Severe Streptococcus equi Subspecies zooepidemicus Outbreak from Unpasteurized Dairy Product Consumption, Italy.

During November 2021-May 2022, we identified 37 clinical cases of Streptococcus equi subspecies zooepidemicus infections in central Italy. Epidemiologic investigations and whole-genome sequencing showed unpasteurized fresh dairy products were the outbreak source. Early diagnosis by using sequencing technology prevented the spread of life-threatening S. equi subsp. zooepidemicus infections.

Histopathological Image Deep Feature Representation for CBIR in Smart PACS.

Pathological Anatomy is moving toward computerizing processes mainly due to the extensive digitization of histology slides that resulted in the availability of many Whole Slide Images (WSIs). Their use is essential, especially in cancer diagnosis and research, and raises the pressing need for increasingly influential information archiving and retrieval systems. Picture Archiving and Communication Systems (PACSs) represent an actual possibility to archive and organize this growing amount of data. The design and implementation of a robust and accurate methodology for querying them in the pathology domain using a novel approach are mandatory. In particular, the Content-Based Image Retrieval (CBIR) methodology can be involved in the PACSs using a query-by-example task. In this context, one of many crucial points of CBIR concerns the representation of images as feature vectors, and the accuracy of retrieval mainly depends on feature extraction. Thus, our study explored different representations of WSI patches by features extracted from pre-trained Convolution Neural Networks (CNNs). In order to perform a helpful comparison, we evaluated features extracted from different layers of state-of-the-art CNNs using different dimensionality reduction techniques. Furthermore, we provided a qualitative analysis of obtained results. The evaluation showed encouraging results for our proposed framework.

Eribulin Mesylate as Third or Subsequent Line Chemotherapy for Elderly Patients with Locally Recurrent or Metastatic Breast Cancer: A Multicentric Observational Study of GIOGer (Italian Group of Geriatric Oncology)-ERIBE.

BACKGROUND: Metastatic breast cancer (MBC) is highly prevalent in middle-aged or elderly patients. Eribulin is a nontaxane microtubule inhibitor, approved for the treatment of pretreated MBC. This multicentric study (sponsored by GIOGer, Italian Group for Geriatric Oncology) was designed to assess the efficacy and tolerability of eribulin, according to parameters usually used in geriatric oncology. SUBJECTS, MATERIALS, AND METHODS: An observational study was conducted on 50 consecutive elderly patients with MBC. The primary endpoint was to evaluate the change in items score of comprehensive geriatric assessment (CGA) and health-related quality of life (HRQL). Italian versions of the CGA and HRQL questionnaires were administered at baseline, before the third and fifth cycles, and then every three cycles until treatment discontinuation. Secondary endpoints were efficacy and safety. RESULTS: Overall, both EQ-5D scores and EQ-5D-3 L visual analogic scale did not significantly change from baseline; the percentage of subjects without problems doing usual activities tended to decrease during treatment (p for linear trend .018), and the percentage of patients with minor problems performing usual activities tended to increase (p for linear trend.012). Among CGA items, Instrumental Activities of Daily Living tended to decrease during treatment and Geriatric Depression Scale tended to increase. After 12 months follow-up, 24 patients (out of 47) showed clinical benefits; median progression-free survival was 4.49 months (2.10-10.33) and median OS was 7.31 months (3.70-14.03). The treatment was associated with mild toxicity. CONCLUSION: Eribulin treatment preserved quality of life and geriatric parameters included in the CGA, except for instrumental functioning and geriatric depression, in elderly patients with MBC. IMPLICATIONS FOR PRACTICE: A collaboration between oncologist and geriatric specialists is essential in the management of patients with metastatic breast cancer, who are frequently elderly or frail. The assessment of geriatric parameters in the decision-making process can contribute to direct toward the most appropriate therapeutic plan and preserve the quality of life of patients. Eribulin does not seem to affect quality of life or worsen the overall geriatric status; therefore, it can be considered a suitable option for elderly patients with metastatic breast cancer.

A Large Set of miRNAs Is Dysregulated from the Earliest Steps of Human Hepatocellular Carcinoma Development.

Hepatocellular carcinoma (HCC) typically results from a stepwise process characterized by the development of premalignant lesions, such as low- or high-grade dysplastic nodules (LGDNs and HGDNs, respectively), in a cirrhotic setting. MicroRNAs (miRNAs) are small noncoding RNAs involved in post-transcriptional regulation of gene expression that can act as oncogenes or tumor suppressors. Whether and which miRNAs are involved in the early stages of HCC development remains elusive. Here, small-RNA sequencing was applied to profile miRNA expression in 55 samples (cirrhotic nodules; CNs), LGDNs, HGDNs, early HCCs, and small progressed HCCs, obtained from 17 patients bearing HCCs of different etiologies. An miRNA expression signature of 62 miRNAs distinguishing small progressed HCCs from matched CNs was identified. Interestingly, 52 of these miRNAs discriminated CNs from LGDNs/HGDNs, regardless of etiology, and remained modified along the tumorigenic process. Functional analysis of the predicted mRNA targets of deregulated miRNAs identified common modifications between the early and late stages of HCC development likely involved in the stepwise process of HCC development. Our results demonstrate that miRNA deregulation happens very early in HCC in humans, implying their crucial role in the tumorigenic process. The identification of miRNAs discriminating CNs from neoplastic nodules may have relevant translational implications in early diagnosis.

iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data.

Summary: The interest in investigating the biological roles of small non-coding RNAs (sncRNAs) is increasing, due to the pleiotropic effects of these molecules exert in many biological contexts. While several methods and tools are available to study microRNAs (miRNAs), only few focus on novel classes of sncRNAs, in particular PIWI-interacting RNAs (piRNAs). To overcome these limitations, we implemented iSmaRT ( i ntegrative Sm all R NA T ool-kit), an automated pipeline to analyze smallRNA-Seq data. Availability and Implementation: iSmaRT is a collection of bioinformatics tools and own algorithms, interconnected through a Graphical User Interface (GUI). In addition to performing comprehensive analyses on miRNAs, it implements specific computational modules to analyze piRNAs, predicting novel ones and identifying their RNA targets. A smallRNA-Seq dataset generated from brain samples of Huntington's Disease patients was used here to illustrate iSmaRT performances, demonstrating how the pipeline can provide, in a rapid and user friendly way, a comprehensive analysis of different classes of sncRNAs. iSmaRT is freely available on the web at ftp://labmedmolge-1.unisa.it (User: iSmart - Password: password). Contact: aweisz@unisa.it or ggiurato@unisa.it. Supplementary information: Supplementary data are available at Bioinformatics online.

Suspending DNA Origami Between Four Gold Nanodots.

Rectangular DNA origami functionalized with thiols in each of the four corners immobilizes by self-assembly between lithographically patterned gold nanodots on a silicon oxide surface.

Estrogen receptor beta impacts hormone-induced alternative mRNA splicing in breast cancer cells.

BACKGROUND: Estrogens play an important role in breast cancer (BC) development and progression; when the two isoforms of the estrogen receptor (ERα and ERß) are co-expressed each of them mediate specific effects of these hormones in BC cells. ERß has been suggested to exert an antagonist role toward the oncogenic activities of ERα, and for this reason it is considered an oncosuppressor. As clinical evidence regarding a prognostic role for this receptor subtype in hormone-responsive BC is still limited and conflicting, more knowledge is required on the biological functions of ERß in cancer cells. We have previously described the ERß and ERα interactomes from BC cells, identifying specific and distinct patterns of protein interactions for the two receptors. In particular, we identified factors involved in mRNA splicing and maturation as important components of both ERα and ERß pathways. Guided by these findings, here we performed RNA sequencing to investigate in depth the differences in the early transcriptional events and RNA splicing patterns induced by estradiol in cells expressing ERα alone or ERα and ERß. RESULTS: Exon skipping was the most abundant splicing event in the post-transcriptional regulation by estradiol. We identified several splicing events induced by ERα alone and by ERα+ERß, demonstrating for the first time that ERß significantly affects estrogen-induced splicing in BC cells, as revealed by modification of a subset of ERα-dependent splicing by ERß, as well as by the presence of splicing isoforms only in ERß+cells. In particular, we observed that ERß+BC cell lines exhibited around 2-fold more splicing events than the ERß- cells. Interestingly, we identified putative direct targets of ERß-mediated alternative splicing by correlating the genomic locations of ERß and ERα binding sites with estradiol-induced differential splicing in the corresponding genes. CONCLUSIONS: Taken together, these results demonstrate that ERß significantly affects estrogen-induced early transcription and mRNA splicing in hormone-responsive BC cells, providing novel information on the biological role of ERß in these tumors.

Timed regulation of P-element-induced wimpy testis-interacting RNA expression during rat liver regeneration.

UNLABELLED: Small noncoding RNAs comprise a growing family of molecules that regulate key cellular processes, including messenger RNA (mRNA) degradation, translational repression, and transcriptional gene silencing. P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) represent a class of small RNAs initially identified in the germline of a variety of species, where they contribute to maintenance of genome stability, and recently found expressed also in stem and somatic cells, where their role and responsiveness to physiopathological signals remain elusive. Here, we investigated piRNA expression in rat liver and its response to the stimuli exerted by regenerative proliferation of this organ. Quantitative polymerase chain reaction analysis identify in the liver the RNAs encoding PIWIL2/HILI, PIWIL4/HIWI2, and other components of the piRNA biogenesis pathways, suggesting that this is indeed functional. RNA sequencing before, during, and after the wave of cell proliferation that follows partial hepatectomy (PH) identified ∼1,400 mammalian germline piRNAs expressed in rat liver, including 72 showing timed changes in expression 24-48 hours post-PH, a timing that corresponds to cell transition through the S phase, returning to basal levels by 168 hours, when organ regeneration is completed and hepatocytes reach quiescence. CONCLUSION: The piRNA pathway is active in somatic cells of the liver and is subject to regulation during the pathophysiological process of organ regeneration, when these molecules are available to exert their regulatory functions on the cell genome and transcriptome, as demonstrated by the identification of several liver mRNAs representing candidate targets of these regulatory RNAs.

Thermal-electric model for piezoelectric ZnO nanowires.

The behavior of ZnO nanowires under uniaxial loading is characterized by means of a numerical model that accounts for all coupled mechanical, electrical, and thermal effects. The paper shows that thermal effects in the nanowires may greatly impact the predicted performance of piezoelectric and piezotronic nanodevices. The pyroelectric effect introduces new equivalent volumic charge in the body of the nanowire and surface charges at the boundaries, where Kapitza resistances are located, that act together with the piezoelectric charges to improve the predicted performance. It is shown that the proposed model is able to reproduce several effects experimentally observed by other research groups, and is a promising tool for the design of ultra-high efficient nanodevices.

Design Concepts, Fabrication and Advanced Characterization Methods of Innovative Piezoelectric Sensors Based on ZnO Nanowires.

Micro- and nano-scale materials and systems based on zinc oxide are expected to explode in their applications in the electronics and photonics, including nano-arrays of addressable optoelectronic devices and sensors, due to their outstanding properties, including semiconductivity and the presence of a direct bandgap, piezoelectricity, pyroelectricity and biocompatibility. Most applications are based on the cooperative and average response of a large number of ZnO micro/nanostructures. However, in order to assess the quality of the materials and their performance, it is fundamental to characterize and then accurately model the specific electrical and piezoelectric properties of single ZnO structures. In this paper, we report on focused ion beam machined high aspect ratio nanowires and their mechanical and electrical (by means of conductive atomic force microscopy) characterization. Then, we investigate the suitability of new power-law design concepts to accurately model the relevant electrical and mechanical size-effects, whose existence has been emphasized in recent reviews.

Electrospun PCL Filtration Membranes Enhanced with an Electrosprayed Lignin Coating to Control Wettability and Anti-Bacterial Properties.

This study reports on the two-step manufacturing process of a filtration media obtained by first electrospinning a layer of polycaprolactone (PCL) non-woven fibers onto a paper filter backing and subsequently coating it by electrospraying with a second layer made of pure acidolysis lignin. The manufacturing of pure lignin coatings by solution electrospraying represents a novel development that requires fine control of the underlying electrodynamic processing. The effect of increasing deposition time on the lignin coating was investigated for electrospray time from 2.5 min to 120 min. Microstructural and physical characterization included SEM, surface roughness analysis, porosity tests, permeability tests by a Gurley densometer, ATR-FTIR analysis, and contact angle measurements vs. both water and oil. The results indicate that, from a functional viewpoint, such a natural coating endowed the membrane with an amphiphilic behavior that enabled modulating the nature of the bare PCL non-woven substrate. Accordingly, the intrinsic hydrophobic behavior of bare PCL electrospun fibers could be reduced, with a marked decrease already for a thin coating of less than 50 nm. Instead, the wettability of PCL vs. apolar liquids was altered in a less predictable manner, i.e., producing an initial increase of the oil contact angles (OCA) for thin lignin coating, followed by a steady decrease in OCA for higher densities of deposited lignin. To highlight the effect of the lignin type on the results, two grades of oak (AL-OA) of the Quercus cerris L. species and eucalyptus (AL-EU) of the Eucalyptus camaldulensis Dehnh species were compared throughout the investigation. All grades of lignin yielded coatings with measurable antibacterial properties, which were investigated against Staphylococcus aureus and Escherichia coli, yielding superior results for AL-EU. Remarkably, the lignin coatings did not change overall porosity but smoothed the surface roughness and allowed modulating air permeability, which is relevant for filtration applications. The findings are relevant for applications of this abundant biopolymer not only for filtration but also in biotechnology, health, packaging, and circular economy applications in general, where the reuse of such natural byproducts also brings a fundamental demanufacturing advantage.

Innovative Multilayer Electrospun Patches for the Slow Release of Natural Oily Extracts as Dressings to Boost Wound Healing.

Electrospinning is an advanced manufacturing strategy used to create innovative medical devices from continuous nanoscale fibers that is endowed with tunable biological, chemical, and physical properties. Innovative medical patches manufactured entirely by electrospinning are discussed in this paper, using a specific plant-derived formulation "1 Primary Wound Dressing©" (1-PWD) as an active pharmaceutical ingredient (API). 1-PWD is composed of neem oil (Azadirachta indica A. Juss.) and the oily extracts of Hypericum perforatum (L.) flowers, according to the formulation patented by the ENEA of proven therapeutic efficacy as wound dressings. The goal of this work is to encapsulate this API and demonstrate that its slow release from an engineered electrospun patch can increase the therapeutic efficacy for wound healing. The prototyped patch is a three-layer core-shell membrane, with a core made of fibers from a 1-PWD-PEO blend, enveloped within two external layers made of medical-grade polycaprolactone (PCL), ensuring mechanical strength and integrity during manipulation. The system was characterized via electron microscopy (SEM) and chemical and contact angle tests. The encapsulation, release, and efficacy of the API were confirmed by FTIR and LC-HRMS and were validated via in vitro toxicology and scratch assays.

Unveiling the pathophysiology of restless legs syndrome through transcriptome analysis.

The aim of this study was to analyze signaling pathways associated with differentially expressed messenger RNAs in people with restless legs syndrome (RLS). Seventeen RLS patients and 18 controls were enrolled. Coding RNA expression profiling of 12,857 gene transcripts by next-generation sequencing was performed. Enrichment analysis by pathfindR tool was carried-out, with p-adjusted ≤0.001 and fold-change ≥2.5. Nine main different network groups were significantly dysregulated in RLS: infections, inflammation, immunology, neurodegeneration, cancer, neurotransmission and biological, blood and metabolic mechanisms. Genetic predisposition plays a key role in RLS and evidence indicates its inflammatory nature; the high involvement of mainly neurotropic viruses and the TORCH complex might trigger inflammatory/immune reactions in genetically predisposed subjects and activate a series of biological pathways-especially IL-17, receptor potential channels, nuclear factor kappa-light-chain-enhancer of activated B cells, NOD-like receptor, mitogen-activated protein kinase, p53, mitophagy, and ferroptosis-involved in neurotransmitter mechanisms, synaptic plasticity, axon guidance, neurodegeneration, carcinogenesis, and metabolism.

iMir: an integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq.

BACKGROUND: Qualitative and quantitative analysis of small non-coding RNAs by next generation sequencing (smallRNA-Seq) represents a novel technology increasingly used to investigate with high sensitivity and specificity RNA population comprising microRNAs and other regulatory small transcripts. Analysis of smallRNA-Seq data to gather biologically relevant information, i.e. detection and differential expression analysis of known and novel non-coding RNAs, target prediction, etc., requires implementation of multiple statistical and bioinformatics tools from different sources, each focusing on a specific step of the analysis pipeline. As a consequence, the analytical workflow is slowed down by the need for continuous interventions by the operator, a critical factor when large numbers of datasets need to be analyzed at once. RESULTS: We designed a novel modular pipeline (iMir) for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, differential expression analysis, biological target prediction and other useful options by integrating multiple open source modules and resources in an automated workflow. As statistics is crucial in deep-sequencing data analysis, we devised and integrated in iMir tools based on different statistical approaches to allow the operator to analyze data rigorously. The pipeline created here proved to be efficient and time-saving than currently available methods and, in addition, flexible enough to allow the user to select the preferred combination of analytical steps. We present here the results obtained by applying this pipeline to analyze simultaneously 6 smallRNA-Seq datasets from either exponentially growing or growth-arrested human breast cancer MCF-7 cells, that led to the rapid and accurate identification, quantitation and differential expression analysis of ~450 miRNAs, including several novel miRNAs and isomiRs, as well as identification of the putative mRNA targets of differentially expressed miRNAs. In addition, iMir allowed also the identification of ~70 piRNAs (piwi-interacting RNAs), some of which differentially expressed in proliferating vs growth arrested cells. CONCLUSION: The integrated data analysis pipeline described here is based on a reliable, flexible and fully automated workflow, useful to rapidly and efficiently analyze high-throughput smallRNA-Seq data, such as those produced by the most recent high-performance next generation sequencers. iMir is available at http://www.labmedmolge.unisa.it/inglese/research/imir.

Computed tomographic colonography for colorectal cancer screening: risk factors for the detection of advanced neoplasia.

BACKGROUND: The objective of this study was to determine whether age, sex, a positive family history of colorectal cancer, and body mass index (BMI) are important predictors of advanced neoplasia in the setting of screening computed tomographic colonography (CTC). METHODS: Consecutive patients who were referred for first-time screening CTC from 2004 to 2011 at a single medical center were enrolled. Results at pathology were recorded for all patients who underwent polypectomy. Logistic regression was used to identify significant predictor variables for advanced neoplasia (any adenoma ≥ 10 mm or with villous component, high-grade dysplasia, or adenocarcinoma). Odds ratios (ORs) were used to express associations between the study variables (age, sex, BMI, and a positive family history of colorectal cancer) and advanced neoplasia. RESULTS: In total, 7620 patients underwent CTC screening. Of these, 276 patients (3.6%; 95% confidence interval [CI], 3.2%-4.1%) ultimately were diagnosed with advanced neoplasia. At multivariate analysis, age (mean OR per 10-year increase, 1.8; 95% CI, 1.6-2.0) and being a man (OR, 1.7; 95% CI, 1.3-2.2) were independent predictors of advanced neoplasia, whereas BMI and a positive family history of colorectal cancer were not. The number needed to screen to detect 1 case of advanced neoplasia varied from 51 among women aged ≤ 55 years to 10 among men aged >65 years. The number of post-CTC colonoscopies needed to detect 1 case of advanced neoplasia varied from 2 to 4. CONCLUSIONS: Age and sex were identified as important independent predictors of advanced neoplasia risk in individuals undergoing screening CTC, whereas BMI and a positive family history of colorectal cancer were not. These results have implications for appropriate patient selection.

Variation in diagnostic performance among radiologists at screening CT colonography.

PURPOSE: To assess the variation in diagnostic performance among radiologists at screening computed tomographic (CT) colonography. MATERIALS AND METHODS: In this HIPAA-compliant, institutional review board-approved study, 6866 asymptomatic adults underwent first-time CT colonographic screening at a single center between January 2005 and November 2011. Results of examinations were interpreted by one of eight board-certified abdominal radiologists (mean number of CT colonographic studies per reader, 858; range, 131-2202). Findings at CT colonography and subsequent colonoscopy were recorded, and key measures of diagnostic performance, including adenoma and advanced neoplasia detection rate, were compared among the radiologists. RESULTS: The overall prevalence of histopathologically confirmed advanced neoplasia was 3.6% and did not differ significantly among radiologists (range, 2.4%-4.4%; P = .067; P = .395 when one outlier was excluded). Overall, 19.5% of polyps detected at CT colonography proved to be advanced neoplasia and did not differ significantly among radiologists (range, 14.4%-23.2%; P = .223). The overall per-polyp endoscopic confirmation rate was 93.5%, ranging from 80.0% to 97.6% among radiologists (P = .585). The overall percentage of nondiagnostic CT colonographic examinations was 0.7% and was consistent among radiologists (range, 0.3%-1.1%; P = .509). CONCLUSION: Consistent performance for adenoma and advanced neoplasia detection, as well as other clinically relevant end points, were observed among radiologists at CT colonographic screening.

Influence of vision and dental occlusion on body posture in pilots.

INTRODUCTION: Air force pilots have great postural control, movement coordination, motor learning, and motor transformation. They undergo abnormal stresses during flight that affect their organs and systems, with consequences such as barodontalgia, bruxism, TMJ dysfunctions, and cervical pain. The aim of this study was to evaluate the influence of dental occlusion and vision on their body posture. METHODS: In collaboration with the "A. Mosso" Legal Medical Institute (Aeronautica Militare), two groups, consisting of 20 air force and 20 civilian pilots, were selected for the study using a protocol approved by the Italian Air Force. An oral examination and a force platform test were performed in order to evaluate the subjects' postural system efficiency. A MANOVA (Multivariate analysis of variance) analysis was performed by using the Wilkes' criterion, in order to statistically evaluate the influence of each factor. RESULTS: Both the sway area and velocity parameters are very strongly influenced by vision: the sway area increases by approximately 32% and the sway velocity increases by approximately 50% when the pilot closes his eyes. Only the sway area parameter was significantly influenced by the mandibular position: the mandibular position with eyes open changed the sway area by about 51% and with eyes closed by about 40%. No statistically significant differences were found between air force and civilian pilots. DISCUSSION: The results of this analysis show that occlusion and visual function could influence posture in air force and civilian pilots.

Towards a Material-by-Design Approach to Electrospun Scaffolds for Tissue Engineering Based on Statistical Design of Experiments (DOE).

Electrospinning bears great potential for the manufacturing of scaffolds for tissue engineering, consisting of a porous mesh of ultrafine fibers that effectively mimic the extracellular matrix (ECM) and aid in directing stem cell fate. However, for engineering purposes, there is a need to develop material-by-design approaches based on predictive models. In this methodological study, a rational methodology based on statistical design of experiments (DOE) is discussed in detail, yielding heuristic models that capture the linkage between process parameters (Xs) of the electrospinning and scaffold properties (Ys). Five scaffolds made of polycaprolactone are produced according to a 22-factorial combinatorial scheme where two Xs, i.e., flow rate and applied voltage, are varied between two given levels plus a center point. The scaffolds were characterized to measure a set of properties (Ys), i.e., fiber diameter distribution, porosity, wettability, Young's modulus, and cell adhesion on murine myoblast C1C12 cells. Simple engineering DOE models were obtained for all Ys. Each Y, for example, the biological response, can be used as a driver for the design process, using the process-property model of interest for accurate interpolation within the design domain, enabling a material-by-design strategy and speeding up the product development cycle. The implications are also illustrated in the context of the design of multilayer scaffolds with microstructural gradients and controlled properties of each layer. The possibility of obtaining statistical models correlating between diverse output properties of the scaffolds is highlighted. Noteworthy, the featured DOE approach can be potentially merged with artificial intelligence tools to manage complexity and it is applicable to several fields including 3D printing.