Miracle-dz/UniFAR-FTUs huggingface dataset:
The management of clival chordomas: an Italian multicentric study.

OBJECTIVE In the last 2 decades, the endoscopic endonasal approach in the treatment of clival chordomas has evolved to be a viable strategy to achieve maximal safe resection of this tumor. Here, the authors present a multicentric national study, intending to analyze the evolution of this approach over a 20-year time frame and its contribution in the treatment of clival chordomas. METHODS Clival chordoma cases surgically treated between 1999 and 2018 at 10 Italian neurosurgical departments were included in this retrospective study. Clinical, radiological, and surgical findings, adjuvant therapy, and outcomes were evaluated and compared according to classification in the treatment eras from 1999 to 2008 and from 2009 to 2018. RESULTS One hundred eighty-two surgical procedures were reviewed, with an increase in case load since 2009. The endoscopic endonasal transclival approach (EETA) was performed in 151 of 182 cases (83.0%) and other approaches were performed in 31 cases (17%). There was an increment in the use of EETA, neuronavigation, and Doppler ultrasound after 2008. The overall postoperative complication rate was 14.3% (26 of 182 cases) consisting of 9 CSF leaks (4.9%), 7 intracranial hemorrhages (3.8%), 5 cases of meningitis (2.7%), and 5 cerebral ischemic injuries (2.7%). Gross-total resection (GTR) was achieved in 93 of 182 cases (51.1%). Extent of resection (EOR) improved in the second era of the study. Signs and/or symptoms at presentation worsened in 27 cases (14.8%), and the Katz Index worsened in 10 cases (5.5%). Previous treatment, dural involvement, EETA, and intraoperative Doppler ultrasound correlated with GTR. Patients received adjuvant proton beam radiation in 115 of 182 cases (63.2%), which was administered more in the latter era. Five-year progression-free survival (PFS) and overall survival (OS) were 62.3% and 73.5%, respectively. GTR, EETA, proton beam therapy, and the chondroid subtype correlated with a better survival rate. The mean follow-up was 62 months. CONCLUSIONS Through multicentric data collection, this study encompasses the largest series in the literature of clival chordomas surgically treated through an EETA. An increase in the use of this approach was found among Italian neurosurgical departments together with an improved extent of resection over time. The satisfactory rate of GTR was marked by low surgical morbidity and the preservation of patient quality of life. Surgical outcome was reinforced, in terms of PFS and OS, by the use of proton beam therapy, which was increasingly performed along the period of study.
Overcoming Symmetry Mismatch in Vaccine Nanoassembly through Spontaneous Amidation

Abstract Matching of symmetry at interfaces is a fundamental obstacle in molecular assembly. Virus‐like particles (VLPs) are important vaccine platforms against pathogenic threats, including Covid‐19. However, symmetry mismatch can prohibit vaccine nanoassembly. We established an approach for coupling VLPs to diverse antigen symmetries. SpyCatcher003 enabled efficient VLP conjugation and extreme thermal resilience. Many people had pre‐existing antibodies to SpyTag:SpyCatcher but less to the 003 variants. We coupled the computer‐designed VLP not only to monomers (SARS‐CoV‐2) but also to cyclic dimers (Newcastle disease, Lyme disease), trimers (influenza hemagglutinins), and tetramers (influenza neuraminidases). Even an antigen with dihedral symmetry could be displayed. For the global challenge of influenza, SpyTag‐mediated display of trimer and tetramer antigens strongly induced neutralizing antibodies. SpyCatcher003 conjugation enables nanodisplay of diverse symmetries towards generation of potent vaccines.
Impact of Simulated Gastrointestinal Digestion on the Biological Activity of an Alcalase Hydrolysate of Orange Seed (Siavaraze, Citrus sinensis) by-Products

In this study, orange seed proteins were hydrolyzed by Alcalase enzyme at different enzyme concentrations 1–3% (v/w) and hydrolysis times (2–5 h), to obtain bioactive peptides showing antioxidant, Angiotensin-converting enzyme (ACE) -inhibitory, and hypoglycemic activities. The highest biological activities (p < 0.05) were achieved by using a hydrolysis time of 5 h and an enzyme concentration of 2%. Orange seed protein hydrolysate (OSPH) was prepared under these conditions, and peptides were isolated and purified by using size-exclusion chromatography and high-performance liquid chromatography, respectively. The fractions that showed the highest biological activities were analyzed by mass spectrometry in tandem, and a total of 63 peptide sequences were found. Moreover, the effect of simulated gastrointestinal digestion on the bioactivity of the fractions was studied, and the novel peptide sequences generated were also identified. Overall, despite there being some differences in the profile of peptide sequences obtained, the main results showed non-significant differences in the analyzed bioactivities after simulated gastrointestinal digestion.
Decoding Susceptibility to Respiratory Viral Infections and Asthma Inception in Children

Human Respiratory Syncytial Virus and Human Rhinovirus are the most frequent cause of respiratory tract infections in infants and children and are major triggers of acute viral bronchiolitis, wheezing and asthma exacerbations. Here, we will discuss the application of the powerful tools of systems biology to decode the molecular mechanisms that determine risk for infection and subsequent asthma. An important conceptual advance is the understanding that the innate immune system is governed by a Bow-tie architecture, where diverse input signals converge onto a few core pathways (e.g., IRF7), which in turn generate diverse outputs that orchestrate effector and regulatory functions. Molecular profiling studies in children with severe exacerbations of asthma/wheeze have identified two major immunological phenotypes. The IRF7hi phenotype is characterised by robust upregulation of antiviral response networks, and the IRF7lo phenotype is characterised by upregulation of markers of TGFβ signalling and type 2 inflammation. Similar phenotypes have been identified in infants and children with severe viral bronchiolitis. Notably, genome-wide association studies supported by experimental validation have identified key pathways that increase susceptibility to HRV infection (ORMDL3 and CHDR3) and modulate TGFβ signalling (GSDMB, TGFBR1, and SMAD3). Moreover, functional deficiencies in the activation of type I and III interferon responses are already evident at birth in children at risk of developing febrile lower respiratory tract infections and persistent asthma/wheeze, suggesting that the trajectory to asthma begins at birth or in utero. Finally, exposure to microbes and their products reprograms innate immunity and provides protection from the development of allergies and asthma in children, and therefore microbial products are logical candidates for the primary prevention of asthma.
Mechanisms of Tolerance and Resistance to Chlorhexidine in Clinical Strains of Klebsiella pneumoniae Producers of Carbapenemase: Role of New Type II Toxin-Antitoxin System, PemIK

Although the failure of antibiotic treatment is normally attributed to resistance, tolerance and persistence display a significant role in the lack of response to antibiotics. Due to the fact that several nosocomial pathogens show a high level of tolerance and/or resistance to chlorhexidine, in this study we analyzed the molecular mechanisms associated with chlorhexidine adaptation in two clinical strains of Klebsiella pneumoniae by phenotypic and transcriptomic studies. These two strains belong to ST258-KPC3 (high-risk clone carrying β-lactamase KPC3) and ST846-OXA48 (low-risk clone carrying β-lactamase OXA48). Our results showed that the K. pneumoniae ST258-KPC3CA and ST846-OXA48CA strains exhibited a different behavior under chlorhexidine (CHLX) pressure, adapting to this biocide through resistance and tolerance mechanisms, respectively. Furthermore, the appearance of cross-resistance to colistin was observed in the ST846-OXA48CA strain (tolerant to CHLX), using the broth microdilution method. Interestingly, this ST846-OXA48CA isolate contained a plasmid that encodes a novel type II toxin/antitoxin (TA) system, PemI/PemK. We characterized this PemI/PemK TA system by cloning both genes into the IPTG-inducible pCA24N plasmid, and found their role in persistence and biofilm formation. Accordingly, the ST846-OXA48CA strain showed a persistence biphasic curve in the presence of a chlorhexidine-imipenem combination, and these results were confirmed by the enzymatic assay (WST-1).
Identification and Expression Profiles of 14 Odorant-Binding Protein Genes From Pieris rapae (Lepidoptera: Pieridae)

Abstract The small white butterfly, Pieris rapae (L.), is an important insect pest of Brassica crops. This species utilize olfactory cues to find their hosts and mates. However, the molecular mechanism underlying the olfactory perception in this species remains unclear. Here, we identified 14 odorant-binding proteins (OBP) genes—essential for insect olfaction—in P. rapae by exploring a previously published transcriptome dataset. Proteins encoded by all of these genes contain N-terminal signal peptides and six positionally conserved cysteine residues, which are characteristic of insect OBPs. These OBPs displayed high amino acid identity with their respective orthologs in other lepidopterans, and several conserved motifs were identified within these OBPs. Phylogenetic analysis showed that these OBPs were well segregated from each other and clustered into different branches. PrapOBP1 and PrapOBP2 were clustered into the ‘general odorant-binding protein’ clade, and PrapOBP3 and PrapOBP4 fall into the ‘pheromone-binding protein’ clade. The 14 OBP genes were located on seven genomic scaffolds. Of these, PrapOBP1, 2, 3, and 4 were located on scaffold332, whereas PrapOBP5, 6, 7, 8, and 9 were located on scaffold116. Ten of the 14 genes had antenna-biased expression. Of these, PrapOBP1, 2, 4, and 13 were enriched in male antennae, whereas PrapOBP7 and PrapOBP10 were female-biased. Our findings suggest that these OBPs may be involved in olfactory communication. To the best of our knowledge, this is the first report on the identification and characterization of OBPs in P. rapae, and our findings provide a solid foundation for studying the functions of these genes.
Performance of a commercial multi-sensor wearable (Fitbit Charge HR) in measuring physical activity and sleep in healthy children

Purpose This study sought to assess the performance of the Fitbit Charge HR, a consumer-level multi-sensor activity tracker, to measure physical activity and sleep in children. Methods 59 healthy boys and girls aged 9–11 years old wore a Fitbit Charge HR, and accuracy of physical activity measures were evaluated relative to research-grade measures taken during a combination of 14 standardized laboratory- and field-based assessments of sitting, stationary cycling, treadmill walking or jogging, stair walking, outdoor walking, and agility drills. Accuracy of sleep measures were evaluated relative to polysomnography (PSG) in 26 boys and girls during an at-home unattended PSG overnight recording. The primary analyses included assessment of the agreement (biases) between measures using the Bland-Altman method, and epoch-by-epoch (EBE) analyses on a minute-by-minute basis. Results Fitbit Charge HR underestimated steps (~11.8 steps per minute), heart rate (~3.58 bpm), and metabolic equivalents (~0.55 METs per minute) and overestimated energy expenditure (~0.34 kcal per minute) relative to research-grade measures (p< 0.05). The device showed an overall accuracy of 84.8% for classifying moderate and vigorous physical activity (MVPA) and sedentary and light physical activity (SLPA) (sensitivity MVPA: 85.4%; specificity SLPA: 83.1%). Mean estimates of bias for measuring total sleep time, wake after sleep onset, and heart rate during sleep were 14 min, 9 min, and 1.06 bpm, respectively, with 95.8% sensitivity in classifying sleep and 56.3% specificity in classifying wake epochs. Conclusions Fitbit Charge HR had adequate sensitivity in classifying moderate and vigorous intensity physical activity and sleep, but had limitations in detecting wake, and was more accurate in detecting heart rate during sleep than during exercise, in healthy children. Further research is needed to understand potential challenges and limitations of these consumer devices.
Role of ultra-processed food in fat mass index between 6 and 11 years of age: a cohort study.

BACKGROUND Ultra-processed food consumption and obesity have been highlighted as an important relationship to public health. We aimed to evaluate the association between ultra-processed food consumption and body fat from 6 to 11 years of age. METHODS We assessed the association between ultra-processed food consumption (from food frequency questionnaires) and body fat (measured by air displacement plethysmography) between 6 and 11 years of age among participants of the Pelotas-Brazil 2004 Birth Cohort. The NOVA classification was used to classify foods according to the processing degree. Body fat was evaluated relative to the height using fat mass index (FMI). Generalized estimating equations were used to answer the main research question and mediation analyses were run to assess the direct and indirect effect of ultra-processed food in body fat. RESULTS At fully adjusted analysis, an increase of 100 g in contribution from ultra-processed food to daily food intake at between 6 and 11 years of age was associated with a gain of 0.14 kg/m² in FMI in the same period; 58% of the total effect of ultra-processed food intake at 6 years (in grams) over the change in FMI from 6 to 11 years was mediated by its calorie content. CONCLUSIONS Ultra-processed food consumption was associated with an increase in body fat from childhood to early adolescence, and this association was not just due to the effect of ultra-processed food on calorie content.
Characterisation of a Teladorsagia circumcincta glutathione transferase

A 615 bp full length cDNA encoding a Teladorsagia circumcincta glutathione transferase (TcGST) was cloned, expressed in Escherichia coli and the recombinant protein purified and its kinetic properties determined. The predicted protein consisted of 205 amino acids and was present as a single band of about 24 kDa on SDS-PAGE. Multiple alignments of the protein sequence of TcGST with homologues from other helminths showed that the highest identity of 53-68% with haem-binding nematode proteins designated as members of the nu class of GSTs. Substrate binding sites and conserved regions were identified and were generally conserved. The predicted 3-dimensional structures of TcGST and HcGST revealed highly open binding cavities typical of this class of GST, considered to allow greater accessibility to diverse ligands compared with other classes of GST. At 25 °C, the optimum pH for TcGST activity was pH 7, the Vmax was 1535 ± 33 nmoles.min-1.mg-1 protein and the apparent Km for the substrate 1-chloro-2,4-dinitrobenzene (CDNB) was 0.22 ± 0.01 mM (mean ± SD, n = 2). Antibodies in both serum and saliva from field-immune, but not nematode-naÏve, sheep, recognised recombinant TcGST in enzyme-linked immunosorbent assays. The recognition of the recombinant protein by antibodies generated by exposure of sheep to the native enzyme indicates similar antigenicity of the two proteins. These findings could aid in the design of novel drugs and vaccine antigens for economically important parasites of livestock.
Digital light microscopy to characterize the scales of two goatfishes (Perciformes; Mullidae)

The normal and lateral line scales from above the head and four flank regions were investigated in two goatfishes by using light microscopy to evaluate the microscopic characteristics of scale surface ornamentation from different body parts of these fishes and to add new morphological data for their discrimination. The body scales were removed and digital images captured with a Dino‐Lite digital camera connected to a Leica compound microscope. The presence of both transverse and longitudinal radii was a distinctive characteristic for the scales of studied goatfishes. The most distinctive features of the key scales discriminating the two goatfishes were the scale shape, the presence of irregular grooves in scale surface, the presence of transverse radii in the lateral fields, and the availability of lepidont at the anterior field. The lateral line scale ornamentations were almost similar in two species; however, the lateral line canal was branching in Parupeneus heptacanthus. Scale extension index indicated that in both species, the dimension of normal key scales tends to the right, while the dimension of lateral line scales tends to the left. This study accentuated that scales from different body regions may exhibit variation in surface ornamentations, that scale morphology could successfully be used to discriminate the examined goatfishes, and that the use of fish scale microscopy is an easy and relatively rapid method and does not require fish sacrifice. Since fish identification is essential for the conservation and management of species, the use of scale morphology to this purpose appears particularly promising.
High-throughput single-cell functional elucidation of neurodevelopmental disease–associated genes reveals convergent mechanisms altering neuronal differentiation

The overwhelming success of exome- and genome-wide association studies in discovering thousands of disease-associated genes necessitates novel high-throughput functional genomics approaches to elucidate the mechanisms of these genes. Here, we have coupled multiplexed repression of neurodevelopmental disease-associated genes to single-cell transcriptional profiling in differentiating human neurons to rapidly assay the functions of multiple genes in a disease-relevant context, assess potentially convergent mechanisms, and prioritize genes for specific functional assays. For a set of 13 autism spectrum disorder (ASD) associated genes, we demonstrate that this approach generated important mechanistic insights, revealing two functionally convergent modules of ASD genes: one that delays neuron differentiation and one that accelerates it. Five genes that delay neuron differentiation (ADNP, ARID1B, ASH1L, CHD2, and DYRK1A) mechanistically converge, as they all dysregulate genes involved in cell-cycle control and progenitor cell proliferation. Live-cell imaging after individual ASD gene repression validated this functional module, confirming that these genes reduce neural progenitor cell proliferation and neurite growth. Finally, these functionally convergent ASD gene modules predicted shared clinical phenotypes among individuals with mutations in these genes. Altogether these results demonstrate the utility of a novel and simple approach for the rapid functional elucidation of neurodevelopmental disease-associated genes.
Design and Microwave-Assisted Synthesis of Aza-Resveratrol Analogues with Potent Cholinesterase Inhibition.

BACKGROUND Currently approved Alzheimer's disease medications mainly comprise acetylcholinesterase inhibitors. Many of these inhibitors are either natural compounds or synthetic molecules inspired in natural compounds. Hybrids molecules that can interact with different target sites of the enzyme could lead to the discovery of effective multitarget drugs. OBJECTIVE Design, synthesize and evaluate a series of new aza-resveratrol analogues as in vitro acetyl- and butyrylcholinesterase inhibitors. METHOD The synthesis is achieved by a simple and efficient microwave-assisted method, from commercially available starting materials. Compounds are designed as hybrids of an aza-stilbene nucleus (Schiff base) connected to a tertiary amine by a hydrocarbon chain of variable length, designed to interact both with the peripheric anionic site and the catalytic site of the enzyme. RESULTS All the derivatives inhibit both enzymes in a concentration dependent manner, acting as moderate to potent cholinesterase inhibitors. The most potent inhibitors are compounds 12b (IC50 = 0.43 µM) and 12a (IC50 = 0.31 µM) for acetyland butyrylcholinesterase, respectively. Compounds 12a and 12b also exhibit significant acetylcholinesterase inhibition in SH-SY5Y human neuroblastoma cells without cytotoxic properties. Enzyme kinetic studies and molecular modelling reveal that inhibitor 12b targets both the catalytic active site and the peripheral anionic site of acetylcholinesterase what makes it able to modulate the self-induced β-amyloid aggregation. Furthermore, the molecular modelling analysis helps to assess the impact of the linker length in the inhibitory activity of this family of new cholinesterase inhibitors. CONCLUSION These compounds have potential to serve as a dual binding site inhibitor and might provide a useful template for the development of new anti- Alzheimer's disease agents.
Impact of Pre-Analytical Factors on MSI Test Accuracy in Mucinous Colorectal Adenocarcinoma: A Multi-Assay Concordance Study

Immunohistochemistry (IHC) and polymerase chain reaction (PCR) and fragment separation by capillary electrophoresis represent the current clinical laboratory standard for the evaluation of microsatellite instability (MSI) status. The importance of reporting MSI status in colorectal cancer is based on its potential for guiding treatment and as a prognostic indicator. It is also used to identify patients for Lynch syndrome testing. Our aim was to evaluate pre-analytical factors, such as age of formalin-fixed and paraffin-embedded (FFPE) block, neoplastic cell percentage, mucinous component, and DNA integrity, that may influence the accuracy of MSI testing and assess the concordance between three different MSI evaluation approaches. We selected the mucinous colorectal cancer (CRC) histotype for this study as it may possibly represent an intrinsic diagnostic issue due to its low tumor cellularity. Seventy-five cases of mucinous CRC and corresponding normal colon tissue samples were retrospectively selected. MMR proteins were evaluated by IHC. After DNA quality and quantity evaluation, the Idylla™ and TapeStation 4200 platforms were adopted for the evaluation of MSI status. Seventy-three (97.3%) cases were successfully analyzed by the three methodologies. Overall, the Idylla™ platform showed a concordance rate with IHC of 98.0% for microsatellite stable (MSS)/proficient MMR (pMMR) cases and 81.8% for MSI/deficient MMR (dMMR) cases. The TapeStation 4200 system showed a concordance rate with IHC of 96.0% for MSS/pMMR cases and 45.4% for MSI/dMMR cases. The concordance rates of the TapeStation 4200 system with respect to the Idylla™ platform were 98.1% for MSS profile and 57.8% for MSI profile. Discordant cases were analyzed using the Titano MSI kit. Considering pre-analytical factors, no significant variation in concordance rate among IHC analyses and molecular systems was observed by considering the presence of an acellular mucus cut-off >50% of the tumor area, FFPE year preparation, and DNA concentration. Conversely, the Idylla™ platform showed a significant variation in concordance rate with the IHC approach by considering a neoplastic cell percentage >50% (p-value = 0.002), and the TapeStation 4200 system showed a significant variation in concordance rate with the IHC approach by considering a DNA integrity number (DIN) ≥4 as cut-off (p-value = 0.009). Our data pinpoint a central role of the pre-analytical phase in the diagnostic outcome of MSI testing in CRC.