020 were selected and divided according to the following topics: prevalence of microbes in patients with CIED infection; characteristics of patients with CIED infection; comparison between patients who underwent and did not undergo replantation after device extraction; and correlation between alteration of hematological parameters and poor prognosis analysis. Results: Epidemiological analysis confirmed high prevalence of male sex, staphylococcal infection, and coagulase-negative staphylococci (CoNS). The most common comorbidity was heart failure. Complete removal of CIED and antimicrobial therapy combination are the gold standard. CIED replacement was associated with higher survival. High preoperative white blood cell count and C-reactive protein levels increased the risk of right ventricular failure (RVF) development. Increased red blood cell distribution width (RDW) value or decreased platelet count was correlated with poor prognosis. No correlation was noted between preoperative leukocytosis and CIED infection. Discussion: A relevant correlation between leukocytosis and RVF was observed. Heart failure may be related to high RDW values and decreased platelet count. Data on the correlation between hematological parameter alteration and poor prognosis are missing in many studies because of delayed implantation in patients showing signs of infection.

Case Report: Unusual Clinical Presentation of a Rare Cardiac Inflammatory Myofibroblastic Tumor in Children: The Differential Diagnosis With Pediatric Emergencies.

Introduction: There are still no guidelines about pediatric cardiac cancers. The purpose of this work is to provide new scientific data facilitating the differential diagnosis of a rare cardiac tumor with an unusual presentation, such as the cardiac inflammatory myofibroblastic tumor (IMT). Case Presentation: A 3-year-old male child presented with several symptoms including unconsciousness, vomiting, and drowsiness. A clinical and neurological examination revealed a unilateral (right) motor delay and positive unilateral Babinski sign. Electrocardiogram (ECG) was normal. Diagnostic Assessment: The total body computed tomography (CT) scans showed hypodensity in the left temporal-parietal lobe, a large hypodense area in the right frontal lobe, and a second area in the left frontal lobe were found with head CT. A magnetic resonance (MR) also noted cerebral areas of hypointensity. The echocardiographic images revealed an ovoid mass, adherent to the anterolateral papillary muscle. The histological exams, performed with hematoxylin-eosin, Masson's trichrome, Alcian blue PAS, Weigert and Van-Gieson stain, allowed observing the microscopic structure of the neoplastic mass. The immunohistochemical analysis was performed through subsequent antibodies: anti-vimentin, anti-actina, anti-ALK, anti-CD8, anti-CD3, anti-CD20, anti-kappa and lambda chains, and anti CD68 antibodies. The healthcare professionals diagnosed a cardiac IMT with brain embolism. Differential Diagnosis: The ventricular localization, observed through radiological exams, required a differential diagnosis with fibroma and rhabdomyoma, the presence of brain embolism with sarcoma, and its morphology with fibroma. Neurological symptoms might be attributed to encephalitis, primitive cerebral cancer, such as astrocytoma or neuroblastoma, cerebral metastases due to any malignancy, or embolic stroke. Conclusion: New studies are encouraged to better define IMT behavior and draw up guidelines confirming the crucial role of multidisciplinary approach and treatment protocol selected on the basis of the characteristics of the tumors, in the case of this rare type of cancer.

Bifocal manifestation of eosinophilic granuloma in a pediatric patient.

BACKGROUND: Eosinophilic granuloma (EG) is a clinical variant of the Langerhans cell histiocytosis (LCH) characterized by unifocal or multifocal bone lesions which predominantly affects children, adolescents, and young adults. CASE REPORT: A case is reported of a 13-year-old Caucasian boy who presented unifocal EG in the mandible as the first clinic manifestation. Radiographic examination and skeletal scintigraphy revealed a further localization with an osteolytic lesion in the right femur. The therapeutic protocol used for the mandibular lesion included causal periodontal therapy, extraction of the compromised teeth, alveolar curettage, and intralesional injections of corticosteroids, in correspondence with femoral and mandibular bone lesions. CONCLUSIONS: Early diagnosis of LCH is considered an important factor which can improve the patient's prognosis and quality of life and also the cost-effectiveness of therapy. Dentists could play a fundamental role in the diagnosis and management of EG. The aim of the treatment is to eradicate EG lesions and provide adequate oral rehabilitation after the tooth loss. A careful multidisciplinary follow-up program is mandatory to identify any signs of local recurrence or dissemination.

Angiogenesis of oral lichen planus: a possible pathogenetic mechanism.

OBJECTIVE: Oral Lichen Planus (OLP) is a chronic inflammatory disease with an autoimmune inflammatory pathogenesis. The aim of the research is to compare the vascular endothelial growth factor (VEGF) and adhesion of molecules in the biopsy samples of patients affected by OLP, in order to research the presence of the angiogenetic phenomenon and to understand its pathogenetic mechanism. MATERIALS AND METHODS: Thirty OLP patients and thirty healthy subjects were enrolled in a study. The immunohistochemical analysis of the VEGF and vascular-endothelial adhesion molecules was carried out by means of primary antibodies and anti-CD34, anti-VEGF, anti-CD106 antigen (VCAM-1) and anti-CD54 antigen (ICAM-1). The statistical significance of the differences was checked with the Mann-Whitney test (MW test). The level of significance was set to P<0.001. Data analysis was carried out with StatView 5.0.1 (SAS Institute Inc., Cary, NC). RESULTS: The results reveal the presence of a significant angiogenesis in OLP patients for the VEGF, CD34, CD106 and CD54 (P < 0.001).. The number of vessels in the biopsies of the patients with OLP (mean +/-SD: 21.27+/-4.85), compared with the healthy subjects (mean +/-SD: 4.74+/-0.97) was significantly more (Mann-Whitney test, P < 0.001). The positive expression rate of VEGF, CD34, VCAM-1 and ICAM-1 in oral lichen samples was 64.2%, 54.3%, 32.5% and 29.7%, respectively. Isolated endothelial cells and newly-formed micro-vessels and endothelial cells with high-immune-positivity to the antibodies anti-ICAM-1 and anti-VCAM-1 were observed. CONCLUSIONS: The results of our immunohistochemical research show that a significant neoangiogenesis occurs in oral lichen planus.

Sex reversal from functional disomy of Xp: prenatal and post-mortem findings.

Translocations involving the short arms of the X and Y chromosomes are uncommon and are often associated with anomalies in gonadal development. Segmental duplications of the X chromosome interfere with the formation of the testis in patients with a 46,XY karyotype. The gene products located within the duplicated segment, when present in double dose, may affect on male sex development. We report on a fetus with karyotype 46,XY,der (14)t(X;14) (p10;p10)dn. Attached to chromosome 14 is the entire short arm of the X chromosome. Therefore, the fetus is affected with a disomy of Xp, resulting in complete male to female sex reversal, as well as other structural defects. To the best of our knowledge, this is the first description of an XY fetus with a pure duplication of the entire short arm of X chromosome.

Early structural degeneration of Mitroflow aortic valve: another issue in addition to the mismatch?

We reported two cases of early structural valve degeneration (SVD) with Mitroflow prosthesis in aortic position in patients above the age of 65 years. Microscopic aspects have been analysed to investigate the intrinsic mechanism of SVD. New techniques to improve the structure and the preservation of this prosthesis are needed in order to reduce potential dangerous early complications.

Hemangiopericytoma of the oral cavity after a ten-year follow-up.

Hemangiopericytoma (HPC) is a mesenchymal tumour that may be benign, malignant, or occur in an intermediate form. We report an unusual case of hemangiopericytoma located in the buccal mucosal region. The histopathologic features showed increased cellularity, necrosis, hemorrhage, low proliferation index, and 4 or less mitotic figures per 10 high-power fields. Since this histological pattern suggests an intermediate form characterized by unpredictable clinical behavior, life-long follow-up is essential. In this patient no recurrences or distant metastases were evident at 10-yr follow-up.

Diagnostic evaluation of serial sections of labial salivary gland biopsies in Sjögren's syndrome.

OBJECTIVES: Sjögren's syndrome is a chronic inflammatory disease. The detection of chronic inflammatory infiltrates containing >50 lymphocytes (lymphocytic focus) per 4 mm2 tissue in minor salivary gland biopsies is a diagnostic parameter of the disease. The aim of the study was to examine if an increase in the tissue area of a single minor labial salivary gland biopsy through serial histological sections in patients affected by primary Sjögren's syndrome could facilitate the detection of the diagnostic focus score (grades >1 or >2). METHODS: We observed 24 labial salivary gland biopsies from patients affected by primary Sjögren's syndrome, diagnosed according to the clinical-laboratory criteria proposed by the American-European Consensus Group. The analysis was carried out on sections (n= 72) obtained at three different levels at 200 micrometers from one another. The serial sections regarding the 3 levels were reviewed by the same oral pathologist, who detected both the total number of foci, and their surface, calculating a cumulative focus score. RESULTS: No significant correlation was found between the number of lobules per histological section and the focus score (Pearson correlation 0.363, p= 0.01). No significant variation in focus score distribution was identified in the three serial histological levels at 200 micrometers from one another. From the comparison between the number of lobules observed and the focus score grade, no direct proportionality between the amount of parenchyma analyzed and the focus score was found. CONCLUSIONS: The focus score remained unchanged in the serial sections at different depths.

Oral necrotizing microvasculitis in a patient affected by Kawasaki disease.

Kawasaki disease (KD) was first described in 1967 by Kawasaki, who defined it as "mucocutaneous lymph node syndrome". KD is an acute systemic vasculitis, which mainly involves medium calibre arteries; its origin is unknown, and it is observed in children under the age of 5, especially in their third year. The principal presentations of KD include fever, bilateral nonexudative conjunctivitis, erythema of the lips and oral mucosa, changes in the extremities, rash, and cervical lymphadenopathy. Within KD, oral mucositis - represented by diffuse mucous membrane erythema, lip and tongue reddening and lingual papillae hypertrophy with subsequent development of strawberry tongue - can occur both in the acute stage of the disease (0-9 days), and in the convalescence stage (>25 days) as a consequence of the pharmacological treatment. KD vascular lesions are defined as systemic vasculitis instead of systemic arteritis. This study analyzed the anatomical-pathological substrata of oral mucositis in a baby affected by Kawasaki disease and suddenly deceased for cardiac tamponade caused by coronary aneurysm rupture (sudden cardiac death of a mechanical type).

When a death apparently associated to sexual assault is instead a natural death due to idiopathic hypereosinophilic syndrome: The importance of gamma-hydroxybutyric acid analysis in vitreous humor.

We here report a case involving a 21-year-old female, found dead in a central square of a city in the south of Italy. Initial evidences and circumstances were suggestive of a death associated with a sexual assault. Two peripheral blood and two vitreous humor samples were collected for the purpose of gamma-hydroxybutyric acid (GHB) testing from the dead body at two different post-mortem intervals (PMIs): approximately 2 (t0) and 36 (t1) hours. The obtained results showed that, between t0 and t1, there was an increase of GHB concentrations in peripheral blood and vitreous humor of 66.3% and 8.1%, respectively. This case was the first evidence of GHB post mortem production in a dead body and not in vitro, showing that vitreous humor is less affected than peripheral blood in GHB post-mortem production. The value detected at t1 in peripheral blood (53.4µg/mL) exceeded the proposed cut-off and if interpreted alone would have led to erroneous conclusions. This was not the case of vitreous humor GHB, whose post-mortem increase was minimal and it allowed to exclude a GHB exposure. Only after a broad forensic investigation including a complete autopsy, serological, histological, toxicological and haematology analyses, a diagnosis of idiopathic hypereosinophilic syndrome, a myeloproliferative disorder characterized by persistent eosinophilia associated with damage to multiple organs, was made and the cause of death was due to a pulmonary eosinophilic vasculitis responsible for an acute respiratory failure.

Food intolerance and chronic constipation: manometry and histology study.

BACKGROUND: Chronic constipation in children can be caused by cows' milk intolerance (CMI), but its pathogenesis is unknown. AIMS: To evaluate the histology and manometry pattern in patients with food intolerance-related constipation. PATIENTS AND METHODS: Thirty-six consecutive children with chronic constipation were enrolled. All underwent an elimination diet and successive double-blind food challenge. All underwent rectal biopsy and anorectal manometry. RESULTS: A total of 14 patients were found to be suffering from CMI and three from multiple food intolerance. They had a normal stool frequency on elimination diet, whereas constipation recurred on food challenge. The patients with food intolerance showed a significantly higher frequency of erosions of the mucosa, and the number of intra-epithelial lymphocytes and eosinophils. The rectal mucous gel layer showed that the food-intolerant patients had a significantly lower thickness of mucus than the other subjects studied. Manometry showed a higher anal sphincter resting pressure and a lower critical volume in food intolerance patients than in the others suffering from constipation unrelated to food intolerance. Both histology and manometry abnormalities disappeared on the elimination diet. CONCLUSIONS: Food intolerance-related constipation is characterized by proctitis. Increased anal resting pressure and a reduced mucous gel layer can be considered to be contributory factors in the pathogenesis of constipation.

Transmural coronary inflammation triggers simultaneous multivessel rupture of unstable plaques.

The authors describe a case of sudden cardiac death caused by the simultaneous multivessel rupture of unstable atherosclerotic plaques, triggered by a transmural inflammatory process (coronaritis). Male subject, 44 years old, apparently in good health until 1 hour before death, when he complained of worsening dyspnea. At autopsy, it was found that the heart weighed 486 g. Evaluation of the coronary arteries revealed the presence of atherosclerotic plaques resulting in a lumen critical stenosis of the left anterior descending artery (LAD), right coronary artery (RCA) and left circumflex artery, and acute occlusive thrombosis of the LAD and RCA. Transverse sections of the ventricular mass highlighted the presence of eccentric hypertrophy of the left ventricle associated with myocardiosclerosis of the posterior interventricular septum and of the posterior wall of the left ventricle. Histology revealed the presence of a coagulative myocytolysis ascribable to the free walls of the left ventricle, and a focus of lymphocytic-active myocarditis. All coronary arteries were sites of intima fibroatheromatous plaques complicated by rupture and thrombosis within the RCA and LAD and by a transmural infiltrate consisting of macrophages and T-lymphocytes associated with consensual medionecrosis and perineuritis. In conclusion, the present case report confirms the hypothesis that inflammation plays a key role in the onset of acute coronary syndromes as it promotes the formation of an unstable plaque as well as its rupture.