genome assembly and annotation reveal diploid genetic traits and stress-induced gene expression patterns.

The green alga (formerly ) is a primary source of astaxanthin, a ketocarotenoid with high antioxidant activity and several industrial applications. Here, the highly repetitive genome was reconstructed by exploiting next-generation sequencing integrated with Hi-C scaffolding, obtaining a 151 Mb genome assembly in 32 scaffolds at a near-chromosome level with high continuity. Surprisingly, the distribution of the single-nucleotide-polymorphisms identified demonstrates a diploid configuration for the genome, further validated by Sanger sequencing of heterozygous regions.

Structural Refinement by Direct Mapping Reveals Assembly Inconsistencies near Hi-C Junctions.

High-throughput chromosome conformation capture (Hi-C) is widely used for scaffolding in de novo assembly because it produces highly contiguous genomes, but its indirect statistical approach can introduce connection errors. We employed optical mapping (Bionano Genomics) as an orthogonal scaffolding technology to assess the structural solidity of Hi-C reconstructed scaffolds. Optical maps were used to assess the correctness of five de novo genome assemblies based on long-read sequencing for contig generation and Hi-C for scaffolding.

Efficacy and Safety of Edoxaban in Cancer-Associated Venous Thromboembolism: A Real World Retrospective Study.

 Few data exist on the use of edoxaban in cancer-associated venous thromboembolism (VTE) outside of clinical trials. Aim of this study was to evaluate the characteristics and outcomes of these patients in a real world clinical setting.  We retrospectively analyzed the characteristics of patients with cancer-associated VTE who were prescribed edoxaban.

Post-Stroke Detection of Subclinical Paroxysmal Atrial Fibrillation in Patients With Embolic Stroke of Undetermined Source in the Real World Practice: The Empoli ESUS Atrial Fibrillation (E 2 AF) Study.

Background: Subclinical paroxysmal atrial fibrillation (AF) is one of the main occult causative mechanisms of embolic stroke of undetermined source (ESUS). Aim of this study was to identify AF predictors, and to develop a score to predict the probability of AF detection in ESUS.

Methods: We retrospectively analyzed ESUS patients undergoing 2-week external electrocardiographic monitoring.

'Nebbiolo' genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.).

Background: 'Nebbiolo' is a grapevine cultivar typical of north-western Italy, appreciated for producing high-quality red wines. Grapevine cultivars are characterized by possessing highly heterozygous genomes, including a great incidence of genomic rearrangements larger than 50 bp, so called structural variations (SVs). Even though abundant, SVs are an under-explored source of genetic variation mainly due to methodological limitations at their detection.

Does the character-based dimension of stories impact narrative processing? An event-related potentials (ERPs) study.

This event-related potentials (ERPs) study investigated online processes of integration of information relating to characters in narrative comprehension. The final sample included twenty-nine participants who read short third-person stories in which the plausibility of the characters' actions was manipulated. Stories were administered in three conditions: a character-based congruent condition including a target word that was consistent with the character's job; a character-based incongruent condition with a target word inconsistent with the character's job; a character-based neutral condition, narrating the action of a character presented by his/her proper name without information about his/her job.

ZNF521 Enhances MLL-AF9-Dependent Hematopoietic Stem Cell Transformation in Acute Myeloid Leukemias by Altering the Gene Expression Landscape.

Leukemias derived from the MLL-AF9 rearrangement rely on dysfunctional transcriptional networks. ZNF521, a transcription co-factor implicated in the control of hematopoiesis, has been proposed to sustain leukemic transformation in collaboration with other oncogenes. Here, we demonstrate that ZNF521 mRNA levels correlate with specific genetic aberrations: in particular, the highest expression is observed in AMLs bearing MLL rearrangements, while the lowest is detected in AMLs with FLT3-ITD, NPM1, or CEBPα double mutations.

Association Between Aldosterone and Parathyroid Hormone Levels in Patients With Adrenocortical Tumors.

Objective: Patients with primary aldosteronism (PA) can present with high PTH levels and negative calcium balance, with some studies speculating that aldosterone could directly stimulate PTH secretion. Either adrenalectomy or mineralocorticoid receptor blockers could reduce PTH levels in patients with PA. The aim of this study was to assess the relationship between aldosterone levels and parathyroid hormone (PTH)-vitamin D-calcium axis in a cohort of patients with PA, compared with patients with nonsecreting adrenocortical tumors in conditions of vitamin D sufficiency.

Disparities in Remote Learning Faced by First-Generation and Underrepresented Minority Students during COVID-19: Insights and Opportunities from a Remote Research Experience.

The COVID-19 pandemic forced an unprecedented shift to remote instruction across higher education, reducing access to critically important undergraduate research experience and potentially magnifying inequities faced by first-generation and underrepresented minority (URM) students in higher education. Through a novel course-based undergraduate research experience (CURE) at UCLA, delivered completely online, results of a unique, student-generated survey showed that the transition to remote learning was challenging for all students, increasing student workload, decreasing ability to focus on school, and limiting their ability to succeed. However, results showed significant disparities in remote learning that disproportionately impacted URM and first-generation students.

ACoRE: Accurate SARS-CoV-2 genome reconstruction for the characterization of intra-host and inter-host viral diversity in clinical samples and for the evaluation of re-infections.

Sequencing the SARS-CoV-2 genome from clinical samples can be challenging, especially in specimens with low viral titer. Here we report Accurate SARS-CoV-2 genome Reconstruction (ACoRE), an amplicon-based viral genome sequencing workflow for the complete and accurate reconstruction of SARS-CoV-2 sequences from clinical samples, including suboptimal ones that would usually be excluded even if unique and irreplaceable. The protocol was optimized to improve flexibility and the combination of technical replicates was established as the central strategy to achieve accurate analysis of low-titer/suboptimal samples.

Characterization of Lysinibacillus fusiformis strain S4C11: In vitro, in planta, and in silico analyses reveal a plant-beneficial microbe.

Despite sharing many of the traits that have allowed the genus Bacillus to gain recognition for its agricultural relevance, the genus Lysinibacillus is not as well-known and studied. The present study employs in vitro, in vivo, in planta, and in silico approaches to characterize Lysinibacillus fusiformis strain S4C11, isolated from the roots of an apple tree in northern Italy. The in vitro and in vivo assays demonstrated that strain S4C11 possesses an antifungal activity against different fungal pathogens, and is capable of interfering with the germination of Botrytis cinerea conidia, as well as of inhibiting its growth through the production of volatile organic molecules.

A Long-Read Sequencing Approach for Direct Haplotype Phasing in Clinical Settings.

The reconstruction of individual haplotypes can facilitate the interpretation of disease risks; however, high costs and technical challenges still hinder their assessment in clinical settings. Second-generation sequencing is the gold standard for variant discovery but, due to the production of short reads covering small genomic regions, allows only indirect haplotyping based on statistical methods. In contrast, third-generation methods such as the nanopore sequencing platform developed by Oxford Nanopore Technologies (ONT) generate long reads that can be used for direct haplotyping, with fewer drawbacks.

Effects of sacubitril valsartan on clinical and echocardiographic parameters of outpatients with heart failure and reduced ejection fraction.

Aim: Sacubitril valsartan (SV) has revolutionized disease history in patients with heart failure and reduced ejection fraction (HFrEF). Our study assessed SV impact on clinical and echocardiographic parameters in HFrEF outpatients previously treated with optimized therapy.

Methods: Forty-nine HFrEF outpatients were retrospectively included in the study.

Zoledronic acid inhibits the growth of leukemic MLL-AF9 transformed hematopoietic cells.

A leukemic model produced by transducing Cord Blood derived-hematopoietic CD34 cells with the MLL-AF9 translocation resulting in the oncogenic fusion protein, is used to assess for sensitivity to Zoledronic acid. These cells are practically immortalized and are of myeloid origin. Proliferation, clonogenic and stromal co-culture assays showed that the MLL-AF9 cells were considerably more sensitive to Zoledronic acid than normal hematopoietic CD34 cells or MS-5 stromal cells.

Prevalence and Incidence of Atrial Fibrillation in a Large Cohort of Adrenal Incidentalomas: A Long-Term Study.

Context: Chronic glucocorticoids excess leads to morphological and functional cardiac alterations, a substrate for arrhythmias. Autonomous cortisol secretion (ACS) in adrenal incidentalomas is a model of chronic endogenous hypercortisolism.

Objective: To investigate prevalence and incidence of atrial fibrillation (AF) in a large cohort of patients with ACS.

Prognostic determinants in patients with non traumatic intracerebral hemorrhage: a real life report.

: Nontraumatic intracerebral hemorrhage (ICH) remains a devastating disease for high in-hospital and long-term mortality and residual neurological disability. The aim of our study was to analyze the prognostic factors in patients managed for ICH in the real-life clinical practice.: We retrospectively analyzed clinical and neuro-radiological data of consecutive patients admitted to our Hospital for ICH along 1 year.

Association Between Gait, Cognition, and Gray Matter Volumes in Mild Cognitive Impairment and Healthy Controls.

Aims: To assess the correlation between cognitive functioning and 3 gait parameters (gait speed, cadence, and stride length) in persons with mild cognitive impairment (MCI) and cognitively healthy controls and investigate linear correlations between gait and gray matter volumes.

Materials And Methods: Participants were recruited at IRCCS San Camillo Hospital, Venice, Italy (MCI=43; age-matched controls=43). Participants underwent comprehensive neuropsychological assessment.

Beneficial Effects of Listening to Classical Music in Patients With Heart Failure: A Randomized Controlled Trial.

Background: Practical recommendations on nonpharmacologic non-device/surgical interventions in patients with heart failure (HF) are well known. Although complementary treatments may have beneficial effects, there is no evidence that these on their own improve mortality, morbidity, or quality of life. We examined the effects of listening to recorded classical music on HF-specific quality of life (QOL), generic QOL, sleep quality, anxiety, depression, and cognitive state in patients with HF in the home-care setting.

Communicative and swallowing disorders in anoxic patients: A retrospective study on clinical outcomes and performance measures.

Background: Anoxic brain injury (ABI) is a neurological condition associated to a severe deterioration of brain functioning, whose symptomatology and clinical outcomes may be heterogeneous: cognitive deficits, language disorders like dysarthria and swallowing impairments. Nevertheless, there is still a lack of information on the rehabilitation outcomes.

Objective: To confirm the occurrence of communication and swallowing deficits in 37 ABI patients and to examine whether intensive rehabilitation may contribute to any improvements and its relation to ABI severity and functional autonomy.