A Novel Affordable and Reliable Framework for Accurate Detection and Comprehensive Analysis of Somatic Mutations in Cancer.

Accurate detection and analysis of somatic variants in cancer involve multiple third-party tools with complex dependencies and configurations, leading to laborious, error-prone, and time-consuming data conversions. This approach lacks accuracy, reproducibility, and portability, limiting clinical application. was developed to address these issues as an end-to-end pipeline for detecting, classifying, and interpreting cancer mutations.

FELASA Working Group report: Capture and transport of live cephalopods - recommendations for scientific purposes.

On 1 January 2013, research using cephalopod molluscs, from hatchlings to adults, became regulated within Directive 2010/63/EU. There are significant difficulties in captive breeding in the great majority of currently utilised species. Thus, scientific research relies upon the use of wild-caught animals.

Management of patients with extensive locally advanced thyroid cancer: results of multimodal treatments.

Purpose: Surgery plays a key role in the treatment of thyroid cancer (TC) patients. Locally advanced cases, however, can require an extensive surgical approach with technical issues and a high risk of complications. In these cases, a multidisciplinary evaluation should be carried out to evaluate pros and cons.

Ultrasound features and risk stratification system in NIFT-P and other follicular-patterned thyroid tumors.

Objective: Noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFT-P) is an encapsulated follicular variant of papillary thyroid carcinoma (PTC) with nonaggressive clinical behavior. However, since its diagnosis is exclusively possible after surgery, it represents a clinical challenge. Neck ultrasound (US) shows good sensitivity and specificity in suggesting malignancy in thyroid nodules.

"Hey Alexa, what do you know about the COVID-19 vaccine?"- (Mis)perceptions of mass immunization and voice assistants.

In this paper, we analyzed the perceived accuracy of COVID-19 vaccine information spoken back by Amazon Alexa. Unlike social media, Amazon Alexa does not apply soft moderation to unverified content, allowing for use of third-party malicious skills to arbitrarily phrase COVID-19 vaccine information. The results from a 210-participant study suggest that a third-party malicious skill could successful reduce the perceived accuracy among the users of information as to who gets the vaccine first, vaccine testing, and the side effects of the vaccine.

In silico characterization of ligand-receptor interactions for U-47700, N,N-didesmethyl-U-47700, U-50488 at mu- and kappa-opioid receptors.

The increasing misuse of novel synthetic opioids (NSOs) represents a serious public health concern. In this regard, U-47700 (trans-3,4-dichloro-N-[2-(dimethylamino)cyclohexyl]-N-methylbenzamide) and related "U-compounds" emerged on recreational drug markets as synthetic substitutes for illicit heroin and constituents of counterfeit pain medications. While the pharmacology of U-compounds has been investigated using in vitro and in vivo methods, there is still a lack of understanding about the details of ligand-receptor interactions at the molecular level.

A combined molecular dynamics simulation and DFT study on mercapto-benzamide inhibitors for the HIV NCp7 protein.

Molecular dynamics and quantum simulations are performed to elucidate some aspects of the action mechanism of mercapto-benzamides, a proposed class of antivirals against HIV-1. These molecules act as prodrugs that, after modifications in the biological environment, are able to denature the HIV nucleocapsid protein 7, a metal binder protein, with two zinc finger motifs, vital for RNA maturation and viral replication. Despite their attractive features, these molecules and their biological target are not well understood.

Indocyanine green fluorescence and near-infrared autofluorescence may improve post-thyroidectomy parathyroid function.

Background: Near-infrared autofluorescence and indocyanine green fluorescence are 2 recent tools introduced to improve postoperative parathyroid function during thyroid surgery.

Methods: We conducted a randomized prospective study. Patients undergoing total thyroidectomy were randomly assigned either to the fluorescence group, in which near-infrared autofluorescence and indocyanine green fluorescence were used, or to the control group.

General and species-specific recommendations for minimal requirements for the use of cephalopods in scientific research.

Here we list species-specific recommendations for housing, care and management of cephalopod molluscs employed for research purposes with the aim of contributing to the standardization of minimum requirements for establishments, care and accommodation of these animals in compliance with the principles stated in Directive 2010/63/EU. Maximizing their psychophysical welfare was our priority. General recommendations on water surface area, water depth and tank shape here reported represent the outcome of the combined action of the analysis of the available literature and an expertise-based consensus reached - under the aegis of the COST Action FA1301 - among researchers working with the most commonly used cephalopod species in Europe.

Cephalopod Behavior: From Neural Plasticity to Consciousness.

It is only in recent decades that subjective experience - or consciousness - has become a legitimate object of scientific inquiry. As such, it represents perhaps the greatest challenge facing neuroscience today. Subsumed within this challenge is the study of subjective experience in non-human animals: a particularly difficult endeavor that becomes even more so, as one crosses the great evolutionary divide between vertebrate and invertebrate phyla.

Impact of energy-based devices in pediatric thyroid surgery.

Background: Energy-based devices are surgical devices increasingly utilized for thyroid surgery, owing to a reduction of operative time and surgical related complications. The aim of the study is to evaluate whether the use of energy-based devices could improve the complication rate in pediatric thyroid surgery.

Methods: This is a retrospective observational study.

Misinformation warnings: Twitter's soft moderation effects on COVID-19 vaccine belief echoes.

Twitter, prompted by the rapid spread of alternative narratives, started actively warning users about the spread of COVID-19 misinformation. This form of soft moderation comes in two forms: as an interstitial cover before the Tweet is displayed to the user or as a contextual tag displayed below the Tweet. We conducted a 319-participants study with both verified and misleading Tweets covered or tagged with the COVID-19 misinformation warnings to investigate how Twitter users perceive the accuracy of COVID-19 vaccine content on Twitter.

The impact of missense mutation in PIGA associated to paroxysmal nocturnal hemoglobinuria and multiple congenital anomalies-hypotonia-seizures syndrome 2: A computational study.

Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired clonal blood disorder that manifests with hemolytic anemia, thrombosis, and peripheral blood cytopenias. The disease is caused by the deficiency of two glycosylphosphatidylinositols (GPI)-anchored proteins (CD55 and CD59) in the hemopoietic stem cells. The deficiency of GPI-anchored proteins has been associated with the somatic mutations in phosphatidylinositol glycan class A ().

Novel 2-pheynlbenzofuran derivatives as selective butyrylcholinesterase inhibitors for Alzheimer's disease.

Alzheimer's disease (AD) is a neurodegenerative disorder representing the leading cause of dementia and is affecting nearly 44 million people worldwide. AD is characterized by a progressive decline in acetylcholine levels in the cholinergic systems, which results in severe memory loss and cognitive impairments. Expression levels and activity of butyrylcholinesterase (BChE) enzyme has been noted to increase significantly in the late stages of AD, thus making it a viable drug target.

Multiple small bowel perforations due to invasive aspergillosis in a patient with acute myeloid leukemia: case report and a systematic review of the literature.

Purpose: Invasive aspergillosis (IA) represents a major cause of morbidity and mortality in immunocompromised patients. Involvement of the gastrointestinal tract by Aspergillus is mostly reported as part of a disseminated infection from a primary pulmonary site and only rarely as an isolated organ infection.

Methods: We report a case of small bowel perforation due to IA in a patient with acute leukemia under chemotherapy and pulmonary aspergillosis.

Duodenal graft complications requiring duodenectomy after pancreas and pancreas-kidney transplantation.

Duodenal graft complications are poorly reported complications of pancreas transplantation that can result in graft loss. Excluding patients with early graft failure, after a median follow-up period of 126 months (range 23-198) duodenectomy was required in 14 of 312 pancreas transplants (4.5%).

2-Phenylbenzofuran derivatives as butyrylcholinesterase inhibitors: Synthesis, biological activity and molecular modeling.

A series of 2-phenylbenzofurans compounds was designed, synthesized and evaluated as cholinesterase inhibitors. The biological assay experiments showed that most of the compounds displayed a clearly selective inhibition for butyrylcholinesterase (BChE), while a weak or no effect towards acetylcholinesterase (AChE) was detected. Among these benzofuran derivatives, compound 16 exhibited the highest BChE inhibition with an IC50 value of 30.

Laparoscopic robot-assisted resection of tumors located in posterosuperior liver segments.

Laparoscopic resection of liver tumors located in the posterosuperior segments is a challenging operation that could be facilitated by robotic assistance. Laparoscopic resection of 12 tumors located in posterosuperior segments (IVa: 1; VII: 5; VIII: 6) was carried out under robotic assistance. All patients had a single tumor nodule.

Metabolomics analysis and modeling suggest a lysophosphocholines-PAF receptor interaction in fibromyalgia.

Fibromyalgia Syndrome (FMS) is a chronic disease characterized by widespread pain, and difficult to diagnose and treat. We analyzed the plasma metabolic profile of patients with FMS by using a metabolomics approach combining Liquid Chromatography-Quadrupole-Time Of Flight/Mass Spectrometry (LC-Q-TOF/MS) with multivariate statistical analysis, aiming to discriminate patients and controls. LC-Q-TOF/MS analysis of plasma (FMS patients: n = 22 and controls: n = 21) identified many lipid compounds, mainly lysophosphocholines (lysoPCs), phosphocholines and ceramides.

Antigenic peptide molecular recognition by the DRB1-DQB1 haplotype modulates multiple sclerosis susceptibility.

Multiple sclerosis (MS) is an autoimmune disease of the central nervous system that has a notably high incidence in Sardinia. Our study focuses on two HLA class II haplotypes associated with the disease in Sardinia, the rare predisposing DRB1*15:01-DQB1*06:02 and the widespread protective DRB1*16:01-DQB1*05:02. This framework enabled the highlighting of HLA binding pocket specificity and peptide recognition mechanisms by employing molecular dynamics simulations of the whole DRB1-DQB1 haplotype interacting with MBP- and EBV-derived peptides.

Identification of calcium binding sites on calsequestrin 1 and their implications for polymerization.

Biophysical studies have shown that each molecule of calsequestrin 1 (CASQ1) can bind about 70-80 Ca(2+) ions. However, the nature of Ca(2+)-binding sites has not yet been fully characterized. In this study, we employed in silico approaches to identify the Ca(2+) binding sites and to understand the molecular basis of CASQ1-Ca(2+) recognition.

Structural and dynamical insights on HLA-DR2 complexes that confer susceptibility to multiple sclerosis in Sardinia: a molecular dynamics simulation study.

Sardinia is a major Island in the Mediterranean with a high incidence of multiple sclerosis, a chronic autoimmune inflammatory disease of the central nervous system. Disease susceptibility in Sardinian population has been associated with five alleles of major histocompatibility complex (MHC) class II DRB1 gene. We performed 120 ns of molecular dynamics simulation on one predisposing and one protective alleles, unbound and in complex with the two relevant peptides: Myelin Basic Protein and Epstein Barr Virus derived peptide.

HLA-DRB1-DQB1 haplotypes confer susceptibility and resistance to multiple sclerosis in Sardinia.

Introduction: Genetic predisposition to multiple sclerosis (MS) in Sardinia (Italy) has been associated with five DRB1*-DQB1* haplotypes of the human leukocyte antigen (HLA). Given the complexity of these associations, an in-depth re-analysis was performed with the specific aims of confirming the haplotype associations; establishing the independence of the associated haplotypes; and assessing patients' genotypic risk of developing MS.

Methods And Results: A transmission disequilibrium test (TDT) of the DRB1*-DQB1* haplotypes in 943 trio families, confirmed a higher than expected transmission rate (over-transmission) of the *13:03-*03:01 (OR = 2.

Inferring gene networks: dream or nightmare?

We describe several algorithms with winning performance in the Dialogue for Reverse Engineering Assessments and Methods (DREAM2) Reverse Engineering Competition 2007. After the gold standards for the challenges were released, the performance of the algorithms could be thoroughly evaluated under different parameters or alternative ways of solving systems of equations. For the analysis of Challenge 4, the "In-silico" challenges, we employed methods to explicitly deal with perturbation data and time-series data.