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Article ; Online: A weighted quantile sum regression with penalized weights and two indices

Stefano Renzetti / Chris Gennings / Stefano Calza

Frontiers in Public Health, Vol

2023 Volume 11

Abstract: BackgroundNew statistical methodologies were developed in the last decade to face the challenges of estimating the effects of exposure to multiple chemicals. Weighted Quantile Sum (WQS) regression is a recent statistical method that allows estimating a ... ...

Abstract	BackgroundNew statistical methodologies were developed in the last decade to face the challenges of estimating the effects of exposure to multiple chemicals. Weighted Quantile Sum (WQS) regression is a recent statistical method that allows estimating a mixture effect associated with a specific health effect and identifying the components that characterize the mixture effect.ObjectivesIn this study, we propose an extension of WQS regression that estimates two mixture effects of chemicals on a health outcome in the same model through the inclusion of two indices, one in the positive direction and one in the negative direction, with the introduction of a penalization term.MethodsTo evaluate the performance of this new model we performed both a simulation study and a real case study where we assessed the effects of nutrients on obesity among adults using the National Health and Nutrition Examination Survey (NHANES) data.ResultsThe method showed good performance in estimating both the regression parameter and the weights associated with the single elements when the penalized term was set equal to the magnitude of the Akaike information criterion of the unpenalized WQS regression. The two indices further helped to give a better estimate of the parameters [Positive direction Median Error (PME): 0.022; Negative direction Median Error (NME): −0.044] compared to the standard WQS without the penalization term (PME: −0.227; NME: 0.215). In the case study, WQS with two indices was able to find a significant effect of nutrients on obesity in both directions identifying sodium and magnesium as the main actors in the positive and negative association, respectively.DiscussionThrough this work, we introduced an extension of WQS regression that improved the accuracy of the parameter estimates when considering a mixture of elements that can have both a protective and a harmful effect on the outcome; and the advantage of adding a penalization term when estimating the weights.
Keywords	environmental mixture ; weighted quantile sum regression ; two indices ; penalized weights ; nutrients ; obesity ; Public aspects of medicine ; RA1-1270
Subject code	310
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Dataset

Davide Capoferri / Paola Chiodelli / Stefano Calza / Marcello Manfredi / Marco Presta

Data, Vol 8, Iss 12, p

Impact of β-Galactosylceramidase Overexpression on the Protein Profile of Braf(V600E) Mutated Melanoma Cells

2023 Volume 177

Abstract: β-Galactosylceramidase (GALC) is a lysosomal enzyme involved in sphingolipid metabolism by removing β-galactosyl moieties from β-galactosyl ceramide and β-galactosyl sphingosine. Previous observations have shown that GALC exerts a pro-oncogenic activity ... ...

Abstract	β-Galactosylceramidase (GALC) is a lysosomal enzyme involved in sphingolipid metabolism by removing β-galactosyl moieties from β-galactosyl ceramide and β-galactosyl sphingosine. Previous observations have shown that GALC exerts a pro-oncogenic activity in human melanoma. Here, the impact of GALC overexpression on the proteomic landscape of BRAF -mutated A2058 and A375 human melanoma cell lines was investigated by liquid chromatography–tandem mass spectrometry analysis of the cell extracts. The results indicate that GALC overexpression causes the upregulation/downregulation of 172/99 proteins in GALC -transduced cells when compared to control cells. Gene ontology categorization of up/down-regulated proteins indicates that GALC may modulate the protein landscape in BRAF -mutated melanoma cells by affecting various biological processes, including RNA metabolism, cell organelle fate, and intracellular redox status. Overall, these data provide further insights into the pro-oncogenic functions of the sphingolipid metabolizing enzyme GALC in human melanoma.
Keywords	melanoma ; proteomics ; sphingolipids ; β-galactosylceramidase ; Bibliography. Library science. Information resources ; Z
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Rapid Point-Of-Care Serology and Clinical History Assessment Increase Protection Provided by RT-PCR Screening

Antonella Savio / Stefano Calza / Gianbattista Guerrini / Valentina Romano / Eleonora Marchina

Frontiers in Public Health, Vol

A Pilot Study Involving Three Nursing Homes in Brescia, a Hotspot of Lombardy

2021 Volume 9

Abstract: Background: COVID-19 outbursts have been registered worldwide within care homes with asymptomatic transmission combined with shortage/inaccuracy of diagnostic tests undermining the efforts at containment of the disease. Nursing facilities in Lombardy ( ... ...

Abstract	Background: COVID-19 outbursts have been registered worldwide within care homes with asymptomatic transmission combined with shortage/inaccuracy of diagnostic tests undermining the efforts at containment of the disease. Nursing facilities in Lombardy (Italy) were left with no, or limited, access to testing for 8 weeks after the outbreak of COVID-19.Methods: This study includes 246 residents and 286 workers of three different nursing homes in Brescia-Lombardy. Clinical questionnaires and rapid serology tests were devised to integrate the data of the first available RT-PCR screening. Follow-up serology after 60-days was performed on 67 of 86 workers with positive serology or clinically suspicious.Findings: Thirty-seven residents and 18 workers had previous positive RT-PCR. Thorough screening disclosed two additional RT-PCR-positive workers. Serology screening revealed antibodies in 59 residents and 48 workers, including 32/37 residents and all workers previously positive at RT-PCR. Follow up serology disclosed antibodies in two additional workers with recent symptoms at the time of screening. The professionals in close contact with residents had more infections (47/226–20.79% vs. 1/60–1.66%; p = 0.00013 Fisher exact-test). A suspicious clinical score was present in 44/64 residents and in 41/50 workers who tested positive with either method with totally asymptomatic disease more frequent among residents 28.1 vs. 10.0% (p = 0.019 Fisher exact-test).Interpretation: Based on the available RT-PCR ± results at the time of symptoms/contacts, our integrated clinical and serological screening demonstrated sensitivity 89% and specificity 87%. This multimodal assessment proved extremely useful in understanding the viral spread in nursing homes, in defining its stage and in implementing protective measures. Rapid serology tests demonstrated efficient and particularly suited for older people less able to move/cooperate.
Keywords	COVID-19 ; SARS–CoV−2 ; asymptomatic transmission ; nursing home ; on-site testing ; COVID-19 symptoms ; Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Estimating the Impact of the COVID-19 Pandemic on Maternal and Perinatal Health Care Services in Italy

Loredana Cena / Matteo Rota / Stefano Calza / Barbara Massardi / Alice Trainini / Alberto Stefana

Frontiers in Public Health, Vol

Results of a Self-Administered Survey

2021 Volume 9

Abstract: The coronavirus disease 2019 (COVID-19) pandemic is strongly changing the way most people live their lives, and disrupting specialist healthcare systems. Such public health disruptions have resulted in significant collateral damage with particular ... ...

Abstract	The coronavirus disease 2019 (COVID-19) pandemic is strongly changing the way most people live their lives, and disrupting specialist healthcare systems. Such public health disruptions have resulted in significant collateral damage with particular implications for vulnerable populations, including the perinatal population. This Study aims to estimate the impact of the COVID-19 pandemic on Italian maternal and perinatal health care services. A questionnaire was designed to evaluate the COVID-19 impact on Italian maternal and perinatal healthcare facilities and their activities and provision of services from March to May 2020. The survey was completed by hospital-based and community-based Italian maternal and perinatal healthcare facilities. Most of these were located in Lombardy or Veneto (the most affected Italian regions). 70% of all facilities reported that the first wave of the COVID-19 pandemic negatively influenced the functioning of one or more aspects of the perinatal service; only 28.4% of facilities all over the country continued to provide outpatient routine visits and examinations as usual; 23.4% of facilities became understaffed during the index period due to various reasons such as ward transfer and sick leave. This is the first Italian study, and among very few international studies that describe the effects of the COVID-19 pandemic on antenatal and postnatal healthcare facilities and their provision of activities and services. Our findings confirm that healthcare systems even in high-income countries were not entirely prepared to handle such a global health emergency; indeed, specialized maternal and perinatal healthcare services have been disrupted by this global health emergency.
Keywords	health services ; antenatal and postnatal healthcare services ; newborn's health ; women's health ; public health ; maternal services ; Public aspects of medicine ; RA1-1270
Subject code	360
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Early prediction of in-hospital death of COVID-19 patients

Emirena Garrafa / Marika Vezzoli / Marco Ravanelli / Davide Farina / Andrea Borghesi / Stefano Calza / Roberto Maroldi

eLife, Vol

a machine-learning model based on age, blood analyses, and chest x-ray score

2021 Volume 10

Abstract: An early-warning model to predict in-hospital mortality on admission of COVID-19 patients at an emergency department (ED) was developed and validated using a machine-learning model. In total, 2782 patients were enrolled between March 2020 and December ... ...

Abstract	An early-warning model to predict in-hospital mortality on admission of COVID-19 patients at an emergency department (ED) was developed and validated using a machine-learning model. In total, 2782 patients were enrolled between March 2020 and December 2020, including 2106 patients (first wave) and 676 patients (second wave) in the COVID-19 outbreak in Italy. The first-wave patients were divided into two groups with 1474 patients used to train the model, and 632 to validate it. The 676 patients in the second wave were used to test the model. Age, 17 blood analytes, and Brescia chest X-ray score were the variables processed using a random forests classification algorithm to build and validate the model. Receiver operating characteristic (ROC) analysis was used to assess the model performances. A web-based death-risk calculator was implemented and integrated within the Laboratory Information System of the hospital. The final score was constructed by age (the most powerful predictor), blood analytes (the strongest predictors were lactate dehydrogenase, D-dimer, neutrophil/lymphocyte ratio, C-reactive protein, lymphocyte %, ferritin std, and monocyte %), and Brescia chest X-ray score (https://bdbiomed.shinyapps.io/covid19score/). The areas under the ROC curve obtained for the three groups (training, validating, and testing) were 0.98, 0.83, and 0.78, respectively. The model predicts in-hospital mortality on the basis of data that can be obtained in a short time, directly at the ED on admission. It functions as a web-based calculator, providing a risk score which is easy to interpret. It can be used in the triage process to support the decision on patient allocation.
Keywords	biomarker ; COVID-19 ; random forests ; VIM ; SMOTE ; PDP ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	310
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mental Health States Experienced by Perinatal Healthcare Workers during COVID-19 Pandemic in Italy

Loredana Cena / Matteo Rota / Stefano Calza / Barbara Massardi / Alice Trainini / Alberto Stefana

International Journal of Environmental Research and Public Health, Vol 18, Iss 6542, p

2021 Volume 6542

Abstract: Background: The ongoing COVID-19 pandemic has had an impact on mental health status in a variety of populations. Methods: An online non-probability sample survey was used to assess psychological distress symptoms and burnout among perinatal healthcare ... ...

Abstract	Background: The ongoing COVID-19 pandemic has had an impact on mental health status in a variety of populations. Methods: An online non-probability sample survey was used to assess psychological distress symptoms and burnout among perinatal healthcare professionals (PHPs) during the pandemic in Italy. The questionnaire included the Depression, Anxiety, and Stress Scale-21 (DASS-21) and the Maslach Burnout Inventory (MBI). Demographic and occupational factors associated with stress, anxiety, and depression symptoms were analyzed. Results: The sample size was 195. The estimated self-reported rates of moderate to severe anxiety symptoms, depression symptoms, and perceived stress levels were 18.7, 18.7, and 21.5%, respectively. Furthermore, 6.2% of respondents reported burnout. One factor associated with all three self-reported psychological distress issues was suffering from trauma unrelated to the pandemic (aOR: 7.34, 95% CI: 2.73–20.28 for depression; aOR: 6.13, 95% CI: 2.28–16.73 for anxiety; aOR: 3.20, 95% CI: 1.14–8.88 for stress). Compared to physicians, psychologists had lower odds of developing clinically significant depressive symptoms (aOR: 0.21, 95% CI: 0.04–0.94) and high stress levels (aOR: 0.19, 95% CI: 0.04–0.80). Conclusions: High rates of self-reported symptoms of depression and anxiety, as well as perceived stress, among PHPs were reported during the COVID-19 pandemic. Health authorities should implement and integrate timely and regular evidence-based assessment of psychological distress targeting PHPs in their work plans.
Keywords	COVID-19 ; pandemic ; depression ; anxiety ; stress ; burnout ; Medicine ; R
Subject code	150 ; 310
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Psychological Distress in Healthcare Workers between the First and Second COVID-19 Waves

Loredana Cena / Matteo Rota / Stefano Calza / Jessica Janos / Alice Trainini / Alberto Stefana

International Journal of Environmental Research and Public Health, Vol 18, Iss 11843, p

The Role of Personality Traits, Attachment Style, and Metacognitive Functioning as Protective and Vulnerability Factors

2021 Volume 11843

Abstract: The COVID-19 pandemic has impacted the mental health of healthcare workers (HCWs) since its outbreak, but little attention has been paid to person-level vulnerability and protective factors. This study aims to determine the prevalence of both general and ...

Abstract	The COVID-19 pandemic has impacted the mental health of healthcare workers (HCWs) since its outbreak, but little attention has been paid to person-level vulnerability and protective factors. This study aims to determine the prevalence of both general and pandemic-related psychological distress among HCWs between the first and second COVID-19 waves in Italy and analyze associations between psychological distress and personality traits, attachment style, and metacognitive functioning. Between June and October 2020, 235 Italian HCWs completed questionnaires concerning psychological stress, personality traits, attachment style, and metacognitive functioning; 26.5% of respondents presented with moderate to extremely severe levels of general psychological distress and 13.8% with moderate to extremely severe levels of pandemic-related psychological distress. After controlling for demographic and occupational variables, significant associations emerged among high emotional stability as a personality trait and both general (aOR: 0.58, 95% CI: 0.41–0.79) and pandemic-related psychological stress (aOR: 0.62, 95% CI: 0.41–0.90). Additionally, higher scores regarding one’s ability to understand others’ emotional states were associated with lower odds of developing psychological distress (aOR: 0.78, 95% CI: 0.63–0.93). Lastly, when comparing those with fearful attachment styles to those with secure attachments, the aOR for psychological distress was 4.73 (95% CI: 1.45–17.04). These results highlight the importance of conducting baseline assessments of HCWs’ person-level factors and providing regular screenings of psychological distress.
Keywords	COVID-19 ; pandemic ; psychological distress ; burnout ; healthcare workers ; personality traits ; Medicine ; R
Subject code	150
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Association between Peri-Implant Soft Tissue Health and Different Prosthetic Emergence Angles in Esthetic Areas

Diego Lops / Eugenio Romeo / Stefano Calza / Antonino Palazzolo / Lorenzo Viviani / Stefano Salgarello / Barbara Buffoli / Magda Mensi

Journal of Clinical Medicine, Vol 11, Iss 6243, p

Digital Evaluation after 3 Years’ Function

2022 Volume 6243

Abstract: Background: The aim of the present retrospective study was to assess peri-implant soft tissue health for implants restored with different prosthetic emergence profile angles. Methods: Patients were treated with implants supporting fixed dentures and were ...

Abstract	Background: The aim of the present retrospective study was to assess peri-implant soft tissue health for implants restored with different prosthetic emergence profile angles. Methods: Patients were treated with implants supporting fixed dentures and were followed for 3 years. Buccal emergence angle (EA) measured at 3 years of follow-up visits (t1) were calculated for two different groups: Group 1 (153 implants) for restorations with angle between implant axis and prosthetic emergence angle from ≥30°, and Group 2 (67 implants) for those with angle ≤30°, respectively. Image J software was used for the measurements. Moreover, peri-implant soft tissue parameters such as pocket probing depth (PPD), plaque index (PI) and gingival index (GI) were assessed, respectively. Results: A total of 57 patients were included in the analysis and a total of 220 implants were examined. Mean (±SD) EA in Groups 1 and 2 was 46.4 ± 12.2 and 24.5 ± 4.7 degrees, respectively. After 3 years of follow-up, a PPD difference of 0.062 mm (CI 95% −0.041 mm; 0.164 mm) was calculated between the two groups and was not statistically significant ( p = 0.238). Similar results were found for PI (OR = 0.78, CI 95% 0.31; 1.98, p = 0.599). Furthermore, GI scores of 2 and 3 were found for nine implants (5.9%) in Group 1, and for five implants in Group 2 (7.5%). A non-significant difference ( p = 0.76) was found. Conclusions: Peri-implant soft-tissue health does not seem to be influenced by EA itself, when a proper emergence profile is provided for implant-supported reconstructions in anterior areas.
Keywords	dental implant ; emergence angle ; retrospective study ; sub-crestal placement ; emergence profile ; Medicine ; R
Subject code	796
Language	English
Publishing date	2022-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Relationship between Lower Limbs Performance and Spinal Alignment in Parkinson’s Disease Patients

Luciano Bissolotti / Matteo Rota / Stefano Calza / Eleuterio A. Sanchez Romero / Andrea Battaglino / Jorge H. Villafañe

Journal of Clinical Medicine, Vol 11, Iss 13, p

An Observational Study with Cross Sectional Design

2022 Volume 3775

Abstract: Parkinson’s disease (PD) is a progressive neurodegenerative disease determining spinal deformities and muscle rigidity, weakness and dystonia that can be related to a change in muscular output during sit-to-stand tasks (STS). Purpose: The aim of this ... ...

Abstract	Parkinson’s disease (PD) is a progressive neurodegenerative disease determining spinal deformities and muscle rigidity, weakness and dystonia that can be related to a change in muscular output during sit-to-stand tasks (STS). Purpose: The aim of this study was to determine the impacts of spinal alignment on lower limbs performance during STS tasks in Parkinson’s disease (PD) patients and healthy controls. Methods: In total, 43 consecutive PD patients (“PD” Group, 25 males and 18 females; age 73.7 ± 7.1) and 42 people not affected by any type of neurological disease (“CON” Group, 22 males, 20 females; age 69.8 ± 6.0) participated in the observational study. The clinical assessment included: IPAQ (International Physical Activity Questionnaire), Hoehn Yahr score, plumb-line distance from the spinous process of C7, kyphosis apex and the spinous process of L3 and S1. We used the Muscle Quality Index test (MQI) to assess muscle power output during STS in both groups. Results: The MQI test measurements of absolute and relative lower limb power was significantly lower in the PD group, in addition to a negative correlation with age and a positive correlation with PL-L3 in that group of patients. Conclusions: A final consideration regarding our results leads to the possibility that the preservation of lumbar lordosis may be one of the factors for maintaining efficient biomechanics of the lower limb muscles, with the preservation of the physiological contractile characteristics of these muscles being the objective for a multidisciplinary rehabilitation based on postural exercises of the spine and a program of training exercises for the lower limb muscles.
Keywords	Parkinson’s disease ; lower limb ; spine ; Medicine ; R
Subject code	796
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: CREDO

Woochang Hwang / Stefano Calza / Marco Silvestri / Yudi Pawitan / Youngjo Lee

Scientific Reports, Vol 9, Iss 1, Pp 1-

Highly confident disease-relevant A-to-I RNA-editing discovery in breast cancer

2019 Volume 8

Abstract: Abstract Adenosine-to-Inosine (A-to-I) RNA editing is the most prevalent post-transcriptional modification of RNA molecules. Researchers have attempted to find reliable RNA editing using next generation sequencing (NGS) data. However, most of these ... ...

Abstract	Abstract Adenosine-to-Inosine (A-to-I) RNA editing is the most prevalent post-transcriptional modification of RNA molecules. Researchers have attempted to find reliable RNA editing using next generation sequencing (NGS) data. However, most of these attempts suffered from a high rate of false positives, and they did not consider the clinical relevance of the identified RNA editing, for example, in disease progression. We devised an effective RNA-editing discovery pipeline called CREDO, which includes novel statistical filtering modules based on integration of DNA- and RNA-seq data from matched tumor-normal tissues. CREDO was compared with three other RNA-editing discovery pipelines and found to give significantly fewer false positives. Application of CREDO to breast cancer data from the Cancer Genome Atlas (TCGA) project discovered highly confident RNA editing with clinical relevance to cancer progression in terms of patient survival. RNA-editing detection using DNA- and RNA-seq data from matched tumor-normal tissues should be more routinely performed as multiple omics data are becoming commonly available from each patient sample. We believe CREDO is an effective and reliable tool for this problem.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2019-03-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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