Environmental DNA metabarcoding reveals the effects of seafloor litter and trawling on marine biodiversity

Environmental DNA (eDNA) techniques are emerging as promising tools for monitoring marine communities. However, they have not been applied to study the integrated effects of anthropogenic pressures on marine biodiversity. This study examined the relationships between demersal community species composition, key environmental features, and anthropogenic impacts such as fishing effort and seafloor litter using eDNA data in the central Tyrrhenian Sea. The results indicated that both fishing effort and seafloor litter influenced species composition and diversity. The adaptive traits of marine species played a critical role in their response to debris accumulation and fishing. Mobile species appeared to use relocation strategies, while sessile species showed flexibility in the face of disturbance. Epibiotic species relied on passive transport. The use of eDNA-based methods is a valuable resource for monitoring anthropogenic impacts during scientific surveys, enhancing our ability to monitor marine ecosystems and more effectively assess the effects of pollution.

Neuronal STING activation in amyotrophic lateral sclerosis and frontotemporal dementia

The stimulator of interferon genes (STING) pathway has been implicated in neurodegenerative diseases, including Parkinson's disease and amyotrophic lateral sclerosis (ALS). While prior studies have focused on STING within immune cells, little is known about STING within neurons. Here, we document neuronal activation of the STING pathway in human postmortem cortical and spinal motor neurons from individuals affected by familial or sporadic ALS. This process takes place selectively in the most vulnerable cortical and spinal motor neurons but not in neurons that are less affected by the disease. Concordant STING activation in layer V cortical motor neurons occurs in a mouse model of C9orf72 repeat-associated ALS and frontotemporal dementia (FTD). To establish that STING activation occurs in a neuron-autonomous manner, we demonstrate the integrity of the STING signaling pathway, including both upstream activators and downstream innate immune response effectors, in dissociated mouse cortical neurons and neurons derived from control human induced pluripotent stem cells (iPSCs). Human iPSC-derived neurons harboring different familial ALS-causing mutations exhibit increased STING signaling with DNA damage as a main driver. The elevated downstream inflammatory markers present in ALS iPSC-derived neurons can be suppressed with a STING inhibitor. Our results reveal an immunophenotype that consists of innate immune signaling driven by the STING pathway and occurs specifically within vulnerable neurons in ALS/FTD.

Unveiling the SOD1-mediated ALS phenotype: insights from a comprehensive meta-analysis

BACKGROUND AND OBJECTIVES

Amyotrophic lateral sclerosis associated with mutations in SOD1 (SOD1-ALS) might be susceptible to specific treatment. The aim of the study is to outline the clinical features of SOD1-ALS patients by comparing them to patients without ALS major gene variants and patients with variants in other major ALS genes. Defining SOD1-ALS phenotype may assist clinicians in identifying patients who should be prioritized for genetic testing.

METHODS

We performed an extensive literature research including original studies which reported the clinical features of SOD1-ALS and at least one of the following patient groups: C9ORF72 hexanucleotide repeat expansion (C9-ALS), TARDBP (TARDBP-ALS), FUS (FUS-ALS) or patients without a positive test for a major-ALS gene (N-ALS). A random effects meta-analytic model was applied to clinical data extracted encompassing sex, site and age of onset. To reconstruct individual patient survival data, the published Kaplan-Meier curves were digitized. Data were measured as odds ratio (OR) or standardized mean difference (SMD) as appropriate. Median survival was compared between groups.

RESULTS

Twenty studies met the inclusion criteria. We identified 721 SOD1-ALS, 470 C9-ALS, 183 TARDBP-ALS, 113 FUS-ALS and 2824 N-ALS. SOD1-ALS showed a higher rate of spinal onset compared with N-ALS and C9-ALS (OR = 4.85, 95% CI = 3.04-7.76; OR = 10.47, 95% CI = 4.32-27.87) and an earlier onset compared with N-ALS (SMD = - 0.45, 95% CI = - 0.72 to - 0.18). SOD1-ALS had a similar survival compared with N-ALS (p = 0.14), a longer survival compared with C9-ALS (p < 0.01) and FUS-ALS (p = 0.019) and a shorter survival compared with TARDBP-ALS (p < 0.01).

DISCUSSION

This study indicates the presence of a specific SOD1-ALS phenotype. Insights in SOD1-ALS clinical features are important in genetic counseling, disease prognosis and support patients' stratification in clinical trials.

What, where, and when: Spatial-temporal distribution of macro-litter on the seafloor of the western and central Mediterranean sea

The progressive increase of marine macro-litter on the bottom of the Mediterranean Sea is an urgent problem that needs accurate information and guidance to identify those areas most at risk of accumulation. In the absence of dedicated monitoring programs, an important source of opportunistic data is fishery-independent monitoring campaigns of demersal resources. These data have long been used but not yet extensively. In this paper, MEDiterranean International Trawl Survey (MEDITS) data was supplemented with 18 layers of information related to major environmental (e.g. depth, sea water and wind velocity, sea waves) and anthropogenic (e.g. river inputs, shipping lanes, urban areas and ports, fishing effort) forcings that influence seafloor macro-litter distribution. The Random Forest (RF), a machine learning approach, was applied to: i) model the distribution of several litter categories at a high spatial resolution (i.e. 1 km2); ii) identify major accumulation hot spots and their temporal trends. Results indicate that RF is a very effective approach to model the distribution of marine macro-litter and provides a consistent picture of the heterogeneous distribution of different macro-litter categories. The most critical situation in the study area was observed in the north-eastern part of the western basin. In addition, the combined analysis of weight and density data identified a tendency for lighter items to accumulate in areas (such as the northern part of the Tyrrhenian Sea) with more stagnant currents. This approach, based on georeferenced information widely available in public databases, seems a natural candidate to be applied in other basins as a support and complement tool to field monitoring activities and strategies for protection and remediation of the most impacted areas.

Structural and Functional Brain Network Connectivity at Different King's Stages in Patients With Amyotrophic Lateral Sclerosis

BACKGROUND AND OBJECTIVES

There is currently no validated disease-stage biomarker for amyotrophic lateral sclerosis (ALS). The identification of quantitative and reproducible markers of disease stratification in ALS is fundamental for study design definition and inclusion of homogenous patient cohorts into clinical trials. Our aim was to assess the rearrangements of structural and functional brain connectivity underlying the clinical stages of ALS, to suggest objective, reproducible measures provided by MRI connectomics mirroring disease staging.

METHODS

In this observational study, patients with ALS and healthy controls (HCs) underwent clinical evaluation and brain MRI on a 3T scanner. Patients were classified into 4 groups, according to the King's staging system. Structural and functional brain connectivity matrices were obtained using diffusion tensor and resting-state fMRI data, respectively. Whole-brain network-based statistics (NBS) analysis and comparisons of intraregional and inter-regional connectivity values using analysis of covariance models were performed between groups. Correlations between MRI and clinical/cognitive measures were tested using Pearson coefficient.

RESULTS

One hundred four patients with ALS and 61 age-matched and sex-matched HCs were included. NBS and regional connectivity analyses demonstrated a progressive decrease of intranetwork and internetwork structural connectivity of sensorimotor regions at increasing ALS stages in our cohort, compared with HCs. By contrast, functional connectivity showed divergent patterns between King's stages 3 (increase in basal ganglia and temporal circuits [p = 0.04 and p = 0.05, respectively]) and 4 (frontotemporal decrease [p = 0.03]), suggesting a complex interplay between opposite phenomena in late stages of the disease. Intraregional sensorimotor structural connectivity was correlated with ALS Functional Rating Scale-revised (ALSFRS-r) score (r = 0.31, p < 0.001) and upper motor neuron burden (r = -0.25, p = 0.01). Inter-regional frontal-sensorimotor structural connectivity was also correlated with ALSFRS-r (r = 0.24, p = 0.02). No correlations with cognitive measures were found.

DISCUSSION

MRI of the brain allows to demonstrate and quantify increasing disruption of structural connectivity involving the sensorimotor networks in ALS, mirroring disease stages. Frontotemporal functional disconnection seems to characterize only advanced disease phases. Our findings support the utility of MRI connectomics to stratify patients and stage brain pathology in ALS in a reproducible way, which may mirror clinical progression.

Meso- and microplastic composition, distribution patterns and drivers: A snapshot of plastic pollution on Brazilian beaches

Pollution by plastics is a worldwide problem on par with climatic change and biological invasions. In coastal sediments, plastic particles tend to accumulate and persist over the long term. We assessed the plastic pollution using a standardized surface sediment sampling protocol on 22 sandy beaches along >4600 km of the Brazilian coast. The abundance, size, color, type, and polymeric composition of all meso- and microplastic items found in the surveys were processed to disclose spatial patterns of distribution and pollution associated drivers. A General Linear Model (GLM) was run to investigate how the predictor variables influenced overall beach plastic amounts and by plastic type and size class. Overall, 3114 plastic items were found, with microplastics comprising just over half of all items (54 %). Most items were either white (60 %) or blue (13 %), while polystyrene foam (45 %) and fragments (39 %) comprised the most abundant plastic types. The principal polymers were Polyethylene (40 %) and Polypropylene (32 %). The analyses indicated that the distribution of plastic litter along beaches is determined by three predictive variables: the distance to the nearest estuary (-), tourism (+), and the number of inhabitants in the nearest urban center (+). Tourist (highly-visited) beaches and those near estuarine runoffs or urban centers presented the highest plastic pollution rates. The unveiling of plastic pollution patterns through a large-scale systematic survey is essential for future management guidance and science-based decisions for mitigating and solving the plastic pollution crisis.

Label-Free Intracellular Multi-Specificity in Yeast Cells by Phase-Contrast Tomographic Flow Cytometry

In-flow phase-contrast tomography provides a 3D refractive index of label-free cells in cytometry systems. Its major limitation, as with any quantitative phase imaging approach, is the lack of specificity compared to fluorescence microscopy, thus restraining its huge potentialities in single-cell analysis and diagnostics. Remarkable results in introducing specificity are obtained through artificial intelligence (AI), but only for adherent cells. However, accessing the 3D fluorescence ground truth and obtaining accurate voxel-level co-registration of image pairs for AI training is not viable for high-throughput cytometry. The recent statistical inference approach is a significant step forward for label-free specificity but remains limited to cells' nuclei. Here, a generalized computational strategy based on a self-consistent statistical inference to achieve intracellular multi-specificity is shown. Various subcellular compartments (i.e., nuclei, cytoplasmic vacuoles, the peri-vacuolar membrane area, cytoplasm, vacuole-nucleus contact site) can be identified and characterized quantitatively at different phases of the cells life cycle by using yeast cells as a biological model. Moreover, for the first time, virtual reality is introduced for handling the information content of multi-specificity in single cells. Full fruition is proofed for exploring and interacting with 3D quantitative biophysical parameters of the identified compartments on demand, thus opening the route to a metaverse for 3D microscopy.

Clinical Features and Biomarkers to Differentiate Primary and Amyotrophic Lateral Sclerosis in Patients With an Upper Motor Neuron Syndrome

OBJECTIVES

Differentiation between primary (PLS) and amyotrophic lateral sclerosis (ALS) entails relevant consequences for prognosis and management but is mostly unreliable at early stages. The objectives of the study are (1) to determine the features at onset that could help to differentiate between PLS and ALS, (2) to evaluate the diagnostic performance of an integrated serum biomarker panel, and (3) to identify the prognostic factors for patients presenting with upper motor neuron (UMN) syndrome.

METHODS

We selected and retrospectively analyzed the clinical data of patients presenting with UMN syndrome. At the first evaluation, when available, serum biomarkers were measured using ultrasensitive single molecule array.

RESULTS

The study population included 55 patients with PLS and 50 patients with ALS. Patients with PLS presented a longer time to first neurologic evaluation (PLS: 35.0 months, interquartile range [IQR] 17.0-38.0 months; ALS: 12.5 months, IQR 7.0-21.3 months; p < 0.01) and lower levels of neurofilament light chain (NfL) (PLS: 81.8 pg/mL, IQR 38.4-111.1 pg/mL; ALS: 155.9 pg/mL, IQR 85.1-366.4 pg/mL; p = 0.01). Two patients with PLS and 3 patients with ALS carried the C9orf72 expansion. NfL resulted an independent predictor of final diagnosis (odds ratio 1.01, 95% CI 1.00-1.02; p = 0.04) and an independent prognostic factor (hazard ratio 1.01, 95% CI 1.00-1.01; p < 0.01).

DISCUSSION

NfL might help to differentiate patients with PLS from patients with ALS and to predict prognosis in patients with UMN syndrome.

Tako-Tsubo Syndrome in Amyotrophic Lateral Sclerosis: Single-Center Case Series and Brief Literature Review

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease with variable phenotypic expressions which has been associated with autonomic dysfunction. The cardiovascular system seems to be affected especially in the context of bulbar involvement. We describe four new cases of Tako-Tsubo syndrome (TTS) in ALS patients with an appraisal of the literature. We present a late-stage ALS patient with prominent bulbar involvement that presented TTS during hospitalization. We then retrospectively identify three additional ALS-TTS cases reporting relevant clinical findings. TTS cardiomyopathy has been observed in different acute neurological conditions, and the co-occurrence of ALS and TTS has already been reported. Cardiovascular autonomic dysfunctions have been described in ALS, especially in the context of an advanced diseases and with bulbar involvement. Noradrenergic hyperfunction linked to sympathetic denervation and ventilatory deficits coupled in different instances with a trigger event could play a synergistic role in the development of TTS in ALS. Sympathetic hyperfunctioning and ventilatory deficits in conjunction with cardiac autonomic nerves impairment may play a role in the development of TTS in a context of ALS.

Role of [68Ga]Ga-PSMA-11 PET radiomics to predict post-surgical ISUP grade in primary prostate cancer

PURPOSE

The aim of this study is to investigate the role of [68Ga]Ga-PSMA-11 PET radiomics for the prediction of post-surgical International Society of Urological Pathology (PSISUP) grade in primary prostate cancer (PCa).

METHODS

This retrospective study included 47 PCa patients who underwent [68Ga]Ga-PSMA-11 PET at IRCCS San Raffaele Scientific Institute before radical prostatectomy. The whole prostate was manually contoured on PET images and 103 image biomarker standardization initiative (IBSI)-compliant radiomic features (RFs) were extracted. Features were then selected using the minimum redundancy maximum relevance algorithm and a combination of the 4 most relevant RFs was used to train 12 radiomics machine learning models for the prediction of PSISUP grade: ISUP ≥ 4 vs ISUP < 4. Machine learning models were validated by means of fivefold repeated cross-validation, and two control models were generated to assess that our findings were not surrogates of spurious associations. Balanced accuracy (bACC) was collected for all generated models and compared with Kruskal-Wallis and Mann-Whitney tests. Sensitivity, specificity, and positive and negative predictive values were also reported to provide a complete overview of models' performance. The predictions of the best performing model were compared against ISUP grade at biopsy.

RESULTS

ISUP grade at biopsy was upgraded in 9/47 patients after prostatectomy, resulting in a bACC = 85.9%, SN = 71.9%, SP = 100%, PPV = 100%, and NPV = 62.5%, while the best-performing radiomic model yielded a bACC = 87.6%, SN = 88.6%, SP = 86.7%, PPV = 94%, and NPV = 82.5%. All radiomic models trained with at least 2 RFs (GLSZM-Zone Entropy and Shape-Least Axis Length) outperformed the control models. Conversely, no significant differences were found for radiomic models trained with 2 or more RFs (Mann-Whitney p > 0.05).

CONCLUSION

These findings support the role of [68Ga]Ga-PSMA-11 PET radiomics for the accurate and non-invasive prediction of PSISUP grade.

Corrigendum to "Going for a stroll on lurasidone: Considerations on an atypical case of acute compartment syndrome of both legs" [Heliyon 9(4) (April 2023) e15047]

[This corrects the article DOI: 10.1016/j.heliyon.2023.e15047.].

Emerging Trends in the Field of Inflammation and Proteinopathy in ALS/FTD Spectrum Disorder

Proteinopathy and neuroinflammation are two main hallmarks of neurodegenerative diseases. They also represent rare common events in an exceptionally broad landscape of genetic, environmental, neuropathologic, and clinical heterogeneity present in patients. Here, we aim to recount the emerging trends in amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD) spectrum disorder. Our review will predominantly focus on neuroinflammation and systemic immune imbalance in ALS and FTD, which have recently been highlighted as novel therapeutic targets. A common mechanism of most ALS and ~50% of FTD patients is dysregulation of TAR DNA-binding protein 43 (TDP-43), an RNA/DNA-binding protein, which becomes depleted from the nucleus and forms cytoplasmic aggregates in neurons and glia. This, in turn, via both gain and loss of function events, alters a variety of TDP-43-mediated cellular events. Experimental attempts to target TDP-43 aggregates or manipulate crosstalk in the context of inflammation will be discussed. Targeting inflammation, and the immune system in general, is of particular interest because of the high plasticity of immune cells compared to neurons.

Impact of prostate imaging quality (PI-QUAL) score on the detection of clinically significant prostate cancer at biopsy

PURPOSE

To investigate the impact of Prostate Imaging Quality (PI-QUAL) scores on the diagnostic performance of multiparametric MRI (mpMRI) in a targeted biopsy cohort.

PATIENTS AND METHODS

300 patients who underwent both mpMRI and biopsy were included. PI-QUAL scores were retrospectively assigned by two radiologists in consensus and were correlated to pre-biopsy PI-RADS scores and biopsy outcomes. Clinically significant prostate cancer (csPCa) was defined as ISUP grade ≥ 2.

RESULTS

Image quality was optimal (PI-QUAL ≥ 4) in 249/300 (83%) and suboptimal (PI-QUAL < 4) in 51/300 (17%). The proportion of PI-RADS 3 scores referred for biopsy was higher in scans of suboptimal vs optimal quality (51% vs 33%). For PI-QUAL < 4 scans, the positive predictive value (PPV) was lower compared to PI-QUAL ≥ 4 (35% [95%CI: 22, 48] vs 48% [95%CI: 41, 55]; difference -13% [95%CI: -27, 2]; p 0.090), as was the detection rate of csPCa in both PI-RADS 3 and PI-RADS 4-5 (15% vs 23% and 56 vs 63%, respectively). The overall MRI quality increased over time.

CONCLUSIONS

Scan quality may affect the diagnostic performance of prostate mpMRI in patients undergoing MRI-guided biopsy. Scans of suboptimal quality (PI-QUAL < 4) were associated with lower PPV for csPCa.

Going for a stroll on lurasidone: Considerations on an atypical case of acute compartment syndrome of both legs

Non-traumatic acute bilateral compartment syndrome is a rare condition that may lead to limb ischemia. We describe a case of this syndrome occurring after a five-kilometer walk in a young woman receiving chronic treatment with lurasidone, leading to a bilateral foot-drop and rhabdomyolysis of the anterolateral compartment of both legs. Due to her late presentation in the emergency department, we opted for a conservative approach, closely monitoring her renal function. We noticed a subsequent clinical and biochemical improvement over the following days, with the patient returning to her daily routine in a matter of weeks, despite a persisting bilateral foot drop. Since atypical antipsychotics are known to be associated with rhabdomyolysis, while possibly exerting a toxic effect on mitochondria, we hypothesize that a mild aerobic physical exertion might have triggered the event, in the context of an iatrogenic muscle susceptibility to oxidative distress.

External validation of a convolutional neural network for the automatic segmentation of intraprostatic tumor lesions on 68Ga-PSMA PET images

Introduction

State of the art artificial intelligence (AI) models have the potential to become a "one-stop shop" to improve diagnosis and prognosis in several oncological settings. The external validation of AI models on independent cohorts is essential to evaluate their generalization ability, hence their potential utility in clinical practice. In this study we tested on a large, separate cohort a recently proposed state-of-the-art convolutional neural network for the automatic segmentation of intraprostatic cancer lesions on PSMA PET images.

Methods

Eighty-five biopsy proven prostate cancer patients who underwent ⁶⁸Ga PSMA PET for staging purposes were enrolled in this study. Images were acquired with either fully hybrid PET/MRI (N = 46) or PET/CT (N = 39); all participants showed at least one intraprostatic pathological finding on PET images that was independently segmented by two Nuclear Medicine physicians. The trained model was available at https://gitlab.com/dejankostyszyn/prostate-gtv-segmentation and data processing has been done in agreement with the reference work.

Results

When compared to the manual contouring, the AI model yielded a median dice score = 0.74, therefore showing a moderately good performance. Results were robust to the modality used to acquire images (PET/CT or PET/MRI) and to the ground truth labels (no significant difference between the model's performance when compared to reader 1 or reader 2 manual contouring).

Discussion

In conclusion, this AI model could be used to automatically segment intraprostatic cancer lesions for research purposes, as instance to define the volume of interest for radiomics or deep learning analysis. However, more robust performance is needed for the generation of AI-based decision support technologies to be proposed in clinical practice.

GLOVE: The Global Plastic Ingestion Initiative for a cleaner world

Plastics are one of the most used materials in the world. Their indiscriminate use and inappropriate disposal have led to inevitable impacts, for instance ingestion, on the environment arousing the attention of the global community. In addition, plastic ingestion studies are often written in scientific jargon or hidden behind paywalls, which makes these studies inaccessible. GLOVE is an online and open-access dashboard database available at gloveinitiative.shinyapps.io/Glove/ to support scientists, decision-makers, and society with information collected from plastic ingestion studies. The platform was created in the R environment, with a web interface developed through Shiny. It already comprises 530 studies, including all biological groups, with 245,366 individual records of 1458 species found in marine, freshwater, and terrestrial environments. The main goal of the GLOVE dashboard database is to improve data accessibility by being a scientifically useful grounded tool for designing effective and innovative actions in the current scenario of upcoming global and local agreements and actions on plastic pollution.

Detection of community-wide impacts of bottom trawl fishing on deep-sea assemblages using environmental DNA metabarcoding

Although considerable research progress on the effects of anthropogenic disturbance in the deep sea has been made in recent years, our understanding of these impacts at community level remains limited. Here, we studied deep-sea assemblages of Sicily (Mediterranean Sea) subject to different intensities of benthic trawling using environmental DNA (eDNA) metabarcoding and taxonomic identification of meiofauna communities. Firstly, eDNA metabarcoding data did not detect trawling impacts using alpha diversity whereas meiofauna data detected a significant effect of trawling. Secondly, both eDNA and meiofauna data detected significantly different communities across distinct levels of trawling intensity when we examined beta diversity. Taxonomic assignment of the eDNA data revealed that Bryozoa was present only at untrawled sites, highlighting their vulnerability to trawling. Our results provide evidence for community-wide impacts of trawling, with different trawling intensities leading to distinct deep-sea communities. Finally, we highlight the need for further studies to unravel understudied deep-sea biodiversity.

Hmga2 protein loss alters nuclear envelope and 3D chromatin structure

BACKGROUND

The high-mobility group Hmga family of proteins are non-histone chromatin-interacting proteins which have been associated with a number of nuclear functions, including heterochromatin formation, replication, recombination, DNA repair, transcription, and formation of enhanceosomes. Due to its role based on dynamic interaction with chromatin, Hmga2 has a pathogenic role in diverse tumors and has been mainly studied in a cancer context; however, whether Hmga2 has similar physiological functions in normal cells remains less explored. Hmga2 was additionally shown to be required during the exit of embryonic stem cells (ESCs) from the ground state of pluripotency, to allow their transition into epiblast-like cells (EpiLCs), and here, we use that system to gain further understanding of normal Hmga2 function.

RESULTS

We demonstrated that Hmga2 KO pluripotent stem cells fail to develop into EpiLCs. By using this experimental system, we studied the chromatin changes that take place upon the induction of EpiLCs and we observed that the loss of Hmga2 affects the histone mark H3K27me3, whose levels are higher in Hmga2 KO cells. Accordingly, a sustained expression of polycomb repressive complex 2 (PRC2), responsible for H3K27me3 deposition, was observed in KO cells. However, gene expression differences between differentiating wt vs Hmga2 KO cells did not show any significant enrichments of PRC2 targets. Similarly, endogenous Hmga2 association to chromatin in epiblast stem cells did not show any clear relationships with gene expression modification observed in Hmga2 KO. Hmga2 ChIP-seq confirmed that this protein preferentially binds to the chromatin regions associated with nuclear lamina. Starting from this observation, we demonstrated that nuclear lamina underwent severe alterations when Hmga2 KO or KD cells were induced to exit from the naïve state and this phenomenon is accompanied by a mislocalization of the heterochromatin mark H3K9me3 within the nucleus. As nuclear lamina (NL) is involved in the organization of 3D chromatin structure, we explored the possible effects of Hmga2 loss on this phenomenon. The analysis of Hi-C data in wt and Hmga2 KO cells allowed us to observe that inter-TAD (topologically associated domains) interactions in Hmga2 KO cells are different from those observed in wt cells. These differences clearly show a peculiar compartmentalization of inter-TAD interactions in chromatin regions associated or not to nuclear lamina.

CONCLUSIONS

Overall, our results indicate that Hmga2 interacts with heterochromatic lamin-associated domains, and highlight a role for Hmga2 in the crosstalk between chromatin and nuclear lamina, affecting the establishment of inter-TAD interactions.

Integrated evaluation of a panel of neurochemical biomarkers to optimize diagnosis and prognosis in amyotrophic lateral sclerosis

BACKGROUND AND PURPOSE

This study was undertaken to determine the diagnostic and prognostic value of a panel of serum biomarkers and to correlate their concentrations with several clinical parameters in a large cohort of patients with amyotrophic lateral sclerosis (ALS).

METHODS

One hundred forty-three consecutive patients with ALS and a control cohort consisting of 70 patients with other neurodegenerative disorders (DEG), 70 patients with ALS mimic disorders (ALSmd), and 45 healthy controls (HC) were included. Serum neurofilament light chain (NfL), ubiquitin carboxyl-terminal hydrolase isozyme L1 (UCHL1), glial fibrillary acidic protein (GFAP), and total tau protein levels were measured using ultrasensitive single molecule array.

RESULTS

NfL correlated with disease progression rate (p < 0.001) and with the measures of upper motor neuron burden (p < 0.001). NfL was higher in the ALS patients with classic and pyramidal phenotype. GFAP was raised in ALS with cognitive-behavioral impairment compared with ALS with normal cognition. NfL displayed the best diagnostic performance in discriminating ALS from HC (area under the curve [AUC] = 0.990), DEG (AUC = 0.946), and ALSmd (AUC = 0.850). UCHL1 performed well in distinguishing ALS from HC (AUC = 0.761), whereas it was not helpful in differentiating ALS from DEG and ALSmd. In multivariate analysis, NfL (p < 0.001) and UCHL1 (p = 0.038) were independent prognostic factors. Survival analysis combining NfL and UCHL1 effectively stratified patients with lower NfL levels (p < 0.001).

CONCLUSIONS

NfL is a useful biomarker for the diagnosis of ALS and the strongest predictor of survival. UCHL1 is an independent prognostic factor helpful in stratifying survival in patients with low NfL levels, likely to have slowly progressive disease. GFAP reflects extramotor involvement, namely cognitive impairment or frontotemporal dementia.

NEK1 Variants in a Cohort of Italian Patients With Amyotrophic Lateral Sclerosis

Introduction

In the last few years, different studies highlighted a significant enrichment of NEK1 loss of function (LoF) variants in amyotrophic lateral sclerosis (ALS), and an additional role for the p.Arg261His missense variant in the disease susceptibility. Several other missense variants have been described so far, whose pathogenic relevance remains however unclear since many of them have been reported in both patients and controls. This study aimed to investigate the presence of NEK1 variants and their correlation with phenotype in a cohort of Italian patients with ALS.

Methods

We sequenced a cohort of 350 unrelated Italian patients with ALS by next-generation sequencing (NGS) and then we analyzed the clinical features of NEK1 carriers.

Results

We detected 20 different NEK1 rare variants (four LoF and 16 missense) in 33 unrelated patients with sporadic ALS (sALS). The four LoF variants (two frameshift and two splice-site variants) were all novel. The p.Arg261His missense variant was enriched in the patients’ cohort (p < 0.001). Excluding this variant from counting, the difference in the frequency of NEK1 rare missense variants between patients and controls was not statistically significant. NEK1 carriers had a higher frequency of flail arm (FA) phenotype compared with the other patients of the cohort (29.2% vs. 6.4%). Nine NEK1 carriers (37.5%) also harbored variants in other ALS-related genes.

Conclusion

This study confirms that NEK1 LoF and p.Arg261. His missense variants are associated with ALS in an Italian ALS cohort and suggests a correlation between the presence of NEK1 variants and FA phenotype.

Disentangling beach litter pollution patterns to provide better guidelines for decision-making in coastal management

Beach litter represents a worldwide problem impacting both terrestrial and aquatic environments. In the present study, we assessed beach litter pollution in a prominent touristic site in Brazil, the Jericoacoara National Park. In particular, we applied a delta-generalized additive modeling (GAM) approach in order to investigate pollution hotspots and to provide better guidelines for coastal environmental managers. A total of 7549 litter items were collected, resulting hard and flexible plastics the most abundant type. Our GAM analysis revealed that the distribution of each type of litter was affected by distinct drivers in the protected area, with the extension of the beach, tourist attractions, wind angle, and the distance to water bodies and villages as the most significant explanatory variables. Our model is suitable in predicting litter pollution hotspots on beaches, which is a valuable tool for future guidelines and effective management strategies to prevent beach pollution worldwide.

Scattered accumulation hotspots of macro-litter on the seafloor: Insights for mitigation actions

Marine litter is an ever-increasing problem that demands immediate reduction plans and mitigation actions that should act synergically to efficiently meet ambitious goals. Since the seafloor has been recognized as the major sink for marine debris, the study of litter accumulation dynamics represent a fundamental tool to evaluate possible removal actions. We analysed a 7 years (2013-2019) standardized data series collected along Sardinian fishing grounds through MEDiterranean International Trawl Survey, for which estimates of density and weight of seafloor macro-litter were calculated for over 707 hauls. Results show the absence of any temporal trend in seafloor macro-litter density and weight, but rather indicate a spatial and bathymetric segregation of different litter categories. Our data showed how different sources and physical features of macro-litter items (i.e., plastic and fishing gear, rubber, glass, metals, and cloth) led to spatially segregated accumulation hotspots. We also point out here how the identification of seafloor macro-litter hotspots using aggregated data that include plastic items could obscure the identification of other segregated but yet relevant hotspots of other macro-litter categories accumulated in the marine environment. These hotspots often occurred at shallower depths and closer to coastlines, thus representing potential spots where eventual future litter removal action could be prioritized.

Evaluation of the combined effect of mobility and seasonality on the COVID-19 pandemic: a Lombardy-based study

Restrictions to human mobility had a significant role in limiting SARS-CoV-2 spread. It has been suggested that seasonality might affect viral transmissibility. Our study retrospectively investigates the combined effect that seasonal environmental factors and human mobility played on transmissibility of SARS-CoV-2 in Lombardy, Italy, in 2020. Environmental data were collected from accredited open-source web services. Aggregated mobility data for different points of interests were collected from Google Community Reports. The Reproduction number (Rt), based on the weekly counts of confirmed symptomatic COVID-19, non-imported cases, was used as a proxy for SARS-CoV-2 transmissibility. Assuming a non-linear correlation between selected variables, we used a Generalized Additive Model (GAM) to investigate with univariate and multivariate analyses the association between seasonal environmental factors (UV-index, temperature, humidity, and atmospheric pressure), location-specific mobility indices, and Rt. UV-index was the most effective environmental variable in predicting Rt. An optimal two-week lag-effect between changes in explanatory variables and Rt was selected. The association between Rt variations and individually taken mobility indices differed: Grocery & Pharmacy, Transit Station and Workplaces displayed the best performances in predicting Rt when individually added to the multivariate model together with UV-index, accounting for 85.0%, 85.5% and 82.6% of Rt variance, respectively. According to our results, both seasonality and social interaction policies played a significant role in curbing the pandemic. Non-linear models including UV-index and location-specific mobility indices can predict a considerable amount of SARS-CoV-2 transmissibility in Lombardy during 2020, emphasizing the importance of social distancing policies to keep viral transmissibility under control, especially during colder months.

Neurofilament light chain as a biological marker for amyotrophic lateral sclerosis: a meta-analysis study

Aim: The aim of the present metanalysis is to evaluate blood and CSF Neurofilament light chain (NfL) concentrations in ALS patients, compared to healthy controls, ALS mimic disorders (ALSmd) and other neurological diseases (OND), and to evaluate their diagnostic yield against ALSmd. Methods: Search engines were systematically investigated for relevant studies. A random effect model was applied to estimate the pooled standard mean difference in NfL levels between ALS and controls and a bivariate mixed-effects model was applied to estimate their diagnostic accuracy on blood and CSF. Results and conclusions: NfL CSF levels were higher in ALS compared with all other control groups. On blood, NfL levels were significantly higher in ALS patients compared with healthy controls and ALSmd. In a subgroup analysis, the use of SIMOA yielded to a better differentiation between ALS and controls on blood, compared with ELISA. Studies performed on CSF (AUC = 0.90) yielded to better diagnostic performances compared with those conducted on blood (AUC = 0.78). Further prospective investigations are needed to determine a diagnostic cutoff, exploitable in clinical practice.

Ecological implications beyond the ecotoxicity of plastic debris on marine phytoplankton assemblage structure and functioning

Plastic pollution is a global issue posing a threat to marine biota with ecological implications on ecosystem functioning. Micro and nanoplastic impact on phytoplankton autotrophic species (e.g., cell growth inhibition, decrease in chlorophyll a and photosynthetic efficiency and hetero-aggregates formation) have been largely documented. However, the heterogeneity of data makes rather difficult a comparison based on size (i.e. micro vs nano). In addition, knowledge gaps on the ecological impact on phytoplankton assemblage structure and functioning are evident. A new virtual meta-analysis on cause-effect relationships of micro and nanoplastics on phytoplankton species revealed the significant effect posed by polymer type on reducing cell density for tested PVC, PS and PE plastics. Linked with autotrophic phytoplankton role in atmospheric CO₂ fixation, a potential impact of plastics on marine carbon pump is discussed. The understanding of the effects of microplastics and nanoplastics on the phytoplankton functioning is fundamental to raise awareness on the overall impact on the first level of marine food web. Interactions between micro and nanoplastics and phytoplankton assemblages have been quite documented by in vitro examinations; but, further studies considering natural plankton assemblages and/or large mesocosm experiments should be performed to evaluate and try predicting ecological impacts on primary producers.

Evidence of large increases in sedimentation rates due to fish trawling in submarine canyons of the Gulf of Palermo (SW Mediterranean)

Bottom trawling in submarine canyons can affect their natural sedimentation rates, but studies addressing this issue are still scarce. In the Gulf of Palermo (SW Mediterranean), bottom trawling occurs on the slope around Oreto, Arenella and Eleuterio canyons. Analyses of excess ²¹⁰Pb concentrations and grain size fractions in sediment cores from their canyon axes revealed that sedimentation rates and silt contents increased in all canyons in the 1980s, due to the expansion of more powerful trawlers (>500 HP) to deeper fishing grounds. In Eleuterio and Arenella canyons, sedimentation rates increased by an order of magnitude (0.1-1.4 cm·yr^-1), whereas they increased less (0.1-0.7 cm·yr^-1) in Oreto Canyon, since the enhanced trawling-derived sediment fluxes into this canyon are affected by sediment resuspension from trawling along its axis. Considering the global expansion of bottom trawling, we anticipate similar alterations in other trawled canyons, with ecological consequences that should be addressed by management strategies.

Scattered accumulation hotspots of macro-litter on the seafloor: Insights for mitigation actions

Marine litter is an ever-increasing problem that demands immediate reduction plans and mitigation actions that should act synergically to efficiently meet ambitious goals. Since the seafloor has been recognized as the major sink for marine debris, the study of litter accumulation dynamics represents a fundamental tool to evaluate future removal actions. We analysed a 7 years (2013-2019) standardized data series collected along Sardinian fishing grounds through MEDiterranean International Trawl Survey, for which estimates of density and weight of seafloor macro-litter were calculated over 707 hauls. Results show the absence of any temporal trend in seafloor macro-litter density and weight, but rather indicate a spatial and bathymetric segregation of different litter categories. Our data showed how different sources and physical features of macro-litter items (i.e., plastic and fishing gears, rubber, glass, metal and textile) led to spatially segregated accumulation hotspots. These hotspots often occurred at shallower depths and closer to coastlines, representing spots where future litter removal action could be prioritized. We also point out here how the identification of seafloor macro-litter hotspots using aggregated data that include plastic items could indeed hide the identification of hotspots of other less abundant but yet detrimental macro-litter categories accumulated in the marine environment.

The potential for aflatoxin predictive risk modelling in sub-Saharan Africa: a review

This review presents the current state of aflatoxin risk prediction models and their potential for value actors throughout the food chain in sub-Saharan Africa, with a specific focus on improving smallholder farmer management practices. Several empirical and mechanistic models have been developed either in academic research or by private sector aggregators and processors in high-income countries including Australia, the USA, and Southern Europe, but these models have been only minimally applied in sub-Saharan Africa, where there is significant potential and increasing need due to climate variability. Predictions can be made based on historic occurrence data using either a mechanistic microbiological framework for aflatoxin accumulation or an empirical model based on statistical correlations with climate conditions and local agronomic factors. Model results can then be distributed to smallholders through private, public, or mobile extension services, used by policymakers for strategy or policy, or utilised by private sector institutions for management decisions. Specific agricultural advice can be given during the three most critical points in the phenological cycle: preseason insight including sowing timing and crop varieties, preharvest advice about management and harvest timing, and postharvest optimal practices including storage, drying, and market information. Model development for sub-Saharan Africa is limited by a dearth of georeferenced aflatoxin occurrence data and real-time high resolution climate data; the wide diversity of farm typologies each with significant information and technology gaps; a prevalence of informal market structures and lack of economic incentives systems; and general lack of awareness around aflatoxins and best management practices to mitigate risk. Given advancements towards solving these challenges, predictive aflatoxin models can be integrated into decision support platforms to focus on optimisation of value for smallholders by minimising yield and nutritional losses, which can propagate value throughout the production and postharvest phases.

Estimating asymptomatic SARS-CoV-2 infections in a geographic area of low disease incidence

Background

The SARS-CoV-2 infection has emerged as a rapidly spreading infection. Today it is relatively easy to isolate Covid-19 symptomatic cases, while remains problematic to control the disease spread by infected but symptom-free individuals. The control of this possible path of contagion requires drastic measures of social distancing, which imply the suspension of most activities and generate economic and social issues. This study is aimed at estimating the percentage of asymptomatic SARS-CoV-2 infection in a geographic area with relatively low incidence of Covid-19.

Methods

Blood serum samples from 388 healthy volunteers were analyzed for the presence of anti-SARS-CoV-2 IgG by using an ELISA assay based on recombinant viral nucleocapsid protein.

Results

We found that 7 out of 388 healthy volunteers, who declared no symptoms of Covid-19, like fever, cough, fatigue etc., in the preceding 5 months, have bona fide serum anti-SARS-CoV-2 IgG, that is 1.8% of the asymptomatic population (95% confidence interval: 0.69–2.91%).

Conclusions

The estimated range of asymptomatic individuals with anti-SARS-CoV-2 IgG should be between 26,565 and 112, 350. In the same geographic area, there are 4665 symptomatic diagnosed cases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06054-2.

All is fish that comes to the net: metabarcoding for rapid fisheries catch assessment

Monitoring marine resource exploitation is a key activity in fisheries science and biodiversity conservation. Since research surveys are time consuming and costly, fishery-dependent data (i.e., derived directly from fishing vessels) are increasingly credited with a key role in expanding the reach of ocean monitoring. Fishing vessels may be seen as widely ranging data-collecting platforms, which could act as a fleet of sentinels for monitoring marine life, in particular exploited stocks. Here, we investigate the possibility of assessing catch composition of single hauls carried out by trawlers by applying DNA metabarcoding to the dense water draining from fishing nets just after the end of hauling operations (hereafter "slush"). We assess the performance of this approach in portraying β-diversity and examining the quantitative relationship between species abundances in the catch and DNA amount in the slush (read counts generated by amplicon sequencing). We demonstrate that the assemblages identified using DNA in the slush satisfactorily mirror those returned by visual inspection of net content (about 71% of species and 86% of families of fish) and detect a strong relationship between read counts and species abundances in the catch. We therefore argue that this approach could be upscaled to serve as a powerful source of information on the structure of demersal assemblages and the impact of fisheries.

All is fish that comes to the net: metabarcoding for rapid fisheries catch assessment

Monitoring marine resource exploitation is a key activity in fisheries science and biodiversity conservation. Since research surveys are time consuming and costly, fishery-dependent data (i.e., derived directly from fishing vessels) are increasingly credited with a key role in expanding the reach of ocean monitoring. Fishing vessels may be seen as widely ranging data-collecting platforms, which could act as a fleet of sentinels for monitoring marine life, in particular exploited stocks. Here, we investigate the possibility of assessing catch composition of single hauls carried out by trawlers by applying DNA metabarcoding to the dense water draining from fishing nets just after the end of hauling operations (hereafter "slush"). We assess the performance of this approach in portraying β-diversity and examining the quantitative relationship between species abundances in the catch and DNA amount in the slush (read counts generated by amplicon sequencing). We demonstrate that the assemblages identified using DNA in the slush satisfactorily mirror those returned by visual inspection of net content (about 71% of species and 86% of families of fish) and detect a strong relationship between read counts and species abundances in the catch. We therefore argue that this approach could be upscaled to serve as a powerful source of information on the structure of demersal assemblages and the impact of fisheries.

Current application of neurofilaments in amyotrophic lateral sclerosis and future perspectives

Motor neuron disease includes a heterogeneous group of relentless progressive neurological disorders defined and characterized by the degeneration of motor neurons. Amyotrophic lateral sclerosis is the most common and aggressive form of motor neuron disease with no effective treatment so far. Unfortunately, diagnostic and prognostic biomarkers are lacking in clinical practice. Neurofilaments are fundamental structural components of the axons and neurofilament light chain and phosphorylated neurofilament heavy chain can be measured in both cerebrospinal fluid and serum. Neurofilament light chain and phosphorylated neurofilament heavy chain levels are elevated in amyotrophic lateral sclerosis, reflecting the extensive damage of motor neurons and axons. Hence, neurofilaments are now increasingly recognized as the most promising candidate biomarker in amyotrophic lateral sclerosis. The potential usefulness of neurofilaments regards various aspects, including diagnosis, prognosis, patient stratification in clinical trials and evaluation of treatment response. In this review paper, we review the body of literature about neurofilaments measurement in amyotrophic lateral sclerosis. We also discuss the open issues concerning the use of neurofilaments clinical practice, as no overall guideline exists to date; finally, we address the most recent evidence and future perspectives.

YAP contributes to DNA methylation remodeling upon mouse embryonic stem cell differentiation

The Yes-associated protein (YAP), one of the major effectors of the Hippo pathway together with its related protein WW-domain-containing transcription regulator 1 (WWTR1; also known as TAZ), mediates a range of cellular processes from proliferation and death to morphogenesis. YAP and WW-domain-containing transcription regulator 1 (WWTR1; also known as TAZ) regulate a large number of target genes, acting as coactivators of DNA-binding transcription factors or as negative regulators of transcription by interacting with the nucleosome remodeling and histone deacetylase complexes. YAP is expressed in self-renewing embryonic stem cells (ESCs), although it is still debated whether it plays any crucial roles in the control of either stemness or differentiation. Here we show that the transient downregulation of YAP in mouse ESCs perturbs cellular homeostasis, leading to the inability to differentiate properly. Bisulfite genomic sequencing revealed that this transient knockdown caused a genome-wide alteration of the DNA methylation remodeling that takes place during the early steps of differentiation, suggesting that the phenotype we observed might be due to the dysregulation of some of the mechanisms involved in regulation of ESC exit from pluripotency. By gene expression analysis, we identified two molecules that could have a role in the altered genome-wide methylation profile: the long noncoding RNA ephemeron, whose rapid upregulation is crucial for the transition of ESCs into epiblast, and the methyltransferase-like protein Dnmt3l, which, during the embryo development, cooperates with Dnmt3a and Dnmt3b to contribute to the de novo DNA methylation that governs early steps of ESC differentiation. These data suggest a new role for YAP in the governance of the epigenetic dynamics of exit from pluripotency.

The MINOUWApp: a web-based tool in support of by-catch and discards management

Current fishing practices often do not allow adequate selection of species or sizes of fish, resulting in unwanted catches, subsequently discarded, with the consequent negative effects on both marine communities and fisheries profitability. The cross-analysis of density patches of potential unwanted catches and distribution of fishing effort can support the identification of spatial-temporal hot-spots in which the fishing pressure should be reduced to limit the amount of discards. The MinouwApp represents a technological and methodological framework to bring different, and structurally complex, sources of georeferenced data together into a simple visual interface aiming to interactively explore temporal ranges and areas of interest. The objective is to improve the understanding of fisheries dynamics, including discards, thus contributing to the implementation of discard management plans in a context of participative, ecosystem-based fisheries management strategies.

Non-invasive CPAP in mild and moderate ARDS secondary to SARS-CoV-2

BACKGROUND

During the COVID-19 outbreak, a very high number of infected patients developed pneumonia and many of them complicated with acute respiratory distress syndrome. The optimal management of respiratory failure and the role of lung ultrasound imaging in the evaluation of efficacy of treatment are unknown.

METHODS

In March 2020 we treated 18 patients with mild and moderate ARDS secondary to SARS-CoV-2 with non-invasive continuous positive airway pressure therapy (NI-CPAP). All patients underwent lung ultrasound imaging to verify the entity of lung recruitment after NI-CPAP initiation.

RESULTS

After one hour of treatment we observed a significant improvement in PaO2/FiO2 ratio in 10 patients. Notably, only 50 % of them reached an effective improvement in lung aeration detectable with lung ultrasound. In the other 50 % or patients the improvement in PaO2/FiO2 might be related to blood redistribution and reverse of hypoxic vasoconstriction.

CONCLUSION

NI- CPAP is a valid therapeutic option in mild and moderate ARDS secondary SARS-CoV-2. Lung recruitment detected by means of lung ultrasound is a relevant but not the exclusive mechanism that underlies the therapeutic efficacy of NI-CPAP in this clinical setting.

Combination of photodynamic therapy with 5-aminolaevulinic acid and microneedling in the treatment of alopecia areata resistant to conventional therapies: our experience with 41 patients

Alopecia areata (AA) is a complex immune-mediated disorder, which is difficult to treat. The available treatment options seem to have limited benefit, help only some patients and have a high relapse rate. We evaluated a new therapeutic option for moderate to severe AA based on the combination of photodynamic therapy (PDT) with 5-aminolaevulinic acid (ALA) and microneedling (MN). In total, 14 patients were enrolled, and these were randomly divided into 3 groups: Group A (MN alone; n = 9), Group B (ALA-PDT alone; n = 15) and Group C (combination of MN and ALA-PDT; n = 17). All patients were treated once every 3 weeks for a total of six treatments. The best clinical outcome was achieved in Group C, with complete hair regrowth observed in three patients, and an improvement of ≥ 50% and < 50% of the treated areas obtained in seven and six patients, respectively. Our report suggests that combination of ALA-PDT with MN could be an additional therapeutic option in moderate to severe AA, as MN allows better skin penetration of ALA and subsequent indirect immunosuppression.

Customised multiphasic nucleus/annulus scaffold for intervertebral disc repair/regeneration

Background: In the case of a degenerated intervertebral disc (IVD), even though spinal fusion has provided good short-term clinical results, an alteration of the spine stability has been demonstrated by long-term studies. In this context, different designs of IVD prostheses have been proposed as alternative to spinal fusion. However, over the past few years, much of the recent research has been devoted to IVD tissue engineering, even if several limitations related to the complex structure of IVD are still presented.Purpose/Aim: Accordingly, the aim of the current paper was to develop a strategy in designing customised multiphasic nucleus/annulus scaffolds for IVD tissue engineering, benefiting from the great potential of reverse engineering, additive manufacturing and gels technology.Materials and Methods: The device consisted of a customised additive-manufactured poly(ε-caprolactone) scaffold with tailored architectural features as annulus and a cell-laden collagen-low molecular weight hyaluronic acid-based material as nucleus with specific rheological and functional properties. To this aim, injectability and viscoelastic properties of the hydrogel were analyzed. Furthermore, a mechanical and biological characterization of cell-laden multiphasic nucleus/annulus scaffold was performed.Results and Conclusions: Analyses on the developed devices demonstrated appropriate viscoelastic and mechanical properties. As evidenced by rheological tests, the hydrogel showed a shear-thinning behaviour, supporting the possibility to inject the material. The mechanical characterization highlighted a compressive modulus which falls in the range of lumbar discs, with the typical initial J-shaped stress-strain curve of natural IVDs. Furthermore, preliminary biological tests showed that human mesenchymal stem cells were viable over the culture period.