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Article ; Online: Host Trait Prediction from High-Resolution Microbial Features.

Bacci, Giovanni

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2242, Page(s) 185–202

Abstract: Predicting host traits from metagenomes presents new challenges that can be difficult to overcome for researchers without a strong background in bioinformatics and/or statistics. Profiling bacterial communities using shotgun metagenomics often leads to ... ...

Abstract	Predicting host traits from metagenomes presents new challenges that can be difficult to overcome for researchers without a strong background in bioinformatics and/or statistics. Profiling bacterial communities using shotgun metagenomics often leads to the generation of a large amount of data that cannot be used directly for training a model. In this chapter we provide a detailed description of how to build a working machine learning model based on taxonomic and functional features of bacterial communities inhabiting the lungs of cystic fibrosis patients. Models are built in the R environment by using different freely available machine learning algorithms.
MeSH term(s)	Bacteria/classification ; Bacteria/genetics ; Bacteria/isolation & purification ; Cystic Fibrosis/genetics ; Cystic Fibrosis/microbiology ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; DNA, Bacterial/metabolism ; Databases, Genetic ; Gene Expression Profiling ; Genome, Bacterial ; Humans ; Lung/microbiology ; Machine Learning ; Metagenome ; Metagenomics ; Mutation ; Phylogeny ; Research Design ; Software ; Transcriptome ; Workflow
Chemical Substances	CFTR protein, human ; DNA, Bacterial ; Cystic Fibrosis Transmembrane Conductance Regulator (126880-72-6)
Language	English
Publishing date	2021-05-07
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1099-2_12
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Article: Value of Diaphragm Ultrasonography for Extubation: A Single-Blinded Randomized Clinical Trial.

Toledo, T G / Bacci, M R

Critical care research and practice

2023 Volume 2023, Page(s) 8403971

Abstract: Introduction: Daily evaluation of mechanically ventilated (MV) patients is essential for successful extubation. Proper withdrawal prevents complications and reduces the cost of hospitalization in the intensive care unit (ICU). Diaphragm ultrasonography ( ...

Abstract	Introduction: Daily evaluation of mechanically ventilated (MV) patients is essential for successful extubation. Proper withdrawal prevents complications and reduces the cost of hospitalization in the intensive care unit (ICU). Diaphragm ultrasonography (DUS) has emerged as a potential instrument for determining whether a patient is ready to be extubated. This study compared the efficacy rate of extubation using a standard withdrawal protocol and DUS in patients with MV. Methods: A randomized, parallel, single-blind, controlled study was conducted on ICU patients undergoing MV. Patients were randomly assigned to either the control (conventional weaning protocol) group or intervention (DUS-guided weaning) group in a 1 : 1 ratio. The primary outcome measure was the rate of reintubation and hospital mortality. Results: Forty patients were randomized to the trial. The mean age of the sample was 70 years, representing an older population. The extubation success rate was 90% in both groups. There was no reintubation in the first 48 hours and only two reintubations in both groups between the second and seventh days. The hospital mortality risk in patients with acute kidney injury was positively correlated with age and the need for hemodialysis.
Language	English
Publishing date	2023-09-19
Publishing country	Egypt
Document type	Journal Article
ZDB-ID	2573849-5
ISSN	2090-1313 ; 2090-1305
ISSN (online)	2090-1313
ISSN	2090-1305
DOI	10.1155/2023/8403971
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Article: The -318 C>G single-nucleotide polymorphism in GNAI2 gene promoter region impairs transcriptional activity through specific binding of Sp1 transcription factor and is associated with high blood pressure in Caucasians from Italy.

Menzaghi, Claudia / Paroni, Giulia / De Bonis, Concetta / Soccio, Teresa / Marucci, Antonella / Bacci, Simonetta / Trischitta, Vincenzo

Journal of the American Society of Nephrology : JASN

2006 Volume 17, Issue 4 Suppl 2, Page(s) S115–9

Abstract: ... synonymous or intronic), six SNP were not studied further. The -318C>G SNP (allelic frequency 6 ... who carry the C/C genotype, G carriers (i.e., individuals who carry either the G/G or the C/G genotype) had ... for hypertension (odds ratio 2.2; 95% confidence interval 1.1 to 4.5). Compared with the C, the G allele had 2.5 ...

Abstract	Inhibiting Galpha subunit 2 protein, which is encoded by the GNAI2 gene, is suggested to be pathogenic for essential hypertension and/or insulin resistance. The aim of this study was to determine whether GNAI2 variations modulate the risk for these abnormalities. Seven single-nucleotide polymorphisms (SNP) at the GNAI2 locus were identified. Because of either low allelic frequency or unlikely biologic relevance (i.e., synonymous or intronic), six SNP were not studied further. The -318C>G SNP (allelic frequency 6%) in the promoter region was studied for association with adiposity, systolic BP (SBP) and diastolic BP, fasting insulin and glucose, and lipids levels in 655 nondiabetic Caucasians from Italy. As compared with individuals who carry the C/C genotype, G carriers (i.e., individuals who carry either the G/G or the C/G genotype) had higher SBP (117.8 +/- 16 versus 113.6 +/- 12.6 mmHg; P = 0.010) and were at increased risk for hypertension (odds ratio 2.2; 95% confidence interval 1.1 to 4.5). Compared with the C, the G allele had 2.5-fold reduced transcriptional activity in transfected HEK293 cells. As predicted by the TRANSFAC database, competition with YY1 or Sp1 transcription factors specifically reduced the binding of HeLa cell nuclear proteins to -318C or -318G allele, respectively, as indicated by shifted electrophoretic mobility. A "supershift" of the nuclear proteins/-318G allele complex was observed after anti-Sp1 was added but not anti-YY1 antibody. The GNAI2 -318 C>G SNP impairs transcriptional activity through specific binding of Sp1 and is associated with high SBP in Caucasians from Italy.
MeSH term(s)	Adult ; Alleles ; Cell Line ; Female ; GTP-Binding Protein alpha Subunit, Gi2/genetics ; Genetic Variation ; HeLa Cells ; Humans ; Hypertension/genetics ; Insulin Resistance/genetics ; Italy ; Male ; Middle Aged ; Polymorphism, Single Nucleotide ; Promoter Regions, Genetic ; Risk ; Sp1 Transcription Factor/metabolism ; Transcription, Genetic ; Transfection
Chemical Substances	Sp1 Transcription Factor ; GNAI2 protein, human (EC 3.6.5.1) ; GTP-Binding Protein alpha Subunit, Gi2 (EC 3.6.5.1)
Language	English
Publishing date	2006-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1085942-1
ISSN	1533-3450 ; 1046-6673
ISSN (online)	1533-3450
ISSN	1046-6673
DOI	10.1681/ASN.2005121340
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Article ; Online: Prognostic impact of Ki-67 in canine splenic hemangiosarcoma: A preliminary study.

Brigandì, Elena / Valenti, Paola / Bacci, Barbara / Brunetti, Barbara / Avallone, Giancarlo

Veterinary pathology

2024 , Page(s) 3009858231225507

Abstract: Canine splenic hemangiosarcoma has a high metastatic rate and short survival time. Currently, the main prognostic parameters are tumor stage and therapy, while data on histologic parameters, such as grade and Ki-67 expression, are scarce. The aims of ... ...

Abstract	Canine splenic hemangiosarcoma has a high metastatic rate and short survival time. Currently, the main prognostic parameters are tumor stage and therapy, while data on histologic parameters, such as grade and Ki-67 expression, are scarce. The aims of this study were to compare two methods of assessment of Ki-67, verify their prognostic impact, and define a threshold value based on survival. Thirty-one cases of histologically diagnosed canine splenic hemangiosarcoma, which were treated with splenectomy and had full staging and follow-up information, were collected. Three were stage I, 17 stage II, and 11 stage III. The mean mitotic count (MC) was 23.9 (standard deviation [SD]: 22.1) and the median was 15 (range, 1-93). Immunohistochemistry for Ki-67 was performed, the Ki-67 labeling index (Ki-67LI) was assessed as a percentage of positive neoplastic nuclei per ≥500 cell, and the Ki-67 count (KI-67C) was defined as the average number of positive nuclei using a 1 cm
Language	English
Publishing date	2024-01-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	188012-3
ISSN	1544-2217 ; 0300-9858
ISSN (online)	1544-2217
ISSN	0300-9858
DOI	10.1177/03009858231225507
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Article ; Online: Impairment of Hypnosis by Nocebo Response and Related Neurovegetative Changes: A Case Report in Oral Surgery.

Queirolo, Luca / Facco, Enrico / Bacci, Christian / Mucignat, Carla / Zanette, Gastone

The International journal of clinical and experimental hypnosis

2024 Volume 72, Issue 2, Page(s) 189–201

Abstract: This article presents the third molar removal in a highly hypnotizable patient, who had been successfully submitted to oral surgery with hypnosis as stand-alone anesthesia in previous sessions. Unexpectedly, hypnosis initially failed, as a result of a ... ...

Abstract	This article presents the third molar removal in a highly hypnotizable patient, who had been successfully submitted to oral surgery with hypnosis as stand-alone anesthesia in previous sessions. Unexpectedly, hypnosis initially failed, as a result of a nocebo response due to a previous dentist's bad communication; two complaints made by the patient were associated with increased sympathetic activity (as defined by increased heart rate and electrodermal activity and decreased heart rate variability). After deepening of hypnosis, the patient achieved a full hypnotic analgesia allowing for a successful conclusion of the intervention, an event associated with decreased heart rate, electrodermal activity, and increased heart rate variability. Hence, the initial failure was paralleled by a decreased parasympathetic activity and increased sympathetic activity, while hypnotic analgesia was associated with the opposite pattern. The patient's postoperative report indicated that the initial failure of hypnosis depended on a strong nocebo effect because of a previous dentist distrusting hypnosis and persuading her that it was not enough to face a third molar removal.
MeSH term(s)	Female ; Humans ; Hypnosis ; Nocebo Effect ; Pain ; Oral Surgical Procedures ; Hypnotics and Sedatives
Chemical Substances	Hypnotics and Sedatives
Language	English
Publishing date	2024-02-16
Publishing country	England
Document type	Case Reports ; Journal Article
ZDB-ID	218267-1
ISSN	1744-5183 ; 0020-7144
ISSN (online)	1744-5183
ISSN	0020-7144
DOI	10.1080/00207144.2024.2311908
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Article ; Online: A Protocol for Teaching Basic Next Generation Sequencing (NGS) Analysis Skills to Undergraduate Students Using Bash and R.

Fondi, Marco / Bacci, Giovanni

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2242, Page(s) 245–265

Abstract: ... of NGS data, from basic and standard operations on sequencing reads (e.g., quality check and trimming ... to more advanced analysis techniques (e.g., data normalization). ...

Abstract	Next generation sequencing (NGS) is routinely used to study crucial aspects of biological systems, including differentially expressed genes identification, microbiome taxonomic composition and structure, enrichment of specific cellular functions in a given environment, and so on. Current research laboratories are facing a serious lack in the availability of properly trained researchers capable of carrying out basic NGS analysis computational pipelines. This reflects a gap in most academic curricula concerning the basics of NGS data management, analysis, and interpretation. Indeed, most of the times, the knowledge necessary to undertake these tasks is acquired through the use of one-shot tutorial, without a thorough explanation of the concepts behind the practical steps. With this protocol we aim to fill this gap by providing teachers with a hands-on protocol to guide bachelor and master students in a more focused analysis of NGS data, from basic and standard operations on sequencing reads (e.g., quality check and trimming) to more advanced analysis techniques (e.g., data normalization).
MeSH term(s)	Computational Biology/education ; Curriculum ; Data Management/education ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Software ; Students ; Teaching
Language	English
Publishing date	2021-05-07
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1099-2_16
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Article: The Perception of Workplace Safety and of Risk of Contagion among Preschool Teachers during the COVID-19 Pandemic.

Bacci, Giulia / Converso, Daniela / Sottimano, Ilaria / Martini, Mara

Children (Basel, Switzerland)

2023 Volume 10, Issue 7

Abstract: The COVID-19 pandemic had a major impact on early childhood educational contexts and on educators' working conditions. This study aims to examine the change over time in personal contribution to workplace safety and perception of risk of infection among ... ...

Abstract	The COVID-19 pandemic had a major impact on early childhood educational contexts and on educators' working conditions. This study aims to examine the change over time in personal contribution to workplace safety and perception of risk of infection among preschool teachers after returning to in-person work during the third wave of the pandemic (spring 2021). Teachers' perceptions of workplace safety can influence their quality of work-life and, as a consequence, the quality of service offered to children. Data were collected using two questionnaires: at T0 (January) and at T1 (May). The results showed relations between organizational and personal actions to manage risk and fear of infection at work. Concern about COVID-19 contagion decreased over time (
Language	English
Publishing date	2023-07-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2732685-8
ISSN	2227-9067
ISSN	2227-9067
DOI	10.3390/children10071222
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Article ; Online: Single session of laser photobiomodulation for symptom management of oral lichen planus: a retrospective study.

Roccon, Andrea / Cavallin, Francesco / Zanette, Gastone / Bacci, Christian

Lasers in medical science

2023 Volume 38, Issue 1, Page(s) 43

Abstract: This study aimed to evaluate the effectiveness of a single session of laser photobiomodulation (PBM) with flat top handpiece in reducing painful symptoms in patients with Oral Lichen Planus (OLP). The clinical charts of 20 patients of the Dental Clinic ... ...

Abstract	This study aimed to evaluate the effectiveness of a single session of laser photobiomodulation (PBM) with flat top handpiece in reducing painful symptoms in patients with Oral Lichen Planus (OLP). The clinical charts of 20 patients of the Dental Clinic of University of Padua (Italy) who underwent a single laser PBM to manage OLP symptomatology were retrospectively analyzed. A 980 nm diode laser and a flat top handpiece with a 1-cm
MeSH term(s)	Humans ; Retrospective Studies ; Lichen Planus, Oral/radiotherapy ; Lichen Planus, Oral/drug therapy ; Low-Level Light Therapy/methods ; Pain ; Lasers, Semiconductor/therapeutic use
Language	English
Publishing date	2023-01-19
Publishing country	England
Document type	Journal Article
ZDB-ID	632808-8
ISSN	1435-604X ; 0268-8921
ISSN (online)	1435-604X
ISSN	0268-8921
DOI	10.1007/s10103-023-03706-4
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Article ; Online: Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome.

Renzi, Sonia / Nenciarini, Stefano / Bacci, Giovanni / Cavalieri, Duccio

Microbiome research reports

2023 Volume 3, Issue 1, Page(s) 2

Abstract: Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association with their hosts. They are ... ...

Abstract	Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association with their hosts. They are involved in the food industry and pharmaceutical production, but they can also cause diseases in other organisms, making the understanding of their biology mandatory. The ongoing loss of biodiversity due to overexploitation of environmental resources is a growing concern in many countries. Therefore, it becomes crucial to understand the ecology and evolutionary history of these organisms to systematically classify them. To achieve this, it is essential that our knowledge of the mycobiota reaches a level similar to that of the bacterial communities. To overcome the existing challenges in the study of fungal communities, the first step should be the establishment of standardized techniques for the correct identification of species, even from complex matrices, both in wet lab practices and in bioinformatic tools.
Language	English
Publishing date	2023-10-23
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2771-5965
ISSN (online)	2771-5965
DOI	10.20517/mrr.2023.27
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Article: The +276 G/T single nucleotide polymorphism of the adiponectin gene is associated with coronary artery disease in type 2 diabetic patients.

Bacci, Simonetta / Menzaghi, Claudia / Ercolino, Tonino / Ma, Xiaowei / Rauseo, Anna / Salvemini, Lucia / Vigna, Carlo / Fanelli, Raffaele / Di Mario, Umberto / Doria, Alessandro / Trischitta, Vincenzo

Diabetes care

2004 Volume 27, Issue 8, Page(s) 2015–2020

Abstract: Objective: Two single nucleotide polymorphisms (SNPs) at the adiponectin locus (+45T>G and +276G>T ... 17 vs. 25 +/- 13 microg/ml).: Conclusions: In conclusion, the +276 G>T polymorphism is ...

Abstract	Objective: Two single nucleotide polymorphisms (SNPs) at the adiponectin locus (+45T>G and +276G>T) have been associated with low circulating adiponectin levels, insulin resistance, and type 2 diabetes. We investigated whether these genetic markers are determinants of coronary artery disease (CAD) in type 2 diabetic patients. Research design and methods: A total of 376 consecutive type 2 diabetic patients were studied: 142 case subjects with coronary stenosis >50% or previous myocardial infarction and 234 control subjects with no symptoms, no electrocardiogram (ECG) signs of myocardial ischemia, and a normal ECG stress test (n = 189) and/or (n = 45) with coronary stenosis <or=50%.<br />Results: No association with CAD was observed for the +45 SNP (P = 0.48). By contrast, a significant association was observed for the +276 SNP, with T/T homozygotes having a lower risk of CAD than carriers of other genotypes (adjusted odds ratio [OR] 0.13 [95% CI 0.037-0.46], P = 0.002). A similarly protective effect of the +276 T/T genotype was observed in 110 case and 45 control subjects for whom the CAD status had been determined by angiography (0.04 [0.006-0.30], P = 0.002). Serum adiponectin, although clearly related to several features of the proatherogenic/insulin-resistant phenotype, was not different between control subjects and CAD patients (26 +/- 17 vs. 25 +/- 13 microg/ml). Conclusions: In conclusion, the +276 G>T polymorphism is a determinant of CAD risk in type 2 diabetic patients. This marker may assist in the identification of diabetic individuals at especially high risk of CAD, so that preventive programs can be targeted at these subjects.
MeSH term(s)	Adiponectin ; Coronary Disease/genetics ; Coronary Stenosis/genetics ; Diabetes Mellitus, Type 2/genetics ; Diabetic Angiopathies/epidemiology ; Electrocardiography ; Exercise Test ; Female ; Genotype ; Homozygote ; Humans ; Intercellular Signaling Peptides and Proteins/genetics ; Male ; Middle Aged ; Polymorphism, Single Nucleotide/genetics ; Reference Values
Chemical Substances	Adiponectin ; Intercellular Signaling Peptides and Proteins
Language	English
Publishing date	2004-05-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	441231-x
ISSN	1935-5548 ; 0149-5992
ISSN (online)	1935-5548
ISSN	0149-5992
DOI	10.2337/diacare.27.8.2015
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