Accelerating SARS-CoV-2 genomic surveillance in a routine clinical setting with nanopore sequencing.

BACKGROUND: SARS-CoV-2 genomic analysis has been key to the provision of valuable data to meet both epidemiological and clinical demands. High-throughput sequencing, generally Illumina-based, has been necessary to ensure the widest coverage in global variant tracking. However, a speedier response is needed for nosocomial outbreak analyses and rapid identification of patients infected by emerging VOCs. An alternative based on nanopore sequencing may be better suited to delivering a faster response when required; however, although there are several studies offering side-by-side comparisons of Illumina and nanopore sequencing, evaluations of the usefulness in the hospital routine of the faster availability of data provided by nanopore are still lacking. RESULTS: We performed a prospective 10-week nanopore-based sequencing in MinION in a routine laboratory setting, including 83 specimens where a faster response time was necessary. The specimens analyzed corresponded to i) international travellers in which lineages were assigned to determine the proper management/special isolation of the patients; ii) nosocomial infections and health-care-worker infections, where SNP-based comparisons were required to rule in/out epidemiological relationships and tailor specific interventions iii) sentinel cases and breakthrough infections to timely report to the Public Health authorities. MinION-based sequencing was compared with the standard procedures, supported on Illumina sequencing; MinION accelerated the delivery of results (anticipating results 1-12 days) and reduced costs per sample by 28€ compared to Illumina, without reducing accuracy in SNP calling. CONCLUSIONS: Parallel integration of Illumina and nanopore sequencing strategies is a suitable solution to ensure both high-throughput and rapid response to cope with accelerating the surveillance demands of SARS-CoV-2 while also maintaining accuracy.

A solution to achieve sequencing from SARS-CoV-2 specimens with low viral loads: concatenation of reads from independent reactions.

BACKGROUND: During the pandemic, whole genome sequencing was critical to characterize SARS-CoV-2 for surveillance, clinical and therapeutical purposes. However, low viral loads in specimens often led to suboptimal sequencing, making lineage assignment and phylogenetic analysis difficult. We propose an alternative approach to sequencing these specimens that involves sequencing in triplicate and concatenation of the reads obtained using bioinformatics. This proposal is based on the hypothesis that the uncovered regions in each replicate differ and that concatenation would compensate for these gaps and recover a larger percentage of the sequenced genome. RESULTS: Whole genome sequencing was performed in triplicate on 30 samples with Ct > 32 and the benefit of replicate read concatenation was assessed. After concatenation: i) 28% of samples reached the standard quality coverage threshold (> 90% genome covered > 30x); ii) 39% of samples did not reach the coverage quality thresholds but coverage improved by more than 40%; and iii) SARS-CoV-2 lineage assignment was possible in 68.7% of samples where it had been impaired. CONCLUSIONS: Concatenation of reads from replicate sequencing reactions provides a simple way to access hidden information in the large proportion of SARS-CoV-2-positive specimens eliminated from analysis in standard sequencing schemes. This approach will enhance our potential to rule out involvement in outbreaks, to characterize reinfections and to identify lineages of concern for surveillance or therapeutical purposes.

Conventional and Contrast-enhanced US of the Lung: From Performance to Diagnosis.

In recent years, lung US has evolved from a marginal tool to an integral component of diagnostic chest imaging. Contrast-enhanced US (CEUS) can improve routine gray-scale imaging of the lung and chest, particularly in diagnosis of peripheral lung diseases (PLDs). Although an underused tool in many centers, and despite inherent limitations in evaluation of central lung disease caused by high acoustic impedance between air and soft tissues, lung CEUS has emerged as a valuable tool in diagnosis of PLDs. Owing to the dual arterial supply to the lungs via pulmonary and bronchial (systemic) arteries, different enhancement patterns can be observed at lung CEUS, thereby enabling accurate differential diagnoses in various PLDs. Lung CEUS also assists in identifying patients who may benefit from complementary diagnostic tests, including image-guided percutaneous biopsy. Moreover, lung CEUS-guided percutaneous biopsy has shown feasibility in accessible subpleural lesions, enabling higher histopathologic performance without significantly increasing either imaging time or expenses compared with conventional US. The authors discuss the technique of and basic normal and pathologic findings at conventional lung US, followed by a more detailed discussion of lung CEUS applications, emphasizing specific aspects of pulmonary physiology, basic concepts in lung US enhancement, and the most commonly encountered enhancement patterns of different PLDs. Finally, they discuss the benefits of lung CEUS in planning and guidance of US-guided lung biopsy. ©RSNA, 2024 Supplemental material is available for this article.

TNFRSF1B Gene Variants in Clinicopathological Aspects and Prognosis of Patients with Cutaneous Melanoma.

Regulatory T lymphocytes play a critical role in immune regulation and are involved in the aberrant cell elimination by facilitating tumor necrosis factor connection to the TNFR2 receptor, encoded by the TNFRSF1B polymorphic gene. We aimed to examine the effects of single nucleotide variants TNFRSF1B c.587T>G, c.*188A>G, c.*215C>T, and c.*922C>T on the clinicopathological characteristics and survival of cutaneous melanoma (CM) patients. Patients were genotyped using RT-PCR. TNFRSF1B levels were measured using qPCR. Luciferase reporter assay evaluated the interaction of miR-96 and miR-1271 with the 3'-UTR of TNFRSF1B. The c.587TT genotype was more common in patients younger than 54 years old than in older patients. Patients with c.*922CT or TT, c.587TG or GG + c.*922CT or TT genotypes, as well as those with the haplotype TATT, presented a higher risk of tumor progression and death due to the disease effects. Individuals with the c.*922TT genotype had a higher TNFRSF1B expression than those with the CC genotype. miR-1271 had less efficient binding with the 3'-UTR of the T allele when compared with the C allele of the SNV c.*922C>T. Our findings, for the first time, demonstrate that TNFRSF1B c.587T>G and c.*922C>T variants can serve as independent prognostic factors in CM patients.

Public Health Implications of Drought in a Climate Change Context: A Critical Review.

Extreme weather events are expected to increase due to climate change, which could pose an additional burden of morbidity and mortality. In recent decades, drought severity has increased in several regions around the world, affecting health by increasing the risk of water-, food-, and vector-borne diseases, malnutrition, cardiovascular and respiratory illness, mental health disorders, and mortality. Drought frequency and severity are expected to worsen across large regions as a result of a decrease in precipitation and an increase in temperature and atmospheric evaporative demand, posing a pressing challenge for public health. Variation in impacts among countries and communities is due to multiple factors, such as aging, socioeconomic status, access to health care, and gender, affecting population resilience. Integrative proactive action plans focused on risk management are required, and resources should be transferred to developing countries to reduce their vulnerability and risk.

A One Health approach revealed the long-term role of Mycobacterium caprae as the hidden cause of human tuberculosis in a region of Spain, 2003 to 2022.

IntroductionMycobacterium caprae is a member of the Mycobacterium tuberculosis complex (MTBC) not routinely identified to species level. It lacks specific clinical features of presentation and may therefore not be identified as the causative agent of tuberculosis. Use of whole genome sequencing (WGS) in the investigation of a family microepidemic of tuberculosis in Almería, Spain, unexpectedly identified the involvement of M. caprae.AimWe aimed to evaluate the presence of additional unidentified M. caprae cases and to determine the magnitude of this occurrence.MethodsFirst-line characterisation of the MTBC isolates was done by MIRU-VNTR, followed by WGS. Human and animal M. caprae isolates were integrated in the analysis.ResultsA comprehensive One Health strategy allowed us to (i) detect other 11 M. caprae infections in humans in a period of 18 years, (ii) systematically analyse M. caprae infections on an epidemiologically related goat farm and (iii) geographically expand the study by including 16 M. caprae isolates from other provinces. Integrative genomic analysis of 41 human and animal M. caprae isolates showed a high diversity of strains. The animal isolates' diversity was compatible with long-term infection, and close genomic relationships existed between isolates from goats on the farm and recent cases of M. caprae infection in humans.DiscussionZoonotic circulation of M. caprae strains had gone unnoticed for 18 years. Systematic characterisation of MTBC at species level and/or extended investigation of the possible sources of exposure in all tuberculosis cases would minimise the risk of overlooking similar zoonotic events.

Deep Learning for chaos detection.

In this article, we study how a chaos detection problem can be solved using Deep Learning techniques. We consider two classical test examples: the Logistic map as a discrete dynamical system and the Lorenz system as a continuous dynamical system. We train three types of artificial neural networks (multi-layer perceptron, convolutional neural network, and long short-term memory cell) to classify time series from the mentioned systems into regular or chaotic. This approach allows us to study biparametric and triparametric regions in the Lorenz system due to their low computational cost compared to traditional techniques.

Evaluation of tolerance to mercaptopurine in patients with inflammatory bowel disease and gastrointestinal intolerance to azathioprine.

BACKGROUND: Thiopurines such as azathioprine (AZA) and mercaptopurine (MP) are commonly utilized to treat inflammatory bowel disease (IBD). Their use is frequently restricted due to gastrointestinal intolerance (GI). Previous retrospective studies have reported that AZA-intolerant patients may benefit from a switch to MP; yet the effectiveness of this strategy has not been prospectively evaluated. AIMS: To assess GI tolerance to MP in patients who are intolerant to AZA, and to identify clinical predictors of GI intolerance to AZA or MP. METHODS: A prospective, observational, single-cohort study was performed in 92 thiopurine-naïve IBD patients. They were started on a 50mg dose of AZA and escalated to 2.5mg/kg per day by week 2. Those with GI intolerance were rechallenged with a 50% dose of AZA, after which another dose escalation attempt was made. If symptoms persisted, they were switched to MP. RESULTS: Thirty (32.6%) of the recruited patients suffered from GI intolerance to AZA. Of these, 15 did not present recurrence of symptoms after rechallenge with lower doses. Of 15 intolerant patients, 14 were switched to MP. Within the MP cohort, 8 patients (57%) were also intolerant to MP, 5 (36%) had no symptoms, and 1 (7%) was lost to follow-up. Female gender was the only independent predictor of GI intolerance to AZA. CONCLUSIONS: Up to half of the AZA-intolerant patients tolerated a 50% dose rechallenge that was successfully escalated. A switch to MP was tolerated in over a third of cases whom rechallenge failed. Our strategy (challenge-rechallenge-switch) achieved an overall GI tolerance to thiopurines in most of the patients.

Cross-sectoral impacts of the 2018-2019 Central European drought and climate resilience in the German part of the Elbe River basin.

The 2018-2019 Central European drought was probably the most extreme in Germany since the early sixteenth century. We assess the multiple consequences of the drought for natural systems, the economy and human health in the German part of the Elbe River basin, an area of 97,175 km2 including the cities of Berlin and Hamburg and contributing about 18% to the German GDP. We employ meteorological, hydrological and socio-economic data to build a comprehensive picture of the drought severity, its multiple effects and cross-sectoral consequences in the basin. Time series of different drought indices illustrate the severity of the 2018-2019 drought and how it progressed from meteorological water deficits via soil water depletion towards low groundwater levels and river runoff, and losses in vegetation productivity. The event resulted in severe production losses in agriculture (minus 20-40% for staple crops) and forestry (especially through forced logging of damaged wood: 25.1 million tons in 2018-2020 compared to only 3.4 million tons in 2015-2017), while other economic sectors remained largely unaffected. However, there is no guarantee that this socio-economic stability will be sustained in future drought events; this is discussed in the light of 2022, another dry year holding the potential for a compound crisis. Given the increased probability for more intense and long-lasting droughts in most parts of Europe, this example of actual cross-sectoral drought impacts will be relevant for drought awareness and preparation planning in other regions. Supplementary Information: The online version contains supplementary material available at 10.1007/s10113-023-02032-3.

Systematic Genomic and Clinical Analysis of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfections and Recurrences Involving the Same Strain.

Estimates of the burden of severe acute respiratory syndrome coronavirus 2 reinfections are limited by the scarcity of population-level studies incorporating genomic support. We conducted a systematic study of reinfections in Madrid, Spain, supported by genomic viral analysis and host genetic analysis, to cleanse laboratory errors and to discriminate between reinfections and recurrences involving the same strain. Among the 41,195 cases diagnosed (March 2020-March 2021), 93 (0.23%) had 2 positive reverse transcription PCR tests (55-346 days apart). After eliminating cases with specimens not stored, of suboptimal sequence quality, or belonging to different persons, we obtained valid data from 22 cases. Of those, 4 (0.01%) cases were recurrences involving the same strain; case-patients were 39-93 years of age, and 3 were immunosuppressed. Eighteen (0.04%) cases were reinfections; patients were 19-84 years of age, and most had no relevant clinical history. The second episode was more severe in 8 cases.

Role of mesenchymal stromal cells derivatives in diabetic foot ulcers: a controlled randomized phase 1/2 clinical trial.

BACKGROUND: Diabetes-related foot complications have been identified as the most common isolated cause of morbidity among patients with diabetes and the leading cause of amputation. Therefore, new strategies to stimulate skin regeneration may provide a novel therapeutic approach to reduce non-healing ulcer disease. Recently, we demonstrated in proof-of-concept in humans that administration of allogeneic bone marrow mesenchymal stromal cellss derivatives (allo-hBM-MSCDs) is effective in a similar way to the use of allogeneic bone marrow mesenchymal stromal cellss (allo-hBM-MSCs) in grade 2 diabetic foot ulcers (DFUs). AIM: To assess the safety and efficacy profile of the allo-hBM-MSCDs relative to the conventional approach (PolyMen® dressing) in 1/2 clinical trial phases in patients with grade 1 and 2 DFUs. METHODS: In the present study, we used 2 doses of allo-hBM-MSCDs (1 mL) or 1 dose of allo-hBM-MSCs (1 × 106 cells) intradermally injected around wounds and assessed their safety and effectiveness, relative to the conventional approach (PolyMem dressing). Allo-hBM-MSCDs and allo-hBM-MSCs were produced in a certified Good Manufacturing Practice-type Laboratory. Patients with grade 1 and 2 DFUs were randomized to receive allo-hBM-MSCDs (n=12), allo-hBM-MSCs (n=6) or conventional treatment (PolyMem dressing) (n=10). The wound-healing process was macroscopically evaluated until the complete closure of the ulcers. RESULTS: No adverse events were reported. Patients with grade 1 and 2 DFUs treated with either allo-hBM-MSCDs or allo-hBM-MSCs, achieved greater percentages of wound closure, enhanced skin regeneration in shorter times and a greater ulcer-free survival relative to the patients who received conventional treatment. Finally, through proteomic analysis, we elucidated the proteins and growth factors that are secreted by allo-hBM-MSCs and relevant to the wound-healing process. In addition, by combining proteomics with Gene Ontology analysis, we comprehensively classified secreted proteins on both biological process and molecular function. CONCLUSIONS: In this phase 1/2 trial, our cumulative results suggest that 2 doses of allo-hBM-MSCDs combined with a wound dressing are a safe and effective treatment for grade 1 and 2 DFUs.

Global drought trends and future projections.

Drought is one of the most difficult natural hazards to quantify and is divided into categories (meteorological, agricultural, ecological and hydrological), which makes assessing recent changes and future scenarios extremely difficult. This opinion piece includes a review of the recent scientific literature on the topic and analyses trends in meteorological droughts by using long-term precipitation records and different drought metrics to evaluate the role of global warming processes in trends of agricultural, hydrological and ecological drought severity over the last four decades, during which a sharp increase in atmospheric evaporative demand (AED) has been recorded. Meteorological droughts do not show any substantial changes at the global scale in at least the last 120 years, but an increase in the severity of agricultural and ecological droughts seems to emerge as a consequence of the increase in the severity of AED. Lastly, this study evaluates drought projections from earth system models and focuses on the most important aspects that need to be considered when evaluating drought processes in a changing climate, such as the use of different metrics and the uncertainty of modelling approaches. This article is part of the Royal Society Science+ meeting issue 'Drought risk in the Anthropocene'.

Good post-transplant outcomes using liver donors after circulatory death when applying strict selection criteria: A propensity-score matched-cohort study.

INTRODUCTION AND OBJECTIVES: Outcomes of liver transplantation (LT) with donors after circulatory death (DCD) have been considered suboptimal due to higher rates of ischemic cholangiopathy, especially when the super-rapid recovery (SRR) technique is used. This study aimed to compare the incidence of complications between recipients receiving DCD vs those receiving donors after brain death (DBD) in a large-volume liver transplant centre. METHODS: We performed a retrospective cohort study (LT from January 2015 to December 2018) comparing recipients who underwent a LT with DCD vs. a control group of LT with DBD, matched 1:1 without replacement by propensity score matching that included the following variables: LT indication, recipient sex and age, donor age and MELD score. RESULTS: 51 recipients with DCD-LT (29 SRR, 22 normothermic regional perfusion [NRP]) were matched with 51 DBD-LT recipients. Biliary complications were more frequent in DCD, 10% (n=5), all with SRR technique, vs 2% (n=1) in the DBD group, p=0.2. Two patients (4%) suffered primary graft non-function in the DCD group (1 SRR and 1 NRP) versus zero in the DBD group (p=0.49). Postoperative bleeding and reinterventions were also higher in the DCD group: 7 (13.7%) vs 1 (1.95%) and 8 (15.7%) vs 2 (3.9%) respectively (p=0.06 and 0.09). On the 1st postoperative day AST/ALT peak was higher in DCD (p≤0001). The incidence of rejection, vascular complications, renal injury, hospital stay, and readmissions were similar in both groups. Cumulative 1-, 2-, 3- and 4-year graft and patient survival were also similar. CONCLUSIONS: DCD donors are an adequate option to increase the donor pool in LT, achieving similar graft and patient survival rates to those achieved with DBD donors, especially when the NRP technique is used.

First importations of SARS-CoV-2 P.1 and P.2 variants from Brazil to Spain and early community transmission.

Introduction: SARS-CoV-2variants of concern (VOC) have been described in the UK (B.1.1.7), South Africa (B.1.351) and Brazil (P.1). Among them, the most scarce information has been obtained from the P.1 variant and more data on its global presence and about its spreading dynamics are needed. Methods: Whole genome sequencing was performed prospectively on travellers arriving from Brazil and on a random selection of SARS-CoV-2 positive cases from our population. Results: In this study we report the first SARS-CoV-2 P.1 and P.2 variants exported from Brazil to Spain. The case infected with the P.1 variant, who had only stayed in Rio de Janeiro, required hospitalisation. The two P.2 cases remained asymptomatic. A wider distribution for P.1 variant beyond the Brazilian Amazonia should be considered. The exportation of the P.2 variant, carrying the E484K mutation, deserves attention. One month after the first description of P.1 and P.2 importations from Brazil to Madrid, these variants were identified circulating in the community, in cases without a travel history, and involved in household transmissions. Conclusion: Whole genome sequencing of SARS-CoV-2 positive travellers arriving from Brazil allowed us to identify the first importations of P.1 and P.2 variants to Spain and their early community transmission.

Introducción: Se han descrito «variantes de preocupación¼ (VOC) de SARS-CoV-2 en el Reino Unido (B.1.1.7), Sudáfrica (B.1.351) y Brasil (P.1). Entre ellas, se dispone de información más escasa para la variante P.1 y se necesitan más datos sobre su presencia global y sobre su dinámica de expansión. Métodos: Se realizó secuenciación del genoma completo de forma prospectiva de SARS-CoV-2 en viajeros procedentes de Brasil y en una selección aleatoria de casos positivos de SARS-CoV-2 de nuestra población. Resultados: En este estudio reportamos las primeras variantes de SARS-CoV-2 P.1 y P.2 exportadas desde Brasil a España. El caso infectado por la variante P.1, que solo había permanecido en Río de Janeiro, requirió hospitalización. Los 2 casos de la variante P.2 permanecieron asintomáticos. Se debe considerar una distribución más amplia para la variante P.1 más allá de la Amazonía brasileña. La exportación de la variante P.2, que porta la mutación E484K, merece asimismo atención adicional. Un mes después de la primera descripción de las importaciones de P.1 y P.2 de Brasil a Madrid, se identificaron estas variantes circulando en la comunidad, en casos sin antecedentes de viaje, e implicadas en transmisiones domiciliarias. Conclusión: La secuenciación de genoma completo de viajeros positivos para SARS-CoV-2 procedentes de Brasil nos permitió identificar las primeras importaciones de variantes P.1 y P.2 a España y su transmisión comunitaria precoz.

Proper Assignation of Reactivation in a COVID-19 Recurrence Initially Interpreted as a Reinfection.

A 77-year-old man (case R) with previous diagnosis of a mild COVID-19 episode was hospitalized 35 days later. On day 23 postadmission, he developed a second COVID-19 episode, now severe, and finally died. Initially, case R's COVID-19 recurrence was interpreted as a reinfection due to the exposure to a SARS-CoV-2 RT-PCR-positive roommate. However, whole-genome sequencing indicated that case R's recurrence corresponded to a reactivation of the strain involved in his first episode. Case R's reactivation had major consequences, leading to a more severe episode, and causing subsequent transmission to another 2 hospitalized patients, 1 of them with fatal outcome.

Order in chaos: Structure of chaotic invariant sets of square-wave neuron models.

Bursting phenomena and, in particular, square-wave or fold/hom bursting, are found in a wide variety of mathematical neuron models. These systems have different behavior regimes depending on the parameters, whether spiking, bursting, or chaotic. We study the topological structure of chaotic invariant sets present in square-wave bursting neuron models, first detailed using the Hindmarsh-Rose neuron model and later exemplary in the more realistic model of a leech heart neuron. We show that the unstable periodic orbits that form the skeleton of the chaotic invariant sets are deeply related to the spike-adding phenomena, typical from these models, and how there are specific symbolic sequences and a symbolic grammar that organize how and where the periodic orbits appear. Linking this information with the topological template analysis permits us to understand how the internal structure of the chaotic invariants is modified and how more symbolic sequences are allowed. Furthermore, the results allow us to conjecture that, for these systems, the limit template when the small parameter ε, which controls the slow gating variable, tends to zero is the complete Smale topological template.

Classification of fold/hom and fold/Hopf spike-adding phenomena.

The Hindmarsh-Rose neural model is widely accepted as an important prototype for fold/hom and fold/Hopf burstings. In this paper, we are interested in the mechanisms for the production of extra spikes in a burst, and we show the whole parametric panorama in an unified way. In the fold/hom case, two types are distinguished: a continuous one, where the bursting periodic orbit goes through bifurcations but persists along the whole process and a discontinuous one, where the transition is abrupt and happens after a sequence of chaotic events. In the former case, we speak about canard-induced spike-adding and in the second one, about chaos-induced spike-adding. For fold/Hopf bursting, a single (and continuous) mechanism is distinguished. Separately, all these mechanisms are presented, to some extent, in the literature. However, our full perspective allows us to construct a spike-adding map and, more significantly, to understand the dynamics exhibited when borders are crossed, that is, transitions between types of processes, a crucial point not previously studied.

Dynamical analysis of early afterdepolarization patterns in a biophysically detailed cardiac model.

Arrhythmogenic early afterdepolarizations (EADs) are investigated in a biophysically detailed mathematical model of a rabbit ventricular myocyte, providing their location in the parameter phase space and describing their dynamical mechanisms. Simulations using the Sato model, defined by 27 state variables and 177 parameters, are conducted to generate electrical action potentials (APs) for different values of the pacing cycle length and other parameters related to sodium and calcium concentrations. A detailed study of the different AP patterns with or without EADs is carried out, showing the presence of a high variety of temporal AP configurations with chaotic and quasiperiodic behaviors. Regions of bistability are identified and, importantly, linked to transitions between different behaviors. Using sweeping techniques, one-, two-, and three-parameter phase spaces are provided, allowing ascertainment of the role of the selected parameters as well as location of the transition regions. A Devil's staircase, with symbolic sequence analysis, is proposed to describe transitions in the ratio between the number of voltage (EAD and AP) peaks and the number of APs. To conclude, the obtained results are linked to recent studies for low-dimensional models and a conjecture is made for the internal dynamical structure of the transition region from non-EAD to EAD behavior using fold and cusp bifurcations and maximal canards.

Somatic Copy Number Alterations and Associated Genes in Clear-Cell Renal-Cell Carcinoma in Brazilian Patients.

Somatic copy number aberrations (CNAs) have been associated with clear-cell renal carcinoma (ccRCC) pathogenesis and are a potential source of new diagnostic, prognostic and therapeutic biomarkers. Recurrent CNAs include loss of chromosome arms 3p, 14q, 9p, and gains of 5q and 8q. Some of these regional CNAs are suspected of altering gene expression and could influence clinical outcomes. Despite many studies of CNAs in RCC, there are currently no descriptions of genomic copy number alterations in a Brazilian ccRCC cohort. This study was designed to evaluate the chromosomal profile of CNAs in Brazilian ccRCC tumors and explore clinical associations. A total of 92 ccRCC Brazilian patients that underwent nephrectomy at Barretos Cancer Hospital were analyzed for CNAs by array comparative genomic hybridization. Most patients in the cohort had early-stage localized disease. The most significant alterations were loss of 3p (87.3%), 14q (35.8%), 6q (29.3%), 9p (28.6%) and 10q (25.0%), and gains of 5q (59.7%), 7p (29.3%) and 16q (20.6%). Bioinformatics analysis revealed 19 genes mapping to CNA significant regions, including SETD2, BAP1, FLT4, PTEN, FGFR4 and NSD1. Moreover, gain of 5q34-q35.3 (FLT4 and NSD1) and loss of 6q23.2-q23.3 (MYB) and 9p21.3 (MLLT3) had gene expression levels that correlated with TCGA data and was also associated with advanced disease features, such as larger tumors, Fuhrman 3, metastasis at diagnosis and death. The loss of region 14q22.1 which encompasses the NIN gene was associated with poor overall survival. Overall, this study provides the first CNA landscape of Brazilian patients and pinpoints genomic regions and specific genes worthy of more detailed investigations. Our results highlight important genes that are associated with copy number changes involving large chromosomal regions that are potentially related to ccRCC tumorigenesis and disease biology for future clinical investigations.

Evidence of non-stationary relationships between climate and forest responses: Increased sensitivity to climate change in Iberian forests.

Climate and forest structure are considered major drivers of forest demography and productivity. However, recent evidence suggests that the relationships between climate and tree growth are generally non-stationary (i.e. non-time stable), and it remains uncertain whether the relationships between climate, forest structure, demography and productivity are stationary or are being altered by recent climatic and structural changes. Here we analysed three surveys from the Spanish Forest Inventory covering c. 30 years of information and we applied mixed and structural equation models to assess temporal trends in forest structure (stand density, basal area, tree size and tree size inequality), forest demography (ingrowth, growth and mortality) and above-ground forest productivity. We also quantified whether the interactive effects of climate and forest structure on forest demography and above-ground forest productivity were stationary over two consecutive time periods. Since the 1980s, density, basal area and tree size increased in Iberian forests, and tree size inequality decreased. In addition, we observed reductions in ingrowth and growth, and increases in mortality. Initial forest structure and water availability mainly modulated the temporal trends in forest structure and demography. The magnitude and direction of the interactive effects of climate and forest structure on forest demography changed over the two time periods analysed indicating non-stationary relationships between climate, forest structure and demography. Above-ground forest productivity increased due to a positive balance between ingrowth, growth and mortality. Despite increasing productivity over time, we observed an aggravation of the negative effects of climate change and increased competition on forest demography, reducing ingrowth and growth, and increasing mortality. Interestingly, our results suggest that the negative effects of climate change on forest demography could be ameliorated through forest management, which has profound implications for forest adaptation to climate change.