Combining germline, tissue and liquid biopsy analysis by comprehensive genomic profiling to improve the yield of actionable variants in a real-world cancer cohort.

BACKGROUND: Comprehensive next-generation sequencing is widely used for precision oncology and precision prevention approaches. We aimed to determine the yield of actionable gene variants, the capacity to uncover hereditary predisposition and liquid biopsy appropriateness instead of, or in addition to, tumor tissue analysis, in a real-world cohort of cancer patients, who may benefit the most from comprehensive genomic profiling. METHODS: Seventy-eight matched germline/tumor tissue/liquid biopsy DNA and RNA samples were profiled using the Hereditary Cancer Panel (germline) and the TruSight Oncology 500 panel (tumor tissue/cfDNA) from 23 patients consecutively enrolled at our center according to at least one of the following criteria: no available therapeutic options; long responding patients potentially fit for other therapies; rare tumor; suspected hereditary cancer; primary cancer with high metastatic potential; tumor of unknown primary origin. Variants were annotated for OncoKB and AMP/ASCO/CAP classification. RESULTS: The overall yield of actionable somatic and germline variants was 57% (13/23 patients), and 43.5%, excluding variants previously identified by somatic or germline routine testing. The accuracy of tumor/cfDNA germline-focused analysis was demonstrated by overlapping results of germline testing. Five germline variants in BRCA1, VHL, CHEK1, ATM genes would have been missed without extended genomic profiling. A previously undetected BRAF p.V600E mutation was emblematic of the clinical utility of this approach in a patient with a liver undifferentiated embryonal sarcoma responsive to BRAF/MEK inhibition. CONCLUSIONS: Our study confirms the clinical relevance of performing extended parallel tumor DNA and cfDNA testing to broaden therapeutic options, to longitudinally monitor cfDNA during patient treatment, and to uncover possible hereditary predisposition following tumor sequencing in patient care.

Preoperative infection risk assessment in hip arthroplasty a matched-pair study of the reliability of 3 validated risk scales.

Peri-prosthetic infection (PJI) represents one of the most devastating complications of total hip arthroplasty (THA). The aim of this study is to assess the reliability of different PJI risk assessment scales between two matched pairs of THA groups. This study included 37 patients with PJI following THA performed between 2012 and 2020 (Group A). Each patient in this group was matched, based on sex, age, and follow-up duration, with a control patient who underwent the same surgical procedure without any septic complications (Group B) during the same period. Each patient's assessment included the American Society of Anesthesiologists (ASA) score and a retrospective evaluation using three different preoperative, specific PJI risk assessment scales: the International Consensus Meeting (ICM) Preoperative Risk Calculator for PJI, the Mayo PJI Risk Score, and the KLIC-score. The two groups were statistically compared using descriptive analyses, both for binomial data and numerical variables. Statistically significant higher values were observed in the preoperative ASA score and surgical time in Group A. Statistically different higher scores were determined only with the ICM risk calculator score in Group A. No significant differences were found using the KLIC score and Mayo score between the two groups. We emphasize the reliability of the ASA score as a nonspecific preoperative assessment scale for PJI. The ICM risk calculator was confirmed as a reliable, specific preoperative assessment scale for PJI, suggesting its routine adoption in THA clinical practice.

Joint Determination of Reactor Antineutrino Spectra from

A joint determination of the reactor antineutrino spectra resulting from the fission of ^{235}U and ^{239}Pu has been carried out by the Daya Bay and PROSPECT Collaborations. This Letter reports the level of consistency of ^{235}U spectrum measurements from the two experiments and presents new results from a joint analysis of both data sets. The measurements are found to be consistent. The combined analysis reduces the degeneracy between the dominant ^{235}U and ^{239}Pu isotopes and improves the uncertainty of the ^{235}U spectral shape to about 3%. The ^{235}U and ^{239}Pu antineutrino energy spectra are unfolded from the jointly deconvolved reactor spectra using the Wiener-SVD unfolding method, providing a data-based reference for other reactor antineutrino experiments and other applications. This is the first measurement of the ^{235}U and ^{239}Pu spectra based on the combination of experiments at low- and highly enriched uranium reactors.

Efficacy of bio- and neurofeedback for depression: a meta-analysis.

BACKGROUND: For many years, biofeedback and neurofeedback have been implemented in the treatment of depression. However, the effectiveness of these techniques on depressive symptomatology is still controversial. Hence, we conducted a meta-analysis of studies extracted from PubMed, Scopus, Web of Science and Embase. METHODS: Two different strings were considered for each of the two objectives of the study: A first group comprising studies patients with major depressive disorder (MDD) and a second group including studies targeting depressive symptomatology reduction in other mental or medical conditions. RESULTS: In the first group of studies including patients with MDD, the within-group analyses yielded an effect size of Hedges' g = 0.717, while the between-group analysis an effect size of Hedges' g = 1.050. Moderator analyses indicate that treatment efficacy is only significant when accounting for experimental design, in favor of randomized controlled trials (RCTs) in comparison to non RCTs, whereas the type of neurofeedback, trial design, year of publication, number of sessions, age, sex and quality of study did not influence treatment efficacy. In the second group of studies, a small but significant effect between groups was found (Hedges' g = 0.303) in favor of bio- and neurofeedback against control groups. Moderator analyses revealed that treatment efficacy was not moderated by any of the sociodemographic and clinical variables. CONCLUSIONS: Heart rate variability (HRV) biofeedback and neurofeedback are associated with a reduction in self-reported depression. Despite the fact that the field has still a large room for improvement in terms of research quality, the results presented in this study suggests that both modalities may become relevant complementary strategies for the treatment of MDD and depressive symptomatology in the coming years.

Cardiac sources of cerebral embolism in people with migraine.

BACKGROUND AND PURPOSE: Whether the reported association between migraine with aura (MA) and cardioembolic stroke may be explained by a higher rate of atrial fibrillation (AF) or by other potential cardiac sources of cerebral embolism remains to be determined. METHODS: In the setting of a single centre cohort study of consecutive patients with acute brain ischaemia stratified by migraine status, the association between AF as well as patent foramen ovale (PFO) and migraine was explored. RESULTS: In all, 1738 patients (1017 [58.5%] men, mean age 67.9 ± 14.9 years) qualified for the analysis. Aging was inversely associated with migraine, whilst women had a >3-fold increased disease risk (odds ratio [OR] 3.82, 95% confidence interval [CI] 2.58-5.66). No association between AF and history of migraine or its pathogenic subtypes was detected. Conversely, migraine was associated with PFO, both in the entire cohort (OR 1.84, 95% CI 1.07-3.16) and in patients aged ≤55 years (OR 2.21, 95% CI 1.16-4.22). This association was significant for MA (OR 2.92, 95% CI 1.32-6.45 in the entire cohort; OR 2.92, 95% CI 1.15-7.41 in patients aged ≤55 years) and in women (OR 8.23, 95% CI 2.06-32.77), but not for migraine without aura. CONCLUSIONS: In patients with brain ischaemia migraine is not associated with AF. Conversely, there is a probable relation between migraine, especially MA, and PFO in patients who are younger and have a more favourable vascular risk factor profile, and in women.

Unilateral multifocal choroiditis following EBV-positive mononucleosis responsive to immunosuppression: a case report.

BACKGROUND: Multifocal choroiditis (MFC) is a relatively uncommon bilateral inflammatory chorioretinopathy affecting Caucasian young women with myopia. We present images from a case of completely unilateral multifocal choroiditis following EBV-positive mononucleosis that demonstrated a dramatic clinical response to immunosuppression. CASE PRESENTATION: A 20-year-old woman with bilateral high myopia (-6D) and a documented normal prior retinal examination presented with visual loss in the right eye 2 months following confirmed Epstein-Barr virus (EBV) positive mononucleosis. Ophthalmoscopic examination showed completely unilateral placoid lesions of variable age. The left eye was unaffected. Fluorescein angiography revealed active leakage, especially in the parafovea. Spectral domain optical coherence tomography (SD-OCT) demonstrated sub-retinal pigment epithelial nodular deposits, some of which were confluent with overlying intra-retinal fluid and indistinct margins. Upon treatment with the immunosuppressant azathioprine there was significant resolution of the lesions in her right eye along with improvement in vision. CONCLUSION: This is a rare case of completely unilateral MFC following an episode of EBV positive mononucleosis that showed a dramatic response to immunosuppression.

Gastrointestinal stromal tumors and second primary malignancies: a retrospective monocentric analysis.

In the post-Imatinib era, the median survival of patients diagnosed with GIST has reached almost 5 years. Prolonging GIST-specific survival, GIST patients have an increased incidence of secondary neoplasia. Data on the prognostic impact of second tumors in GIST patients are very poor with few and small retrospective analyses available in the literature. We conducted a retrospective monocentric analysis on 145 patients diagnosed with GIST between April 2001 and October 2018. Kaplan-Meier and Cox hazard methods were used for survival analysis. A total of 154 GIST patients were included and 31 patients of them (21%) were diagnosed with at least one additional malignancy. The most common second tumors associated with GIST were gastrointestinal tumors. GIST patients with additional malignancies showed to have lower size (>5 cm: 35% vs 45%; p=0.75), higher mitotic rate (>5/50 HPFs: 42% vs 29%; p=0.24), higher presence of c-KIT mutation (85% vs 69%), a lower presence of PDGFRα mutation (8% vs 17%; p=0.05) and shorter survival (mOS: 9.6 vs 15.5 years; p=0.30). In conclusion, our study did not find any significant correlation between clinicopathological characteristics and the development of a second tumor in GIST patients. Further analyses and strict follow up protocols are needed in order to early diagnose and promptly treat a second primary tumor in the GIST population.

Global Health Professions Student Survey among Healthcare students: a cross sectional study.

BACKGROUND: Healthcare professionals have the potential to influence patients' smoking status; however, their smoking habits and their opinions about tobacco use can hamper an effective counselling about smoking to patients. METHODS: A cross-sectional survey was carried out among healthcare students from the Sapienza University of Rome using a previously validated Italian version of Global Health Professions Student Survey (GHPSS) online questionnaire. RESULTS: Overall, 349 students filled out the online survey: 158 (45%) were current smokers and 191 (55%) were nonsmokers. Nurses students had the highest percentage of smokers (55%). Healthcare students declared they had learned about the health consequences about tobacco use during their academic course (90%), however, only 24% received specific training on smoking cessation. CONCLUSIONS: It is necessary to implement a smoking cessation course in the undergraduate curriculum in order to train healthcare professionals to provide patients an effective counselling against smoking.

Epidemiological, clinical and pathological characteristics of gastric neoplasms in the province of Cremona: the experience of the first population-based specialized gastric cancer registry in Italy.

BACKGROUND: The gastric cancer incidence rate differs widely across geographical areas. In Italy, in the province of Cremona the incidence is high, compared to the national situation. For this reason a specialized population-based registry was set up. METHODS: The collection encompasses all gastric cancers diagnosed in the three districts of the province since January 1, 2010. The main data sources were the pathological and Hospital Discharge Records and patient clinical charts. Only diagnoses of primary gastric cancer were considered. For each case the following variables were registered: personal data, medical history and symptoms at diagnosis; imaging assessments performed, details on surgery and other treatments received; genetic background and biomolecular characteristics; social and environmental factors. RESULTS: As of November 2017, 1087 cases were collected; of which 876, diagnosed up to December 2015, were analyzed. Male/female ratio was 1.4. The European Age-standardized Incidence Rate was 41.4 for males and 28.3 for females as compared to a national average of 33.3 and 17.0 respectively. Median age at diagnosis was 73 for male and 78 for female. Helicobacter Pylori infection was present in fewer than 20% of cases. HER-2 gene was amplified in about 25% of cases. Primary tumour location was the gastro-esophageal junction or cardia in 17.5% in males and 8.3% in females. The majority of cases (58.3%) were diagnosed at an advanced stage and overall only 41.2% underwent surgery. Median overall survival was 14.8 months for men and 18.5 for women. Age standardized 5-year relative survival was 31.4% for men and 40.5% for females. Neoadjuvant treatment was performed in fewer than 10% of patients who underwent surgery, and the rate of postoperative therapy adherence was low. DISCUSSION: This study shows a high gastric cancer incidence in the province of Cremona, with a geographical spread across different districts. Moreover, a high percentage of gastric cancers were detected at an advanced stage of disease and a low rate of 5-year relative survival was registered. Based on these findings, effective preventive interventional health strategies and screening procedures need to be implemented to reduce the impact of this pathology in this geographical area.

The revolution of personalized psychiatry: will technology make it happen sooner?

Personalized medicine (PM) aims to establish a new approach in clinical decision-making, based upon a patient's individual profile in order to tailor treatment to each patient's characteristics. Although this has become a focus of the discussion also in the psychiatric field, with evidence of its high potential coming from several proof-of-concept studies, nearly no tools have been developed by now that are ready to be applied in clinical practice. In this paper, we discuss recent technological advances that can make a shift toward a clinical application of the PM paradigm. We focus specifically on those technologies that allow both the collection of massive as much as real-time data, i.e., electronic medical records and smart wearable devices, and to achieve relevant predictions using these data, i.e. the application of machine learning techniques.

Evolution of the Reactor Antineutrino Flux and Spectrum at Daya Bay.

The Daya Bay experiment has observed correlations between reactor core fuel evolution and changes in the reactor antineutrino flux and energy spectrum. Four antineutrino detectors in two experimental halls were used to identify 2.2 million inverse beta decays (IBDs) over 1230 days spanning multiple fuel cycles for each of six 2.9 GW_{th} reactor cores at the Daya Bay and Ling Ao nuclear power plants. Using detector data spanning effective ^{239}Pu fission fractions F_{239} from 0.25 to 0.35, Daya Bay measures an average IBD yield σ[over ¯]_{f} of (5.90±0.13)×10^{-43} cm^{2}/fission and a fuel-dependent variation in the IBD yield, dσ_{f}/dF_{239}, of (-1.86±0.18)×10^{-43} cm^{2}/fission. This observation rejects the hypothesis of a constant antineutrino flux as a function of the ^{239}Pu fission fraction at 10 standard deviations. The variation in IBD yield is found to be energy dependent, rejecting the hypothesis of a constant antineutrino energy spectrum at 5.1 standard deviations. While measurements of the evolution in the IBD spectrum show general agreement with predictions from recent reactor models, the measured evolution in total IBD yield disagrees with recent predictions at 3.1σ. This discrepancy indicates that an overall deficit in the measured flux with respect to predictions does not result from equal fractional deficits from the primary fission isotopes ^{235}U, ^{239}Pu, ^{238}U, and ^{241}Pu. Based on measured IBD yield variations, yields of (6.17±0.17) and (4.27±0.26)×10^{-43} cm^{2}/fission have been determined for the two dominant fission parent isotopes ^{235}U and ^{239}Pu. A 7.8% discrepancy between the observed and predicted ^{235}U yields suggests that this isotope may be the primary contributor to the reactor antineutrino anomaly.

Improved Search for a Light Sterile Neutrino with the Full Configuration of the Daya Bay Experiment.

This Letter reports an improved search for light sterile neutrino mixing in the electron antineutrino disappearance channel with the full configuration of the Daya Bay Reactor Neutrino Experiment. With an additional 404 days of data collected in eight antineutrino detectors, this search benefits from 3.6 times the statistics available to the previous publication, as well as from improvements in energy calibration and background reduction. A relative comparison of the rate and energy spectrum of reactor antineutrinos in the three experimental halls yields no evidence of sterile neutrino mixing in the 2×10^{-4}≲|Δm_{41}^{2}|≲0.3 eV^{2} mass range. The resulting limits on sin^{2}2θ_{14} are improved by approx imately a factor of 2 over previous results and constitute the most stringent constraints to date in the |Δm_{41}^{2}|≲0.2 eV^{2} region.

Measurement of the Reactor Antineutrino Flux and Spectrum at Daya Bay.

This Letter reports a measurement of the flux and energy spectrum of electron antineutrinos from six 2.9 GWth nuclear reactors with six detectors deployed in two near (effective baselines 512 and 561 m) and one far (1579 m) underground experimental halls in the Daya Bay experiment. Using 217 days of data, 296 721 and 41 589 inverse ß decay (IBD) candidates were detected in the near and far halls, respectively. The measured IBD yield is (1.55±0.04) ×10(-18) cm(2) GW(-1) day(-1) or (5.92±0.14) ×10(-43) cm(2) fission(-1). This flux measurement is consistent with previous short-baseline reactor antineutrino experiments and is 0.946±0.022 (0.991±0.023) relative to the flux predicted with the Huber-Mueller (ILL-Vogel) fissile antineutrino model. The measured IBD positron energy spectrum deviates from both spectral predictions by more than 2σ over the full energy range with a local significance of up to ∼4σ between 4-6 MeV. A reactor antineutrino spectrum of IBD reactions is extracted from the measured positron energy spectrum for model-independent predictions.

Detection, identification, and typing of Listeria species from baled silages fed to dairy cows.

Anaerobiosis, critical for successful ensilage, constitutes a challenge in baled silages. The loss of complete anaerobiosis causes aerobic deterioration and silages undergo dry matter and nutrient losses, pathogen growth, and mycotoxin production. Silage may represent an ideal substrate for Listeria monocytogenes, a pathogen of primary concern in several cheeses. The aim of this research was to investigate the occurrence of Listeria in baled silage fed to cows producing milk for a protected designation of origin cheese, and to characterize isolates by repetitive sequence-based PCR. Listeria spp. were detected in 21 silages and L. monocytogenes in 6 out of 80 of the analyzed silages; 67% of positives were found in molded zones. Results of the PCR typing showed genotypic homogeneity: 72.9 and 78.8% similarity between strains of Listeria spp. (n=56) and L. monocytogenes (n=24), respectively. Identical profiles were recovered in molded and nonmolded areas, indicating that contamination may have occurred during production. The application of PCR allowed the unambiguous identification of Listeria isolated from baled silages, and repetitive sequence-based PCR allowed a rapid and effective typing of isolates. Results disclose the potential of the systematic typing of Listeria in primary production, which is needed for the understanding of its transmission pathways.

Effects of ecologically relevant concentrations of cadmium in a freshwater fish.

Sub-chronic effects of ecologically relevant concentrations of cadmium (Cd) were evaluated in the catfish Rhamdia quelen. The fish were exposed to Cd (0, 0.1, 1, 10 and 100µgL(-1)) for 15 days. Bioconcentration was observed in the liver of fish exposed to 10 and 100µgL(-1) of cadmium. The liver glutathione S-transferase activity decreased at 0.1 and 1µgL(-1) and increased at 100µgL(-1) and lipoperoxidation increased in all tested concentrations. Fish exposed to 0.1, 1 and 100µgL(-1) Cd presented increase in hepatic lesion index. In the kidney, the catalase activity and LPO reduced in all exposed groups. The gluthatione peroxidase, etoxiresorufin-O-deethylase activities and metallothionein increased at the highest concentration of Cd, but the level of reduced glutathione decreased. The genotoxicity was observed at 0.1 and 100µgL(-1). Neurotoxicity was not observed. The results showed that low concentrations (range of µgL(-1)) of Cd caused hepato-, nephro- and hematological alterations in this freshwater fish species.

New measurement of antineutrino oscillation with the full detector configuration at Daya Bay.

We report a new measurement of electron antineutrino disappearance using the fully constructed Daya Bay Reactor Neutrino Experiment. The final two of eight antineutrino detectors were installed in the summer of 2012. Including the 404 days of data collected from October 2012 to November 2013 resulted in a total exposure of 6.9×10^{5} GW_{th} ton days, a 3.6 times increase over our previous results. Improvements in energy calibration limited variations between detectors to 0.2%. Removal of six ^{241}Am-^{13}C radioactive calibration sources reduced the background by a factor of 2 for the detectors in the experimental hall furthest from the reactors. Direct prediction of the antineutrino signal in the far detectors based on the measurements in the near detectors explicitly minimized the dependence of the measurement on models of reactor antineutrino emission. The uncertainties in our estimates of sin^{2}2θ_{13} and |Δm_{ee}^{2}| were halved as a result of these improvements. An analysis of the relative antineutrino rates and energy spectra between detectors gave sin^{2}2θ_{13}=0.084±0.005 and |Δm_{ee}^{2}|=(2.42±0.11)×10^{-3} eV^{2} in the three-neutrino framework.

Probing the factor structure of metabolic syndrome in Sardinian genetic isolates.

BACKGROUND AND AIMS: Owing to the multiplicity of the key components of metabolic syndrome (MetS), its diagnosis is very complex. The lack of a unique definition is responsible for the prevalence variability observed among studies; therefore, a definition based on continuous variables was recommended. The aim of this study was to compare competing models of the MetS factor structure for selecting the one that explains the best clustering pattern and to propose an algorithm for computing MetS as a continuous variable. METHODS AND RESULTS: Data were from isolated Sardinian populations (n = 8102). Confirmatory factor analysis (CFA) and two-group CFA by gender were performed to evaluate the sex-specific factor structure of MetS. After selecting the best model, an algorithm was obtained using factor loadings/residual variances. The quality of the MetS score was evaluated by the receiver operating characteristics curve and the area under the curve. Cross-validation was performed to validate the score and to determine the best cut point. The best fit model was a bifactor one with a general factor (MetS) and three specific factors (f1: obesity/adiposity trait; f2: hypertension/blood pressure trait; and f3: lipid trait). Gender-specific algorithms were implemented to obtain MetS scores showing a good diagnostic performance (0.80 specificity and 0.80 sensitivity for the cut point). Furthermore, cross-validation confirmed these results. CONCLUSION: These analyses suggested that the bifactor model was the most representative one. In addition, they provided a score and a cut point that are both clinically accessible and interpretable measures for MetS diagnosis and likely useful for evaluating the association with adverse cardiovascular disease and diabetes and for investigating the MetS genetic component.

Search for a light sterile neutrino at Daya Bay.

A search for light sterile neutrino mixing was performed with the first 217 days of data from the Daya Bay Reactor Antineutrino Experiment. The experiment's unique configuration of multiple baselines from six 2.9 GW(th) nuclear reactors to six antineutrino detectors deployed in two near (effective baselines 512 m and 561 m) and one far (1579 m) underground experimental halls makes it possible to test for oscillations to a fourth (sterile) neutrino in the 10(-3) eV(2)<|Δm(41)(2) |< 0.3 eV(2) range. The relative spectral distortion due to the disappearance of electron antineutrinos was found to be consistent with that of the three-flavor oscillation model. The derived limits on sin(2) 2θ(14) cover the 10(-3) eV(2) ≲ |Δm(41)(2)| ≲ 0.1 eV(2) region, which was largely unexplored.

Lateral ankle and hindfoot instability: a new clinical based classification.

Ankle sprains are one of the most common soft tissue injuries accounting for nearly 40% of sports injuries. There are large number of procedures for its treatment reported in the literature with largely good results. The ankle forms a functional unit with the subtalar joint. We present a new classification for peritalar lateral instability. There are two intents of this classification. Firstly, the classification demonstrates an assessment and treatment guideline for the many causes of peritalar lateral instability. The second use of the classification is for research purposes so that cohorts of patients can be accurately described and the efficacy of different operations in different groups can be properly assessed.

New constraint on the existence of the µ+ → e+ γ decay.

The analysis of a combined data set, totaling 3.6 × 10(14) stopped muons on target, in the search for the lepton flavor violating decay µ(+) → e(+)γ is presented. The data collected by the MEG experiment at the Paul Scherrer Institut show no excess of events compared to background expectations and yield a new upper limit on the branching ratio of this decay of 5.7 × 10(-13) (90% confidence level). This represents a four times more stringent limit than the previous world best limit set by MEG.