Pangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery

The HXB/BXH family of recombinant inbred rat strains is a unique genetic resource that has been extensively phenotyped over 25 years, resulting in a vast dataset of quantitative molecular and physiological phenotypes. We built a pangenome graph from 10x Genomics Linked-Read data for 31 recombinant inbred rats to study genetic variation and association mapping. The pangenome includes 0.2Gb of sequence that is not present the reference mRatBN7.2, confirming the capture of substantial additional variation. We validated variants in challenging regions, including complex structural variants resolving into multiple haplotypes. Phenome-wide association analysis of validated SNPs uncovered variants associated with glucose/insulin levels and hippocampal gene expression. We propose an interaction between Pirl1l1 , chromogranin expression, TNF-α levels, and insulin regulation. This study demonstrates the utility of linked-read pangenomes for comprehensive variant detection and mapping phenotypic diversity in a widely used rat genetic reference panel.

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

Pangenome graph construction from genome alignments with Minigraph-Cactus

Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be used to construct pangenome graphs, but advances in long-read sequencing are leading to widely available, high-quality phased assemblies. Constructing a pangenome graph directly from assemblies, as opposed to variant calls, leverages the graph's ability to represent variation at different scales. Here we present the Minigraph-Cactus pangenome pipeline, which creates pangenomes directly from whole-genome alignments, and demonstrate its ability to scale to 90 human haplotypes from the Human Pangenome Reference Consortium. The method builds graphs containing all forms of genetic variation while allowing use of current mapping and genotyping tools. We measure the effect of the quality and completeness of reference genomes used for analysis within the pangenomes and show that using the CHM13 reference from the Telomere-to-Telomere Consortium improves the accuracy of our methods. We also demonstrate construction of a Drosophila melanogaster pangenome.

Pleiotropic influence of DNA methylation QTLs on physiological and ageing traits

DNA methylation is influenced by genetic and non-genetic factors. Here, we chart quantitative trait loci (QTLs) that modulate levels of methylation at highly conserved CpGs using liver methylome data from mouse strains belonging to the BXD family. A regulatory hotspot on chromosome 5 had the highest density of trans-acting methylation QTLs (trans-meQTLs) associated with multiple distant CpGs. We refer to this locus as meQTL.5a. Trans-modulated CpGs showed age-dependent changes and were enriched in developmental genes, including several members of the MODY pathway (maturity onset diabetes of the young). The joint modulation by genotype and ageing resulted in a more 'aged methylome' for BXD strains that inherited the DBA/2J parental allele at meQTL.5a. Further, several gene expression traits, body weight, and lipid levels mapped to meQTL.5a, and there was a modest linkage with lifespan. DNA binding motif and protein-protein interaction enrichment analyses identified the hepatic nuclear factor, Hnf1a (MODY3 gene in humans), as a strong candidate. The pleiotropic effects of meQTL.5a could contribute to variations in body size and metabolic traits, and influence CpG methylation and epigenetic ageing that could have an impact on lifespan.

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared to its predecessor. Gene annotations are now more complete, significantly improving the mapping precision of genomic, transcriptomic, and proteomics data sets. We jointly analyzed 163 short-read whole genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ~20.0 million sequence variations, of which 18.7 thousand are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice

Short tandem repeats (STRs) are a class of rapidly mutating genetic elements typically characterized by repeated units of 1-6 bp. We leveraged whole-genome sequencing data for 152 recombinant inbred (RI) strains from the BXD family of mice to map loci that modulate genome-wide patterns of new mutations arising during parent-to-offspring transmission at STRs. We defined quantitative phenotypes describing the numbers and types of germline STR mutations in each strain and performed quantitative trait locus (QTL) analyses for each of these phenotypes. We identified a locus on Chromosome 13 at which strains inheriting the C57BL/6J (B) haplotype have a higher rate of STR expansions than those inheriting the DBA/2J (D) haplotype. The strongest candidate gene in this locus is Msh3, a known modifier of STR stability in cancer and at pathogenic repeat expansions in mice and humans, as well as a current drug target against Huntington's disease. The D haplotype at this locus harbors a cluster of variants near the 5' end of Msh3, including multiple missense variants near the DNA mismatch recognition domain. In contrast, the B haplotype contains a unique retrotransposon insertion. The rate of expansion covaries positively with Msh3 expression-with higher expression from the B haplotype. Finally, detailed analysis of mutation patterns showed that strains carrying the B allele have higher expansion rates, but slightly lower overall total mutation rates, compared with those with the D allele, particularly at tetranucleotide repeats. Our results suggest an important role for inherited variants in Msh3 in modulating genome-wide patterns of germline mutations at STRs.

A draft human pangenome reference

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

Building pangenome graphs

Pangenome graphs can represent all variation between multiple genomes, but existing methods for constructing them are biased due to reference-guided approaches. In response, we have developed PanGenome Graph Builder (PGGB), a reference-free pipeline for constructing unbi-ased pangenome graphs. PGGB uses all-to-all whole-genome alignments and learned graph embeddings to build and iteratively refine a model in which we can identify variation, measure conservation, detect recombination events, and infer phylogenetic relationships.

First-line levetiracetam versus enzyme-inducing antiseizure medication in glioma patients with epilepsy

OBJECTIVE

This study aimed to directly compare the effectiveness of first-line monotherapy levetiracetam (LEV) versus enzyme-inducing antiseizure medications (EIASMs) in glioma patients.

METHODS

In this nationwide retrospective observational cohort study, Grade 2-4 glioma patients were included, with a maximum duration of follow-up of 36 months. Primary outcome was antiseizure medication (ASM) treatment failure for any reason, and secondary outcomes were treatment failure due to uncontrolled seizures and due to adverse effects. For estimation of the association between ASM treatment and ASM treatment failure, multivariate cause-specific cox proportional hazard models were estimated, adjusting for potential confounders.

RESULTS

In the original cohort, a total of 808 brain tumor patients with epilepsy were included, of whom 109 glioma patients were prescribed first-line LEV and 183 glioma patients first-line EIASMs. The EIASM group had a significantly higher risk of treatment failure for any reason compared to LEV (adjusted hazard ratio [aHR] = 1.82, 95% confidence interval [CI] = 1.20-2.75, p = .005). Treatment failure due to uncontrolled seizures did not differ significantly between EIASMs and LEV (aHR = 1.32, 95% CI = .78-2.25, p = .300), but treatment failure due to adverse effects differed significantly (aHR = 4.87, 95% CI = 1.89-12.55, p = .001).

SIGNIFICANCE

In this study, it was demonstrated that LEV had a significantly better effectiveness (i.e., less ASM treatment failure for any reason or due to adverse effects) compared to EIASMs, supporting the current neuro-oncology guideline recommendations to avoid EIASMs in glioma patients.

AB1169 IMMUNOMODULATORY EFFECTS OF SARS-CoV-2 VACCINATION: INCREASE OF REGULATORY T CELLS AFTER mRNA VACCINE

Background

Besides the ability to induce antigen-specific responses, vaccines can be endowed with immunomodulatory properties including the capacity to induce or downregulate regulatory T cells (Treg) that suppress adaptative and autoreactive immune responses (1).

Objectives

We asked if an anti-SARS-CoV-2 mRNA vaccine could also induce an accumulation of Treg cells in patients with mixed cryoglobulinemia vasculitis (MCV), who have a deficiency of Treg cells (2) and in healthy individuals. We also investigated immunologic variables possibly associated with a low immunogenicity of SARS-CoV-2 mRNA vaccine in patients with MCV (3).

Methods

We analyzed peripheral blood lymphocyte subpopulations and anti-SARS-CoV-2 serological response in 24 patients with MCV and 9 Healthy donors (HD) before and after 2 weeks after the second dose of the Pfizer/BioNTech vaccine.

Results

Among MCV patients we found 15 serological responders and 9 non-responders. All 5 seronegative patients treated recently with rituximab had <5 B cells/µL, whereas the absolute B cell count was increased in 2 of 4 untreated patients due to monoclonal B cell lymphocytosis, with monoclonal cells representing more than 90% of B cells, associated with non-Hodgkin lymphoma. The percentage of pathologic CD21low B cells was significantly increased in seronegative patients.

Before receiving the Pfizer/BioNTech vaccine, patients with MCV had a significantly reduced frequency of Treg cells among CD4+ T cells compared to HD. After the second dose of the vaccine, there was in MCV patients a significant increase in the percent and absolute count of Treg among CD4+ T cells

Concerning the pre-vaccination distribution of T cells subpopulations, including the percentages and absolute counts of total CD3+, CD4+, CD8+, HLA-DR+ activated, Treg or CD56+ natural killer T cells, we could not reveal any pattern significantly associated with lack of serological response to vaccine.

Conclusion

Our findings show that lack of immunoreactivity in patients with MCV may be associated with expansion of pathologic B cells and that anti-SARS-CoV2 mRNA vaccine may induce an increase of Treg cells.

References

[1]Krienke C. et al. A noninflammatory mRNA vaccine for treatment of experimental autoimmune encephalomyelitis. Science. 2021 Jan 8;371(6525):145-153.

[2]Boyer O. et al. CD4+CD25+ regulatory T-cell deficiency in patients with hepatitis C-mixed cryoglobulinemia vasculitis. Blood. 2004 May 1;103(9):3428-30.

[3]Visentini M. et al. Flares of mixed cryoglobulinaemia vasculitis after vaccination against SARS-CoV-2. Ann Rheum Dis. 2021 Nov 24:annrheumdis-2021-221248.

Disclosure of Interests

None declared

A global analysis of conservative and non-conservative mutations in SARS-CoV-2 detected in the first year of the COVID-19 world-wide diffusion

The ability of SARS-CoV-2 to rapidly mutate represents a remarkable complicancy. Quantitative evaluations of the effects that these mutations have on the virus structure/function is of great relevance and the availability of a large number of SARS-CoV-2 sequences since the early phases of the pandemic represents a unique opportunity to follow the adaptation of the virus to humans. Here, we evaluated the SARS-CoV-2 amino acid mutations and their progression by analyzing publicly available viral genomes at three stages of the pandemic (2020 March 15th and October 7th, 2021 February 7th). Mutations were classified in conservative and non-conservative based on the probability to be accepted during the evolution according to the Point Accepted Mutation substitution matrices and on the similarity of the encoding codons. We found that the most frequent substitutions are T > I, L > F, and A > V and we observe accumulation of hydrophobic residues. These findings are consistent among the three stages analyzed. We also found that non-conservative mutations are less frequent than conservative ones. This finding may be ascribed to a progressive adaptation of the virus to the host. In conclusion, the present study provides indications of the early evolution of the virus and tools for the global and genome-specific evaluation of the possible impact of mutations on the structure/function of SARS-CoV-2 variants.

Efficient dynamic variation graphs

MOTIVATION

Pangenomics is a growing field within computational genomics. Many pangenomic analyses use bidirected sequence graphs as their core data model. However, implementing and correctly using this data model can be difficult, and the scale of pangenomic datasets can be challenging to work at. These challenges have impeded progress in this field.

RESULTS

Here, we present a stack of two C++ libraries, libbdsg and libhandlegraph, which use a simple, field-proven interface, designed to expose elementary features of these graphs while preventing common graph manipulation mistakes. The libraries also provide a Python binding. Using a diverse collection of pangenome graphs, we demonstrate that these tools allow for efficient construction and manipulation of large genome graphs with dense variation. For instance, the speed and memory usage are up to an order of magnitude better than the prior graph implementation in the VG toolkit, which has now transitioned to using libbdsg's implementations.

AVAILABILITY AND IMPLEMENTATION

libhandlegraph and libbdsg are available under an MIT License from https://github.com/vgteam/libhandlegraph and https://github.com/vgteam/libbdsg.

Surface ruptures database related to the 26 December 2018, MW 4.9 Mt. Etna earthquake, southern Italy

We provide a database of the surface ruptures produced by the 26 December 2018 Mw 4.9 earthquake that struck the eastern flank of Mt. Etna volcano in Sicily (southern Italy). Despite its relatively small magnitude, this shallow earthquake caused about 8 km of surface faulting, along the trace of the NNW-trending active Fiandaca Fault. Detailed field surveys have been performed in the epicentral area to map the ruptures and to characterize their kinematics. The surface ruptures show a dominant right-oblique sense of displacement with an average slip of about 0.09 m and a maximum value of 0.35 m. We have parsed and organized all observations in a concise database, with 932 homogeneous georeferenced records. The Fiandaca Fault is part of the complex active Timpe faults system affecting the eastern flank of Etna, and its seismic history indicates a prominent surface-faulting potential. Therefore, this database is essential for unravelling the seismotectonics of shallow earthquakes in volcanic areas, and contributes updating empirical scaling regressions that relate magnitude and extent of surface faulting.

Relationship between Doxorubicin-Induced Ecg Changes and Myocardial Alterations in Rats

The aim of the present study was to evaluate the dose- and time-dependence of the effect displayed by doxorubicin (DXR) on the electrocardiogram (ECG) and to establish the relationship between structural alterations of the myocardium and ECG changes in rats administered DXR, at a dose of 1.5 or 3.0 mg/kg, every 3 days for a total of three administrations. The most interesting findings consisted of a dose-dependent, but reversible prolongation of the QRS complex, and in a dose-dependent and progressive irreversible increase in QaT and, in particular, in SaT duration. Furthermore, animals treated with the higher DXR dose showed a slight increase in serum K+ concentration and a significant decrease in serum Ca2+ levels. A good correlation was found between the morphologic score indicating the degree of observed tissue damage and SaT prolongation. These results therefore support the usefulness of measuring this ECG parameter for monitoring the development of DXR-induced cardiotoxicity in rats.

Evaluation of the PMMA microlens efficiency for the realization of a solar micro-concentrator array

In order to assess the performance of solar micro-concentrators, specific methods and protocols need to be developed, tested, and applied. In detail, as in conventional concentration modules, one of the fundamental parameters to consider is the efficiency of optical concentrators. In fact, optical concentrators give fundamental information on the current potentially generated from solar microcells that receive the concentrated light radiation. To develop a measurement method for micrometer-size optical components, a suitable optical system was implemented and used. Moreover, the potential application of the printed microstructures in an optical system for solar micro-concentrators was demonstrated.

A Phase II Study of the Administration of Recombinant Interleukin 2 (rIL-2) Plus Lymphokine Activated Killer (LAK) Cells in Stage IV Melanoma Patients

From January 1987 to February 1988, 15 stage IV melanoma patients were treated with two courses of bolus injection of rIL-2 plus LAK cell infusions at the National Cancer Institute of Milan. The original treatment regimen included a first course of rIL-2 administration (400 μg/m5 bolus injection 3 times a day [TID] for 4 days) and a second course of rIL-2 administration (800 μg/m2 bolus injection TID for 7 days) separated by 4 consecutive daily leukaphereses. Autologous lymphokine activated killer (LAK) cells were reinfused into each patient on three occasions during the second period of rIL-2 administration. Due to the appearance of grade III–IV neurological, hepatic and cardiopulmonary toxicity, 7 patients discontinued dosing before the end of treatment, one patient desired to be withdrawn and one patient died from rapidly progressive disease, although complications of rIL-2 administration may have contributed to her death. Only 6 patients completed the schedule without evidence of major intolerance, even though the planned dose during the second course of rIL-2 was reduced to 400 μg/m2. The complete duration of treatment ranged from 11 to 19 days. The total dose of rIL-2 injected ranged from 12.6 to 30.4 mg. The number of infused LAK cells ranged from 15.5x109 to 60x109/patient. Two of the 14 evaluable patients showed a minor anti-tumor response. In 5 patients new metastases in other sites were documented from 2 to 5 months after completion of dosing. No apparent association was found between progression of the disease (or the appearance of new metastases) and the total dose of rIL-2 injected, the number of LAK cells administered or the number of days of treatment. By December 1988, all patients had died of their disease in a period ranging from 3 to 14 months from the last injection of rIL-2. The lack of significant clinical responses in this study and the high toxicity of this treatment lead us to conclude that at least as far as melanoma patients are concerned, adoptive immunotherapy with rIL-2 plus LAK cells (as described here) is not a justifiable treatment option unless new evidence presents itself.

The Rat Model in the Comparative Evaluation of Anthracyclines Cardiotoxicity

In the present investigation, the cardiotoxic effects of three anthracycline analogs (doxorubicin, 4′-epi-doxorubicin and 4′-deoxy-doxorubicin) were compared. For this purpose, 9.0 mg/kg of doxorubicin, divided into three closely spaced sub-doses, were injected intravenously in rats. The two derivatives were administered according to the same time schedule and their doses were chosen on the basis of the clinically adopted ratio, doxorubicin : 4′-epidoxorubicin : 4′-deoxy-doxorubicin = 1:1: 0.5. The degree of cardiomyopathy induced by the three anthracyclines was evaluated by ECG changes and morphological alterations. Doxorubicin was found to produce a significant degree of cardiotoxicity, thus confirming the validity of the experimental model adopted. Both 4′-substituted derivatives proved to be less cardiotoxic than the parent compound, although not completely devoid of this side effect.

Cardiac Arrhythmia: Possible Complication from Treatment with Cisplatin

Cardiotoxicity is rarely observed during cisplatin chemotherapy. A possible synergistic toxic effect of cisplatin with etoposide on cardiac electrical activity is discussed. A case of a 60-year-old woman with squamous cell lung carcinoma who developed paroxysmal supraventricular tachycardia during cisplatin chemotherapy is reported. The potential cardiotoxicity should be considered when cisplatin is combined with other cardiotoxic agents or used in patients with cardiac disease.

Cardiac Function Evaluation in Amsa-Treated Patients

Cardiac function was monitored by means of ECG and systolic time intervals in 13 patients submitted to treatment with 4′-(9-acridinylamino) methanesulfon-m-aniside (AMSA) without the classical reconstitution vehicle N1N-dimethylacetamide. ECG changes were represented by flattening of T waves (100%), sporadic atrial extrasystoles (23 %), and sporadic or coupled ventricular premature beats (7.6 %). These alterations were transient and not dose related. The systolic time interval ratio, recorded at the end of infusion and 2 h after drug administration, did not change significantly from pretreatment values. Systolic time intervals recorded in 6 patients after the mean cumulative dose of 550 mg/m2, and in 3 patients after the mean cumulative dose of 1000 mg/m2, did not change from mean basal values. Present data failed to confirm the occurrence of a significantly cardiotoxic activity of AMSA.

Relationship between Pulmonary Function Tests and Morphologic Changes in the Lung in Bleomycin-Treated Patients

The transfer factor of the lung for carbon monoxide (TLCO) and the respiratory response to moderate exercise were determined in 16 patients with pulmonary metastasis pretreated with bleomycin who underwent pulmonary partial resection. The results of pulmonary function tests were related to histologic findings. No significant correlation was found between pulmonary morphologic changes and the TLCO: this questions the usefulness of TLCO as a predictive method for detecting subclinical bleomycin pulmonary toxicity. No significant correlation was found between morphologic findings and cumulative dose of bleomycin: this confirms the limit of a dose limitation strategy. In contrast, evaluation of pulmonary response to exercise seemed to improve the sensitivity of monitoring such patients for clinical evidence of latent pulmonary toxicity; however, it seems that critical morphologic changes must occur before pulmonary performance begins to deteriorate.

Mitoxantrone as First-Salvage Chemotherapy in Relapsed Breast Cancer

Mitoxantrone was administered at the dose of 14 mg/m2 i.v. every 3 weeks to 25 consecutive women with measurable progressive disease who relapsed after adjuvant CMF and endocrine therapy. The treatment plan consisted in the delivery of 6 cycles, unless disease progression or severe toxicity occurred. All patients were evaluable for drug response and toxicity. One patient achieved complete remission and 6 partial remission, for a total response rate of 28%. Objective tumor response was observed in all major sites of disease. The median time to achieve remission was 3 months. The median duration of response was 7 months (range, 5–39+), and the median survival for the entire group was 10 months (range, 3–39). Results were influenced only by the duration of diseasefree status from the end of adjuvant CMF chemotherapy. In fact, all tumor responses were documented in woman with free intervals exceeding 1 year (7 of 17 or 41 %). Treatment was generally well tolerated, with 10 patients developing leukopenia at some time during treatment. Only 2 patients received less than 75 % of the projected dose because of granulocytopenia. Complete alopecia occurred in only 2 cases. Three patients developed a fall > 15 % in left ventricular ejection fraction, but no episode of congestive heart failure was observed. We conclude that mitoxantrone is an effective and safe drug which can be utilized in women relapsing after adjuvant CMF.

5-Fuorouracil Cardiotoxicity

Two cases of 5-fluorouracil cardiotoxicity, resulting in one patient in myocardial infarction, are described. A review of the literature confirms that cardiotoxicity is a rare but genuine complication of 5-fluorouracil treatment; the cardiotoxic effect seems to range from mild angina without persistent electrocardiographic changes to severe myocardial infarction. No factors predictive of this complication were identified. The authors therefore feel it is advisable to stop 5-fluorouracil treatment when precordial pain occurs, even if the ECG (after angina) is normal, since angina can in some cases result in myocardial infarction.

Interaction between Doxorubicin and Mitomycin C on Mortality and Myocardial Contractility in Guinea PIG

The present investigations were carried out in guinea pig to ascertain whether mitomycin C has a direct cardiotoxic effect or interacts with doxorubicin-induced cardiotoxicity. I.p. administration of mitomycin C did not modify the survival rate up to 30 days, whereas the combined administration of doxorubicin and mitomycin C significantly decreased the survival time in comparison to the doxorubicin-treated group. On isolated atria, mitomycin C did not cause significant inhibition of the contractile force or an enhancement of the doxorubicin-induced negative inotropic effect. These results do not support the possibility that mitomycin C potentiates the acute cardiotoxic effects produced by doxorubicin.

Relationship between the Effect on Calcium Turnover and Early Cardiotoxicity of Doxorubicin and 4'-EPI-Doxorubicin in Guinea Pig Heart Muscle

Doxorubicin and 4'-epi-doxorubicin, two anthracycline derivatives with different cardiotoxic effects in experimental models, were found to decrease myocardial contractility in isolated guinea pig atria by significantly modifying calcium turnover. This effect seems to be mainly localized on the fast exchanging membrane-bound calcium, while these drugs do not significantly influence the intracellular stores of calcium. 4'-epi-doxorubicin, which induces a less negative inotropic effect than doxorubicin, produces a smaller inhibition of calcium turnover. This supports the hypothesis that the inhibition of calcium turnover and particularly of the fast exchanging calcium compartment is a general mechanism involved in the early anthracycline-induced cardiotoxicity.

Evaluation of Doxorubicin Cardiotoxicity in Patients Treated Intermittently with Beta-Methyldigoxin

Twenty-one patients with various advanced neoplasms were treated with 60 to 75 mg/m2 of doxorubicin every 3 to 4 weeks and monitored by ECG and systolic time intervals (PEP/LVET) with the aim to establish whether a pretreatment with beta-methyldigoxin, administered intermittently, could prevent doxorubicin-induced cardiotoxicity. It was found that until patients received digitalis pretreatment the PEP/LVET ratio did not change significantly from mean basal values even after the highest cumulative dosages of doxorubicin. However, after interruption of the therapy with both drugs, PEP/LVET increased reaching a value not significantly different from that observed in a comparable group of patients treated only with doxorubicin. Moreover, of 9 patients who reached the cumulative limiting dose, 2 developed congestive heart failure. These results question the possibility that digitalis administered according to an intermittent treatment scheme may prevent doxorubicin cardiomyopathy.

A Phase I Study of Recombinant Interleukin 2 in Melanoma Patients. Toxicity and Clinical Effects

Toxicity and clinical effects of a new brand of recombinant interleukin 2 (rIL2, Bioleukin™, Biogen, Geneva) were evaluated by a phase I study in 12 patients with stage III melanoma. Escalating doses from 100 μg/m2 to 800 μg/m2 were administered thrice a day with bolus injections given via a peripheral venous catheter for up to a maximum of 7 days. All patients showed malaise, fever and chills and mild gastrointestinal side effects. A modest electrolyte imbalance (hypocalcemia and hypokalemia) was detected in all 12 patients. Renal toxicity as judged by serum creatinine was not observed, and hepatic toxicity was moderate with the possible exception of one patient who had an unclear previous history of liver dysfunction. Mild, transient leukopenia was found in several patients, whereas thrombocytopenia developed in 4 patients; no anemia was observed. Cutaneous rash was seen in half of the patients treated. Fluid retention was minimal, with a weight gain associated to treatment that never exceeded 10% of pretreatment body weight. Electrocardiographic alterations developed in 2 patients in the form of ventricular and supraventricular extrasystoles. In 2 patients given the highest dose of rIL2, a significant reduction in transfer lung factor for carbon monoxide was seen, indicating alterations in pulmonary functions. Other dose-related toxicities were thrombocytopenia and malaise. All side effects disappeared 2-3 days after the end of rIL2 administration. No major responses were seen in association with the 4-8 days of treatment given in this study.

Genetic Heterogeneity of Variable Number Tandem Repeats in Thymidylate Synthase Gene in Colorectal Cancer Patients

Purpose

To analyze the genetic variability in a variable number of tandem repeats (VNTR) in the thymidylate synthase (TS) enhancer promoter region and assess the influence of functional alterations in mismatch repair genes by analyzing constitutional and tumoral DNA from patients with colorectal adenocarcinoma with a high microsatellite instability (MSI-H) or microsatellite stability (MSS) status.

Patients and methods

Patients who underwent surgery for colorectal adenocarcinoma were selected from the colorectal database of our institute and, on the basis of MSI status, assigned to a study group and a control group: group A, MSI-H; group B, MSS. Microsatellite status was investigated using the Bethesda recommended panel (BAT-26, BAT-25, D2S123, D5S346, D17S250). In MSI-H patients an additional analysis was made of the microsatellite loci D18S61 and D18S58, both mapping in the region containing the TS gene (18p11.2–11.32). Based on the number of altered microsatellites (≥2, 1, or 0), tumors were considered as having high (MSI-H) or low (MSI-L) instability or microsatellite stability (MSS), respectively. Genotyping for thymidylate synthase promoter polymorphism was carried out on constitutional and tumor DNA of each patient by PCR amplification of the polymorphic region.

Results

MSI-H was found in 55 patients (group A) and MSS in 50 patients (group B). In none of the MSI-H patients was microsatellite instability found in the additional D18S61 and D18S58 loci. In five group A and ten group B cases the analysis was not performed because constitutional DNA and/or tumoral DNA were not amplifiable. Homozygotes for the triple repeat variant (3R/3R) displayed only the large PCR product, homozygotes for the double repeat variant (2R/2R) displayed only the smaller PCR product, while heterozygotes (2R/3R) displayed both the larger and smaller PCR products. In 3/50 (6%) group A patients and 5/40 (12%) group B patients repeat variations were found in tumoral DNA.

Conclusion

Our findings demonstrate that there is genetic homogeneity between constitutional and tumoral DNA but do not support the hypothesis that mismatch repair genes are involved in VNTR recombinant events in TS gene variability.

Study of the correlation between sensing performance and surface morphology of inkjet-printed aqueous graphene-based chemiresistors for NO2 detection

The extremely high sensitivity to the external environment and the high specific surface area, as well as the absence of bulk phenomena that could interfere with the response signal, make graphene highly attractive for the applications in the field of sensing. Among the various methods for producing graphene over large areas, liquid phase exfoliation (LPE) appears to be very promising, especially if combined with inkjet printing (IJP), which offers several advantages, including the selective and controlled deposition of small ink volumes and the versatility of the exploitable inks and substrates. Herein we present a feasibility study of chemiresistive gas sensors inkjet-printed onto paper substrates, in which a LPE graphene suspension dispersed in a water/isopropanol (H₂O/IPA) mixture is used as sensing ink. The device performances, in terms of relative conductance variations, upon exposure to NO₂ at standard ambient temperature and pressure, are analysed. In addition, we examine the effect of the substrate morphology and, more specifically, of the ink/substrate interaction on the device performances, by comparing the response of different chemiresistors fabricated by dispensing the same suspension also onto Al₂O₃ and Si/SiO₂ substrates and carrying out a supportive atomic force microscopy analysis. The results prove the possibility to produce sensor devices by means of a wholly environmentally friendly, low-cost process that meets the requests coming from the increasing field of paper-based electronics and paving the way towards a flexible, green-by-design mass production.

The course of language functions after temporal lobe epilepsy surgery: a prospective study

BACKGROUND AND PURPOSE

Anterior temporal lobectomy (ATL) within the language-dominant hemisphere can impair naming. This prospective study examined the pre-operative to post-operative course of different language components, clarifying which changes are relevant within the short-term and long-term outcome of language.

METHODS

Patients with drug-resistant temporal lobe epilepsy (TLE) were evaluated using the Token, Boston Naming and Word Fluency tests assessing sentence comprehension and word-finding on visual, semantic or phonemic cues.

RESULTS

A total of 106 patients were evaluated before and 6 months, 1 and 2 years after ATL; 60 patients were also evaluated after 5 years and 38 controls were assessed at baseline. Seizure outcome was comparable between the left and right TLE patients. Before surgery, naming and word fluency were impaired in the left and right TLE patients, whereas sentence comprehension was normal. After left or right ATL, word fluency progressively improved, naming showed early worsening and late improvement after left ATL and progressive improvement after right ATL, and sentence comprehension did not change. At the 5-year follow-up, naming improvement was clinically significant in 31% and 71% of the left and right TLE patients, respectively. Pre-operative naming, ATL laterality, schooling, and post-operative seizure frequency and number of antiepileptic drugs predicted post-operative naming. Pre-operative word fluency and schooling predicted post-operative word fluency.

CONCLUSIONS

Left or right TLE can impair word-finding but not sentence comprehension. After ATL, word-finding may improve for a long time, depending on TLE laterality, seizure control and mental reserve. These findings may clarify prognosis prior to treatment.

Graded-size microlens array by the pyro-electrohydrodynamic continuous printing method

In the present work, the pyro-electrohydrodynamic technique was used for the realization of tunable-size microlens arrays. Poly(methyl methacrylate) dissolved in different solvent mixtures was used as the polymeric material for the realization of the microstructures. By controlling the experimental parameters and in particular, the volume of the drop reservoir, graded-size square arrays of tens of microlenses with focal length in the range 1.5-3 mm were produced. Moreover, the optical quality and geometrical features were investigated by profilometric and interferometric analysis.

Preoperative language lateralization in temporal lobe epilepsy (TLE) predicts peri-ictal, pre- and post-operative language performance: An fMRI study

In patients with temporal lobe epilepsy (TLE), assessment of language lateralization is important as anterior temporal lobectomy may lead to language impairments. Despite the widespread use of fMRI, evidence of its usefulness in predicting postsurgical language performance is scant. We investigated whether preoperative functional lateralization is related to the preoperative language performance, peri-ictal aphasia, and can predict language outcome one year post-surgery. We studied a total of 72 TLE patients (42 left, 30 right), by using three fMRI tasks: Naming, Verb Generation and Fluency. Functional lateralization indices were analyzed with neuropsychological scores and presence of peri-ictal aphasia. The key findings are:1)Both left and right TLE patients show decreased left lateralization compared to controls.2)Lateralization correlates with language performance before surgery. In left TLE, decreased left lateralization correlates with better fluency performance. In right TLE, increased left lateralization during the Naming task correlates with better naming.3)Left lateralization correlates with peri-ictal aphasia in left TLE patients.4)Lateralization correlates with language performance after surgery. In a subgroup of left TLE who underwent surgery (17 left), decreased left lateralization is predictive of better naming performance at 6 and 12 months after surgery. The present study highlights the clinical relevance of fMRI language lateralization in TLE, especially to predict language outcome one year post-surgery. We also underline the importance of using fMRI tasks eliciting frontal and anterior temporal activations, when studying left and right TLE patients.

Perineural fat grafting in the treatment of painful end-neuromas of the upper limb: a pilot study

The purpose of this study was to evaluate the effectiveness and middle-term durability of the results achieved with perineural fat grafting of painful neuromas of the upper limb. We retrospectively analysed eight patients, affected by eight neuromas, treated by neuroma excision and fat grafting around the proximal nerve stump. Clinical parameters, the disabilities of the arm shoulder and hand score, and the visual analogue scale were recorded at 2, 6 and 12 months after surgery. A reduction of 23.2% was observed in the mean disabilities of the arm shoulder and hand scores at 12 months. The spontaneous baseline visual analogue scale score showed a mean improvement of 22% at 12 months, although not this was not statistically significant. Perineural fat grafting is a quick and useful procedure and could represent a useful primary operation in the treatment of pain syndromes of neuropatic origin.

Printing of polymer microlenses by a pyroelectrohydrodynamic dispensing approach

The investigation of a method for fabricating microlenses by a nozzle-free inkjet printing approach is reported. The new method, based on a pyroelectrohydrodynamic mechanism, is also able to dispense viscous liquids and to draw liquid phase drops directly from the reservoir. Specifically, by dispensing optical grade polymer dissolved in different solvent mixtures, microlenses were printed with a pattern defined directly through this deposition method. The reliability of the microlenses and the tunability of their focal properties were demonstrated through profilometric and inteferometric analyses.

Proximal interphalangeal joint arthroplasty with silicone implants (NeuFlex) by a lateral approach: a series of 51 cases

The aim of this study is to assess outcomes of a lateral surgical approach for proximal interphalangeal joint arthroplasty with NeuFlex(®) silicone implants for primary degenerative osteoarthritis. We reviewed 51 arthroplasties performed on 43 patients. The mean follow up period was 36 months (range 18-42). The average preoperative range of motion (ROM) was 38°. The average postoperative ROM was 63°. In 21/51 (41%) cases, there was an average axial deviation of 17° (range 10-30°). VAS and Quick DASH scores improved. In 5/51 (10%) cases, further surgery was required. Our lateral approach seems to be effective and minimally invasive, providing adequate exposure. Contralateral incision and contralateral ligament reinforcement should be performed, whenever necessary, to improve lateral stability.

Shelf life prediction of fresh Italian pork sausage modified atmosphere packed

The shelf life of fresh Italian pork sausages packed in modified atmosphere was studied. Samples were packed using different levels of oxygen (high and low) with different levels of carbon dioxide (high-low) in the atmospheres headspace and were stored at 4 °C for 9 days. Microbial, physiochemical and sensory parameters were analyzed during storage. A consumer test was performed to determine the critical acceptability levels. Sensory data were mathematically modelled to estimate product shelf life. A first-order kinetic model and a Weibull-type model aptly described, respectively, the changes in fresh pork sausage odor and color over storage time. These models may be used to predict the sensory shelf life of fresh pork sausage. Results showed that 20% O(2) and 70% CO(2) extend fresh pork sausage shelf life to 9 days at 4 °C. The microbial quality of the samples at the critical sensory level of acceptability was within the range of microbial acceptability.

Isolation of Saccharomyces cerevisiae strains from different food matrices and their preliminary selection for a potential use as probiotics

AIMS

To isolate acid- and bile-resistant Saccharomyces cerevisiae strains directly from food samples and to preliminarily select them on the basis of fundamental probiotic properties.

METHODS AND RESULTS

A rapid screening method allowed the isolation and selection of 20 acid- and bile-resistant yeasts from foods, avoiding time-consuming isolation steps. The strains were characterized for their specific survival in simulated gastric juice and in intestinal fluid after pre-exposure at low pH. Ten isolates demonstrated a satisfactory survival percentage in intestinal fluid after pre-exposure to gastric juice and appreciable lipolytic and proteolytic properties, as demonstrated by the API-ZYM test. By using molecular methods five strains were identified as Saccharomyces cerevisiae, three as Candida spp., one as Candida pararugosa and one as Pichia spp. The Saccharomyces cerevisiae strains showed considerable probiotic properties, achieving a 80< % <90 survival through the simulated gastrointestinal tract, as well as interesting glucosidase activities.

CONCLUSIONS

The research represents an efficient strategy to select and identify Saccharomyces cerevisiae strains with desirable acid and bile resistances.

SIGNIFICANCE AND IMPACT OF THE STUDY

This paper reports the direct selection of potentially probiotic yeasts from foods and provides indications about the ability of Saccharomyces cerevisiae strains to survive conditions simulating the human gastrointestinal tract.

Engagement of the medial temporal lobe in verbal and nonverbal memory: assessment with functional MR imaging in healthy subjects

BACKGROUND AND PURPOSE

The hippocampus and parahippocampal gyrus have a central role in the acquisition of new memories. Although functional MR imaging (fMRI) can provide information on the functional status of these brain regions, it has not reached widespread use in the presurgical assessment of patients undergoing temporal lobectomy. We aimed to evaluate whether simple memory-encoding paradigms could be used to elicit robust activations in the hippocampus and parahippocampal gyrus and to determine the lateralization of verbal and nonverbal memory. We also studied the relative contribution of the anterior and posterior portions of these structures.

MATERIALS AND METHODS

We conducted this study on 16 healthy subjects by performing event-related fMRI using 3 memory encoding tasks with words, objects, and faces. In addition to a second-level group analysis, region-of-interest (ROI)-based measurements of the signal intensity percent change and of the percentage of activated voxels, determined at 2 thresholds, were performed. ROIs were drawn on the hippocampus and parahippocampal gyrus, divided into anterior and posterior segments.

RESULTS

We found overall left-lateralized activation with words, bilateral activation with objects, and right-lateralized activation with faces. In particular, significant hippocampal activations were observed with all 3 categories of stimuli, and the head of the hippocampus was generally more engaged than its body and tail. Data on the signal intensity percent change and percentage of activated voxels are provided for each ROI and task.

CONCLUSIONS

The combination of these 3 undemanding memory tasks could be considered, following appropriate validation, as a tool to assess the functional status of the medial temporal lobe in clinical settings.

Cardiopulmonary response to exercise in patients with different degrees of lung toxicity after radio-chemotherapy for Hodgkin's disease

The combination of mediastinal radiotherapy (RT) and polychemotherapy (CT) regimens can produce late toxic pulmonary and cardiac effects which often remain at the subclinical level. The aim of the present study was to investigate the cardiopulmonary response to exercise in this kind of patient. Therefore, 126 patients suffering from Hodgkin's disease were investigated after a follow-up of at least 5 years from the completion of the combined treatment. Sixty-two patients had been submitted to ABVD (doxorubicin, bleomycin, vinblastine, dacarbazine)-RT, 40 to ABVD-MOPP (mechloretamine, vincristine, procarbazine, prednisone)-RT and 24 to VEBEP (vincristine, epidoxorubicin, bleomycin, cyclophosphamide, etoposide, prednisone)-RT. The patients were divided into three groups on the basis of respiratory function: group 1 (67 patients), normal spirometry and lung transfer function for carbon monoxide (DLCO); group 2 (52 patients), normal spirometry and DLCO less than 80% of predicted; and group 3 (7 patients), total lung capacity and DLCO less than 80% of predicted. The patients were submitted to respiratory function evaluation and 2D-echocardiography before exercise, and to the determination of cardiac output by the acetylene rebreathing method before and during symptom-limited exercise on a cycloergometer using an incremental protocol. The patients of group 3 and to a lesser extent the patients of group 2 showed, in comparison to patients of group 1, a lower tolerance to exercise, a lower oxygen consumption, a higher respiratory rate, a lower O2 pulse and a lower cardiac output per oxygen uptake. These data indicated an abnormal exercise physiology in the patients with persistent pulmonary impairment, especially when the reduction of DLCO was associated with a decrease of total lung capacity. The lower exercise capacity seems to be due to a combination of decreased cardiac performance and an impairment of gas diffusion capacity.

Correlation between complication rate and perioperative risk-factors in superior pedicle reduction mammaplasty: our experience in 127 patients

Reduction mammaplasty, one of the most common plastic surgery procedures, has been shown to confer significant sustained health benefits for patients with symptomatic breast enlargement providing a remedy for back, neck, and shoulder pain. Unfortunately, operations of breast reduction may lead to patient dissatisfaction for poor aesthetic outcome due to complications. Complications, including infection, hematoma, seroma, dehiscence, fat necrosis, and skin loss, may occur in as many as 50% of patients. Unacceptable scarring has also been reported. Complication data revealed several significant features, although there isn't much objective evidence to support that. Over the period 2004-2008, 127 consecutive patients were admitted for breast reduction surgery, data have been analyzed retrospectively to determine whether any correlation could be found between complication rate and perioperative risk-factors using a multifactorial ANOVA F-test. Analysis of variables associated with complications showed that, after adjusting for age and smoking status, only BMI was associated with any complication (p < 0.05). By power analysis, based on a comparison of three proportions, a power of 92% with a significance level of 0.05 was found for the hypothesis that the outcomes of the procedures depends on BMI.