The role of ion homeostasis in adaptation and tolerance to acetic acid stress in yeasts.

Maintenance of asymmetric ion concentrations across cellular membranes is crucial for proper yeast cellular function. Disruptions of these ionic gradients can significantly impact membrane electrochemical potential and the balance of other ions, particularly under stressful conditions such as exposure to acetic acid. This weak acid, ubiquitous to both yeast metabolism and industrial processes, is a major inhibitor of yeast cell growth in industrial settings and a key determinant of host colonization by pathogenic yeast. Acetic acid toxicity depends on medium composition, especially on the pH (H+ concentration), but also on other ions' concentrations. Regulation of ion fluxes is essential for effective yeast response and adaptation to acetic acid stress. However, the intricate interplay among ion balancing systems and stress response mechanisms still presents significant knowledge gaps. This review offers a comprehensive overview of the mechanisms governing ion homeostasis, including H+, K+, Zn2+, Fe2+/3+, and acetate, in the context of acetic acid toxicity, adaptation, and tolerance. While focus is given on Saccharomyces cerevisiae due to its extensive physiological characterization, insights are also provided for biotechnologically and clinically relevant yeast species whenever available.

A bothremydid turtle (Pleurodira) from the middle Cenomanian of Vale de Figueira (Belas, Portugal).

An unpublished turtle shell from the middle Cenomanian of Vale de Figueira, near Belas (Lisbon District, Portugal), is recognized by us as collected in 1880 under the direction of Carlos Ribeiro. No turtle remains from that region had so far been figured, described or discussed from a systematic point of view. The specimen corresponds to a partial but articulated shell. It is attributed to Pleurodira and, more specifically, to Bothremydidae. Only one pre-Campanian turtle specimen was previously identified at the infrafamilial level in the Cretaceous record of Portugal. It was a partial shell from the middle Cenomanian of Nazaré (Leiria District) attributed to the bothremydid Algorachelus peregrina, a species defined in a Spanish synchronous locality (Algora, in Central Spain). Several anatomical regions in the specimen from Vale de Figueira were not preserved in the partial carapace from Nazaré, and differences in the morphology of some elements are recognized between both shells. However, the individual studied here is also ascribed to Algorachelus peregrina, these differences being justified by intraspecific variability. Therefore, the specimen represents the second evidence on the species in Portugal, being the only one recognized for the Lisbon District.

A pan-cheloniid turtle from the Middle Miocene of Portugal.

Currently, there is no information on the fossil record of Pan-Cheloniidae from the Neogene of the Iberian Peninsula. A well-preserved partial skeleton attributable to this lineage of turtles, from the Middle Miocene of Portugal, is presented here. It preserves much of the anterior half of its carapace, in which the plates remain articulated, as well as several articulated dorsal vertebrae, and an isolated cervical and a caudal vertebrae. The analysis of this Serravallian find shows that it cannot be attributed to a hitherto described taxon. Thus, a new member of Pan-Cheloniidae is defined, Lusochelys emilianoi gen. et sp. nov., improving the relatively limited knowledge about this lineage for the Middle Miocene global record. It represents the first generic and specific systematic attribution for a member of Pan-Chelonioidea in the Neogene record of the Iberian Peninsula.

Point Cloud Painting for 3D Object Detection with Camera and Automotive 3+1D RADAR Fusion.

RADARs and cameras have been present in automotives since the advent of ADAS, as they possess complementary strengths and weaknesses but have been underlooked in the context of learning-based methods. In this work, we propose a method to perform object detection in autonomous driving based on a geometrical and sequential sensor fusion of 3+1D RADAR and semantics extracted from camera data through point cloud painting from the perspective view. To achieve this objective, we adapt PointPainting from the LiDAR and camera domains to the sensors mentioned above. We first apply YOLOv8-seg to obtain instance segmentation masks and project their results to the point cloud. As a refinement stage, we design a set of heuristic rules to minimize the propagation of errors from the segmentation to the detection stage. Our pipeline concludes by applying PointPillars as an object detection network to the painted RADAR point cloud. We validate our approach in the novel View of Delft dataset, which includes 3+1D RADAR data sequences in urban environments. Experimental results show that this fusion is also suitable for RADAR and cameras as we obtain a significant improvement over the RADAR-only baseline, increasing mAP from 41.18 to 52.67 (+27.9%).

Very-early detection of atrial fibrillation after ablation evaluated by a wearable ECG-patch predicts late blanking period recurrence: Preliminary data from a prospective registry.

Introduction: Atrial fibrillation (AF) ablation represents a safe and effective procedure to restore sinus rhythm. The idea that post-procedural AF episodes - during the blanking period - are not considered treatment failure has been increasingly challenged. The E-Patch, a single-use adhesive electrode, facilitates extended continuous ECG monitoring for 120 h. This pilot study aims to assess the effectiveness of this ambulatory monitoring device and investigate whether very-early AF recurrence correlates with delayed blanking period ablation outcomes. Methods: We conducted a single-center, prospective, longitudinal study, including consecutive post-ablation patients monitored with the E-patch. The ability of the device to continuously record was analyzed, as well as the occurrence of AF episodes during external 7-day loop-recorder in the 2nd-month post-ablation. Results: We included 40 patients, median age 62 years (IQR 56-70). E-Patch monitoring was obtained for a median of 118 h (IQR 112-120), with no discomfort nor interpretation artefacts. Very-early AF recurrence was detected in 11 (27.5 %) patients, with a median AF burden of 7 % (IQR 6 %-33 %). Late-blanking period AF was detected in 13 (33 %) of the external 7-day loop recordings. Of the 11 patients that had very-early AF recurrence, 10 (91 %) had late-blanking AF. Very-early AF detection showed 77 % (95 % CI 64 %-90 %) sensitivity and 96 % (95 % CI 90-100 %) specificity in predicting late-blanking AF, with a non-parametric ROC curve AUC of 0.903 (95 % 0.797--1.0). Conclusion: The E-Patch was able to detect very-early AF during an extended period. Very-early AF detection emerges as a predictor of AF recurrence during the late blanking period post-ablation.

The Hrk1 kinase is a determinant of acetic acid tolerance in yeast by modulating H+ and K+ homeostasis.

Acetic acid-induced stress is a common challenge in natural environments and industrial bioprocesses, significantly affecting the growth and metabolic performance of Saccharomyces cerevisiae. The adaptive response and tolerance to this stress involves the activation of a complex network of molecular pathways. This study aims to delve deeper into these mechanisms in S. cerevisiae, particularly focusing on the role of the Hrk1 kinase. Hrk1 is a key determinant of acetic acid tolerance, belonging to the NPR/Hal family, whose members are implicated in the modulation of the activity of plasma membrane transporters that orchestrate nutrient uptake and ion homeostasis. The influence of Hrk1 on S. cerevisiae adaptation to acetic acid-induced stress was explored by employing a physiological approach based on previous phosphoproteomics analyses. The results from this study reflect the multifunctional roles of Hrk1 in maintaining proton and potassium homeostasis during different phases of acetic acid-stressed cultivation. Hrk1 is shown to play a role in the activation of plasma membrane H+-ATPase, maintaining pH homeostasis, and in the modulation of plasma membrane potential under acetic acid stressed cultivation. Potassium (K+) supplementation of the growth medium, particularly when provided at limiting concentrations, led to a notable improvement in acetic acid stress tolerance of the hrk1Δ strain. Moreover, abrogation of this kinase expression is shown to confer a physiological advantage to growth under K+ limitation also in the absence of acetic acid stress. The involvement of the alkali metal cation/H+ exchanger Nha1, another proposed molecular target of Hrk1, in improving yeast growth under K+ limitation or acetic acid stress, is proposed.

Dilated Cardiomyopathy: A Comprehensive Approach to Diagnosis and Risk Stratification.

Dilated cardiomyopathy (DCM) represents one of the most common causes of non-ischemic heart failure, characterised by ventricular dilation alongside systolic dysfunction. Despite advances in therapy, DCM mortality rates remain high, and it is one of the leading causes of heart transplantation. It was recently recognised that many patients present minor structural cardiac abnormalities and express different arrhythmogenic phenotypes before overt heart-failure symptoms. This has raised several diagnostic and management challenges, including the differential diagnosis with other phenotypically similar conditions, the identification of patients at increased risk of malignant arrhythmias, and of those who will have a worse response to medical therapy. Recent developments in complementary diagnostic procedures, namely cardiac magnetic resonance and genetic testing, have shed new light on DCM understanding and management. The present review proposes a comprehensive and systematic approach to evaluating DCM, focusing on an improved diagnostic pathway and a structured stratification of arrhythmic risk that incorporates novel imaging modalities and genetic test results, which are critical for guiding clinical decision-making and improving outcomes.

YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis.

YEASTRACT+ (http://yeastract-plus.org/) is a tool for the analysis, prediction and modelling of transcription regulatory data at the gene and genomic levels in yeasts. It incorporates three integrated databases: YEASTRACT (http://yeastract-plus.org/yeastract/), PathoYeastract (http://yeastract-plus.org/pathoyeastract/) and NCYeastract (http://yeastract-plus.org/ncyeastract/), focused on Saccharomyces cerevisiae, pathogenic yeasts of the Candida genus, and non-conventional yeasts of biotechnological relevance. In this release, YEASTRACT+ offers upgraded information on transcription regulation for the ten previously incorporated yeast species, while extending the database to another pathogenic yeast, Candida auris. Since the last release of YEASTRACT+ (January 2020), a fourth database has been integrated. CommunityYeastract (http://yeastract-plus.org/community/) offers a platform for the creation, use, and future update of YEASTRACT-like databases for any yeast of the users' choice. CommunityYeastract currently provides information for two Saccharomyces boulardii strains, Rhodotorula toruloides NP11 oleaginous yeast, and Schizosaccharomyces pombe 972h-. In addition, YEASTRACT+ portal currently gathers 304 547 documented regulatory associations between transcription factors (TF) and target genes and 480 DNA binding sites, considering 2771 TFs from 11 yeast species. A new set of tools, currently implemented for S. cerevisiae and C. albicans, is further offered, combining regulatory information with genome-scale metabolic models to provide predictions on the most promising transcription factors to be exploited in cell factory optimisation or to be used as novel drug targets. The expansion of these new tools to the remaining YEASTRACT+ species is ongoing.

Ancestry of victims of 1755 Lisbon earthquake based on tooth morphology.

The present investigation comprises the characterization of skeletal remains recovered from the 2004 archaeological excavations carried out in the Cloister's Southwest Wing of the Academy of Sciences of Lisbon, attributed to the 1755 earthquake. Among the remains, many teeth were found. Our goal is to use dental morphological characteristics to assess the geographic ancestry of the combined sample using the methods of biodistance and web-based application of the Arizona State University Dental Anthropology System 2. The crown and root traits of the ASUDAS were scored in a sample of 1068 disarticulated teeth, 65 skulls, 138 adult and 42 sub-adult jaws. Eight characteristics of 34 specimens (7 skulls and 27 jaws) were analyzed using rASUDAS2. Results demonstrate that 73.5% of this sample can be assigned to Western Eurasian ancestry, with the remaining 26.5% divided between Sub-Saharan Africa, non-Arctic and Arctic America, and East Asia. Euclidean and Bray-Curtis distance measures were used to put this Portuguese sample in a world context. From both distance matrixes, cluster analyses were used to generate dendrograms. Based on Bray-Curtis values, Portugal is closest to Western Europe, followed by India and Eastern Europe. For the tree based on Euclidean distances, India is the first to join Portugal, followed by Eastern and Western Europe. Therefore, on both an individual and group level, the Portuguese sample is most closely tied to Western Eurasia. However, there may be other ancestries in the sample, such as Sub-Saharan Africa, due to non-European migrants in Portugal along with the African slave trade to Brazil that reached its peak in 18th century Lisbon.

The NPR/Hal family of protein kinases in yeasts: biological role, phylogeny and regulation under environmental challenges.

Protein phosphorylation is the most common and versatile post-translational modification occurring in eukaryotes. In yeast, protein phosphorylation is fundamental for maintaining cell growth and adapting to sudden changes in environmental conditions by regulating cellular processes and activating signal transduction pathways. Protein kinases catalyze the reversible addition of phosphate groups to target proteins, thereby regulating their activity. In Saccharomyces cerevisiae, kinases are classified into six major groups based on structural and functional similarities. The NPR/Hal family of kinases comprises nine fungal-specific kinases that, due to lack of similarity with the remaining kinases, were classified to the "Other" group. These kinases are primarily implicated in regulating fundamental cellular processes such as maintaining ion homeostasis and controlling nutrient transporters' concentration at the plasma membrane. Despite their biological relevance, these kinases remain poorly characterized and explored. This review provides an overview of the information available regarding each of the kinases from the NPR/Hal family, including their known biological functions, mechanisms of regulation, and integration in signaling pathways in S. cerevisiae. Information gathered for non-Saccharomyces species of biotechnological or clinical relevance is also included.

The genomic history and global expansion of domestic donkeys.

Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant ~200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.

Reconstruction of full antibody sequences in NGS datasets and accurate VL:VH coupling by cluster coordinate matching of non-overlapping reads.

Next-generation sequencing (NGS) is an indispensable tool in antibody discovery projects. However, the limits on NGS read length make it difficult to reconstruct full antibody sequences from the sequencing runs, especially if the six CDRs are randomized. To overcome that, we took advantage of Illumina's cluster mapping capabilities to pair non-overlapping reads and reconstruct full Fab sequences with accurate VL:VH pairings. The method relies on in silico cluster coordinate information, and not on extensive in vitro manipulation, making the protocol easily deployable and less prone to PCR-derived errors. This work maintains the throughput necessary for antibody discovery campaigns, and a high degree of fidelity, which potentiates not only phage-display and synthetic library-based discovery methods, but also the NGS-driven analysis of naïve and immune libraries.

Systematic reviews and meta-analysis published in indexed Portuguese medical journals: time trends and critical appraisal.

INTRODUCTION: Over the last years, the number of systematic reviews published is steadily increasing due to the global interest in this type of evidence synthesis. However, little is known about the characteristics of this research published in Portuguese medical journals. This study aims to evaluate the publication trends and overall quality of these systematic reviews. MATERIAL AND METHODS: This was a methodological study. We aimed the most visible Portuguese medical journals indexed in MEDLINE. Systematic reviews were identified through an electronic search (through PUBMED). We included systematic reviews published up to August 2020. Systematic reviews selection and data extraction were done independently by three authors. The overall quality critical appraisal using the A MeaSurement Tool to Assess systematic Reviews (AMSTAR-2) was independently assessed by three authors. Disagreements were solved by consensus. RESULTS: Sixty-six systematic reviews published in 5 Portuguese medical journals were included. Most (n = 53; 80.3%) were systematic reviews without meta-analysis. Up to 2010 there was a steady increase in the number of systematic reviews published, followed by a period of great variability of publication, ranging from 1 to 10 in a given year. According to the systematic reviews' typology, most have been predominantly conducted to assess the effectiveness/efficacy of health interventions (n = 27; 40.9%). General and Internal Medicine (n = 20; 30.3%) was the most addressed field. Most systematic reviews (n = 46; 69.7%) were rated as being of "critically low-quality". CONCLUSIONS: There were consistent flaws in the methodological quality report of the systematic reviews included, particularly in establishing a prior protocol and not assessing the potential impact of the risk of bias on the results. Through the years, the number of systematic reviews published increased, yet their quality is suboptimal. There is a need to improve the reporting of systematic reviews in Portuguese medical journals, which can be achieved by better adherence to quality checklists/tools.

The high-risk bleeding category of different scores in patients with venous thromboembolism: Systematic review and meta-analysis.

BACKGROUND: In patients with venous thromboembolism (VTE), bleeding risk should be carefully assessed but none of the available risk scores is currently recommended. The aim of this study was to systematically evaluate the performance of bleeding scores in patients with VTE focusing on high-risk patients. METHODS: Longitudinal studies were searched in Medline and Cochrane Library, as well as reviews and references of retrieved articles. Studies were identified, data were extracted, and reporting quality was evaluated. We determined the sensitivity, specificity, positive likelihood ratio (LR+), and diagnostic odds ratio (DOR) of the 'high risk' category of each bleeding score. Random effects meta-analysis was performed in order to derive the central estimates and 95% confidence intervals (95% CI). RESULTS: Twenty-one studies and ten bleeding scores fulfilled the inclusion criteria. VTE-BLEED showed the highest sensitivity but the second-lowest specificity (Se 76%; Sp 61%), followed by ACCP (Se 59%; Sp 57%). The remaining scores had high specificity (> 80%) but a low sensitivity (< 20%). HEMORR2HAGES and Niewenhuis score showed the best performance regarding LR+ that was 2.67 and 5.91, respectively. Regarding DOR, the Niewenhuis score and VTE-BLEED were the best performers with 9.04; 95% CI 3.87-21.09 and 4.94 95% CI 2.66-9.09, respectively. In a cohort with patients predominantly treated with direct oral anticoagulants (DOACs), VTE-BLEED had the highest sensitivity (Se 77%; Sp 60%). CONCLUSIONS: Overall, the majority of the risk scores showed a moderate ability to forecast major bleeding events, with the VTE-BLEED as the most sensitive in patients treated with DOACs.

The N.C.Yeastract and CommunityYeastract databases to study gene and genomic transcription regulation in non-conventional yeasts.

Responding to the recent interest of the yeast research community in non-Saccharomyces cerevisiae species of biotechnological relevance, the N.C.Yeastract (http://yeastract-plus.org/ncyeastract/) was associated to YEASTRACT + (http://yeastract-plus.org/). The YEASTRACT + portal is a curated repository of known regulatory associations between transcription factors (TFs) and target genes in yeasts. N.C.Yeastract gathers all published regulatory associations and TF-binding sites for Komagataellaphaffii (formerly Pichia pastoris), the oleaginous yeast Yarrowia lipolytica, the lactose fermenting species Kluyveromyces lactis and Kluyveromyces marxianus, and the remarkably weak acid-tolerant food spoilage yeast Zygosaccharomyces bailii. The objective of this review paper is to advertise the update of the existing information since the release of N.C.Yeastract in 2019, and to raise awareness in the community about its potential to help the day-to-day work on these species, exploring all the information available in the global YEASTRACT + portal. Using simple and widely used examples, a guided exploitation is offered for several tools: (i) inference of orthologous genes; (ii) search for putative TF binding sites and (iii) inter-species comparison of transcription regulatory networks and prediction of TF-regulated networks based on documented regulatory associations available in YEASTRACT + for well-studied species. The usage potentialities of the new CommunityYeastract platform by the yeast community are also discussed.

From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon.

Numerous genomes are sequenced and made available to the community through the NCBI portal. However, and, unlike what happens for gene function annotation, annotation of promoter sequences and the underlying prediction of regulatory associations is mostly unavailable, severely limiting the ability to interpret genome sequences in a functional genomics perspective. Here we present an approach where one can download a genome of interest from NCBI in the GenBank Flat File (.gbff) format and, with a minimum set of commands, have all the information parsed, organized and made available through the platform web interface. Also, the new genomes are compared with a given genome of reference in search of homologous genes, shared regulatory elements and predicted transcription associations. We present this approach within the context of Community YEASTRACT of the YEASTRACT + portal, thus benefiting from immediate access to all the comparative genomics queries offered in the YEASTRACT + portal. Besides the yeast community, other communities can install the platform independently, without any constraints. In this work, we exemplify the usefulness of the presented tool, within Community YEASTRACT, in constructing a dedicated database and analysing the genome of the highly promising oleaginous red yeast species Rhodotorula toruloides currently poorly studied at the genome and transcriptome levels and with limited genome editing tools. Regulatory prediction is based on the conservation of promoter sequences and available regulatory networks. The case-study examined is focused on the Haa1 transcription factor-a key regulator of yeast resistance to acetic acid, an important inhibitor of industrial bioconversion of lignocellulosic hydrolysates. The new tool described here led to the prediction of a RtHaa1 regulon with expected impact in the optimization of R. toruloides robustness for lignocellulosic and pectin-rich residue biorefinery processes.

Pneumococcal vaccination in adults at very high risk or with established cardiovascular disease: systematic review and meta-analysis.

AIMS: There are several guidelines that recommend pneumococcal vaccination (PPSV23 and/or PCV13) in adults with a history of cardiovascular disease (established heart failure, coronary disease, and cerebrovascular disease) or at a very high risk of cardiovascular disease. However, there is no randomized controlled trial (RCT) systematic review that evaluates the impact of vaccination on all-cause mortality compared to no vaccination in this particular population. Our objective is to conduct a systematic review and meta-analysis of the impact of pneumococcal vaccination in the referred population. METHODS AND RESULTS: We searched CENTRAL and MEDLINE for relevant RCTs and observational studies. Data were screened, extracted, and appraised by two independent reviewers. We pooled results using a random effects model, and used hazard ratios (HRs) with 95% confidence intervals (CIs) to assess measure of effect. The primary outcome was all-cause mortality and we assessed the confidence in the evidence using the GRADE framework. No RCTs were found. Seven observational studies were included for analyses. Pooled results from five studies enrolling a total of 163 756 participants showed a significant decrease in all-cause mortality (HR 0.78, 95% CI 0.73-0.83, very low confidence), without statistically significant heterogeneity (χ2 test P = 0.21; I2 = 32%). CONCLUSIONS: Pneumococcal vaccination was associated with a 22% decrease of all-cause mortality in patients with cardiovascular disease or at a very high cardiovascular risk. However, limitations due to study design and the serious risk of bias in three of the included studies leads to a decreased level of result confidence.

YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts.

The YEASTRACT+ information system (http://YEASTRACT-PLUS.org/) is a wide-scope tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in yeasts of biotechnological or human health relevance. YEASTRACT+ is a new portal that integrates the previously existing YEASTRACT (http://www.yeastract.com/) and PathoYeastract (http://pathoyeastract.org/) databases and introduces the NCYeastract (Non-Conventional Yeastract) database (http://ncyeastract.org/), focused on the so-called non-conventional yeasts. The information in the YEASTRACT database, focused on Saccharomyces cerevisiae, was updated. PathoYeastract was extended to include two additional pathogenic yeast species: Candida parapsilosis and Candida tropicalis. Furthermore, the NCYeastract database was created, including five biotechnologically relevant yeast species: Zygosaccharomyces baillii, Kluyveromyces lactis, Kluyveromyces marxianus, Yarrowia lipolytica and Komagataella phaffii. The YEASTRACT+ portal gathers 289 706 unique documented regulatory associations between transcription factors (TF) and target genes and 420 DNA binding sites, considering 247 TFs from 10 yeast species. YEASTRACT+ continues to make available tools for the prediction of the TFs involved in the regulation of gene/genomic expression. In this release, these tools were upgraded to enable predictions based on orthologous regulatory associations described for other yeast species, including two new tools for cross-species transcription regulation comparison, based on multi-species promoter and TF regulatory network analyses.