Analysis of a two-layer energy balance model: Long time behavior and greenhouse effect

We study a two-layer energy balance model that allows for vertical exchanges between a surface layer and the atmosphere. The evolution equations of the surface temperature and the atmospheric temperature are coupled by the emission of infrared radiation by one level, that emission being partly captured by the other layer, and the effect of all non-radiative vertical exchanges of energy. Therefore, an essential parameter is the absorptivity of the atmosphere, denoted εa. The value of εa depends critically on greenhouse gases: increasing concentrations of CO2 and CH4 lead to a more opaque atmosphere with higher values of ϵa. First, we prove that global existence of solutions of the system holds if and only if εa∈(0,2) and blow up in finite time occurs if εa>2. (Note that the physical range of values for εa is (0,1].) Next, we explain the long time dynamics for εa∈(0,2), and we prove that all solutions converge to some equilibrium point. Finally, motivated by the physical context, we study the dependence of the equilibrium points with respect to the involved parameters, and we prove, in particular, that the surface temperature increases monotonically with respect to εa. This is the key mathematical manifestation of the greenhouse effect.

Articulating the "stem cell niche" paradigm through the lens of non-model aquatic invertebrates

Stem cells (SCs) in vertebrates typically reside in "stem cell niches" (SCNs), morphologically restricted tissue microenvironments that are important for SC survival and proliferation. SCNs are broadly defined by properties including physical location, but in contrast to vertebrates and other "model" organisms, aquatic invertebrate SCs do not have clearly documented niche outlines or properties. Life strategies such as regeneration or asexual reproduction may have conditioned the niche architectural variability in aquatic or marine animal groups. By both establishing the invertebrates SCNs as independent types, yet allowing inclusiveness among them, the comparative analysis will allow the future functional characterization of SCNs.

Femtosecond Resolution of the Nonballistic Electron Energy Transport in Warm Dense Copper

The ultrafast electron energy transport is investigated in laser-heated warm dense copper in a high flux regime (2.5±0.7×10^{13}  W/cm^{2} absorbed). The dynamics of the electron temperature is retrieved from femtosecond time-resolved x-ray absorption near-edge spectroscopy near the Cu L3 edge. A characteristic time of ∼1  ps is observed for the increase in the average temperature in a 100 nm thick sample. Data are well reproduced by two-temperature hydrodynamic simulations, which support energy transport dominated by thermal conduction rather than ballistic electrons.

Resource use during systematic review production varies widely: a scoping review

OBJECTIVE

We aimed to map the resource use during systematic review (SR) production and reasons why steps of the SR production are resource intensive to discover where the largest gain in improving efficiency might be possible.

STUDY DESIGN AND SETTING

We conducted a scoping review. An information specialist searched multiple databases (e.g., Ovid MEDLINE, Scopus) and implemented citation-based and grey literature searching. We employed dual and independent screenings of records at the title/abstract and full-text levels and data extraction.

RESULTS

We included 34 studies. Thirty-two reported on the resource use-mostly time; four described reasons why steps of the review process are resource intensive. Study selection, data extraction, and critical appraisal seem to be very resource intensive, while protocol development, literature search, or study retrieval take less time. Project management and administration required a large proportion of SR production time. Lack of experience, domain knowledge, use of collaborative and SR-tailored software, and good communication and management can be reasons why SR steps are resource intensive.

CONCLUSION

Resource use during SR production varies widely. Areas with the largest resource use are administration and project management, study selection, data extraction, and critical appraisal of studies.

The Mutational Landscape of Acute Myeloid Leukaemia Predicts Responses and Outcomes in Elderly Patients from the PETHEMA-FLUGAZA Phase 3 Clinical Trial

We sought to predict treatment responses and outcomes in older patients with newly diagnosed acute myeloid leukemia (AML) from our FLUGAZA phase III clinical trial (PETHEMA group) based on mutational status, comparing azacytidine (AZA) with fludarabine plus low-dose cytarabine (FLUGA). Mutational profiling using a custom 43-gene next-generation sequencing panel revealed differences in profiles between older and younger patients, and several prognostic markers that were useful in young patients were ineffective in older patients. We examined the associations between variables and overall responses at the end of the third cycle. Patients with mutated DNMT3A or EZH2 were shown to benefit from azacytidine in the treatment-adjusted subgroup analysis. An analysis of the associations with tumor burden using variant allele frequency (VAF) quantification showed that a higher overall response was associated with an increase in TET2 VAF (odds ratio (OR), 1.014; p = 0.030) and lower TP53 VAF (OR, 0.981; p = 0.003). In the treatment-adjusted multivariate survival analyses, only the NRAS (hazard ratio (HR), 1.9, p = 0.005) and TP53 (HR, 2.6, p = 9.8 × 10^-7) variants were associated with shorter overall survival (OS), whereas only mutated BCOR (HR, 3.6, p = 0.0003) was associated with a shorter relapse-free survival (RFS). Subgroup analyses of OS according to biological and genomic characteristics showed that patients with low-intermediate cytogenetic risk (HR, 1.51, p = 0.045) and mutated NRAS (HR, 3.66, p = 0.047) benefited from azacytidine therapy. In the subgroup analyses, patients with mutated TP53 (HR, 4.71, p = 0.009) showed a better RFS in the azacytidine arm. In conclusion, differential mutational profiling might anticipate the outcomes of first-line treatment choices (AZA or FLUGA) in older patients with AML. The study is registered at ClinicalTrials.gov as NCT02319135.

COVID-19 and the forgotten pandemic: follow-up of neurocognitive disorders during lockdown in Argentina

Introduction

Health systems in numerous countries around the world are suffering a serious burden as a consequence of the COVID-19 pandemic. As a result of this situation, the follow-up of such chronic diseases as dementia may be at risk. Similarly, neuropsychiatric complications related to lockdown measures may also be neglected; Argentina’s lockdown has been the longest implemented in Latin America. This study aims to determine the frequency of the different types of medical consultations for neurocognitive disorders and the predictors for requiring consultation since the beginning of the lockdown.

Methods

We performed a descriptive, observational, cross-sectional study based on data collected through an online survey.

Results

Data were collected on 324 participants, with 165 (50.9%) having had at least one medical consultation. Consultations were held by telephone in 109 cases (33.6%), by e-mail in 62 (19.1%), by video conference in 30 (9.3%), and at the emergency department in 23 (7.1%). Predictors of requiring consultation were Clinical Dementia Rating scores ≥1 (P < .001) and diagnosis of Alzheimer disease (P = .017). Higher Neuropsychiatric Inventory scores were found in the group of respondents who did require medical consultation (P < .001), but no significant differences were found between groups for Zarit Burden Interview scores.

Conclusion

We identified a high prevalence of behavioural disorders and caregiver burden during lockdown. Nevertheless, only 50% of respondents had sought medical consultation (by telephone or email in 52.7% of cases). Care of people with dementia must be emphasised, guaranteeing follow-up of these patients.

Aurore: A platform for ultrafast sciences

We present the Aurore platform for ultrafast sciences. This platform is based on a unique 20 W, 1 kHz, 26 fs Ti:sapphire laser system designed for reliable operation and high intensity temporal contrast. The specific design ensures the high stability in terms of pulse duration, energy, and beam pointing necessary for extended experimental campaigns. The laser supplies 5 different beamlines, all dedicated to a specific field: attosecond science (Aurore 1), ultrafast phase transitions in solids (Aurore 2 and 3), ultrafast luminescence in solids (Aurore 4), and femtochemistry (Aurore 5). The technical specifications of these five beamlines are described in detail, and examples of the recent results are given.

The digestive system of xenacoelomorphs

Interest in the study of Xenacoelomorpha has recently been revived due to realization of its key phylogenetic position as the putative sister group of the remaining Bilateria. Phylogenomic studies have attracted the attention of researchers interested in the evolution of animals and the origin of novelties. However, it is clear that a proper understanding of novelties can only be gained in the context of thorough descriptions of the anatomy of the different members of this phylum. A considerable literature, based mainly on conventional histological techniques, describes different aspects of xenacoelomorphs' tissue architecture. However, the focus has been somewhat uneven; some tissues, such as the neuro-muscular system, are relatively well described in most groups, whereas others, including the digestive system, are only poorly understood. Our lack of knowledge of the xenacoelomorph digestive system is exacerbated by the assumption that, at least in Acoela, which possess a syncytial gut, the digestive system is a derived and specialized tissue with little bearing on what is observed in other bilaterian animals. Here, we try to remedy this lack of attention by revisiting the different studies of the xenacoelomorph digestive system, and we discuss the diversity present in the light of new evolutionary knowledge.

Genetic analyses of aplastic anemia and idiopathic pulmonary fibrosis patients with short telomeres, possible implication of DNA-repair genes

Background

Telomeres are nucleoprotein structures present at the terminal region of the chromosomes. Mutations in genes coding for proteins involved in telomere maintenance are causative of a number of disorders known as telomeropathies. The genetic origin of these diseases is heterogeneous and has not been determined for a significant proportion of patients.

Methods

This article describes the genetic characterization of a cohort of patients. Telomere length was determined by Southern blot and quantitative PCR. Nucleotide variants were analyzed either by high-resolution melting analysis and Sanger sequencing of selected exons or by massive sequencing of a panel of genes.

Results

Forty-seven patients with telomere length below the 10% of normal population, affected with three telomeropathies: dyskeratosis congenita (4), aplastic anemia (22) or pulmonary fibrosis (21) were analyzed. Eighteen of these patients presented known pathogenic or novel possibly pathogenic variants in the telomere-related genes TERT, TERC, RTEL1, CTC1 and ACD. In addition, the analyses of a panel of 188 genes related to haematological disorders indicated that a relevant proportion of the patients (up to 35%) presented rare variants in genes related to DNA repair or in genes coding for proteins involved in the resolution of complex DNA structures, that participate in telomere replication. Mutations in some of these genes are causative of several syndromes previously associated to telomere shortening.

Conclusion

Novel variants in telomere, DNA repair and replication genes are described that might indicate the contribution of variants in these genes to the development of telomeropathies. Patients carrying variants in telomere-related genes presented worse evolution after diagnosis than the rest of patients analyzed.

Electronic supplementary material

The online version of this article (10.1186/s13023-019-1046-0) contains supplementary material, which is available to authorized users.

Insights on the relationship between complement component C4 serum concentrations and C4 gene copy numbers in a Western Australian systemic lupus erythematosus cohort

The relationship between serum concentration of complement C4 ([C4]) and C4 gene copy number (GCN) was investigated in 56 systemic lupus erythematosus (SLE) patients and 33 age and sex-matched controls in a Western Australian population. C4A and C4B gene copy numbers (C4A & B GCN) together with the presence or absence of the ≈6.4-kb human endogenous retroviral element type K (hereafter HERV-K) in intron 9 were estimated by two TaqMan™ real-time PCR (RT-PCR) assays that measured total C4 and HERV-K GCNs, respectively. There was good correlation between the two methods; however, the HERV-K GCN method showed a positive bias (≈6%) relative to the C4A & B total GCN. Despite individual variation, excellent correlation between total C4 GCN and mean [C4] per GCN was observed for both the SLE and control cohorts ( R²= 88% and R²= 99%, respectively). It was noted that serum [C4] was significantly lower in the SLE patients than the controls ( p = 0.006) despite there being no difference between C4A and C4B GCN in both cohorts. The data therefore confirm previous reports that the C4A genes are preferentially associated with the presence of the HERV-K insertion relative to C4B genes and does not support the hypothesis that low [C4] in SLE is explained by low C4A GCNs. There was no evidence also that the presence of the HERV-K insertion in C4 genes influenced [C4]. This study supports the view that low [C4] in SLE patients is due to consumption rather than deficient synthesis related to lower C4A & B GCN.

Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species

The development of Genotyping-By-Sequencing (GBS) technologies enables cost-effective analysis of large numbers of Single Nucleotide Polymorphisms (SNPs), especially in "non-model" species. Nevertheless, as such technologies enter a mature phase, biases and errors inherent to GBS are becoming evident. Here, we evaluated the performance of double digest Restriction enzyme Associated DNA (ddRAD) sequencing in SNP genotyping studies including high number of samples. Datasets of sequence data were generated from three marine teleost species (>5500 samples, >2.5 × 10¹² bases in total), using a standardized protocol. A common bioinformatics pipeline based on STACKS was established, with and without the use of a reference genome. We performed analyses throughout the production and analysis of ddRAD data in order to explore (i) the loss of information due to heterogeneous raw read number across samples; (ii) the discrepancy between expected and observed tag length and coverage; (iii) the performances of reference based vs. de novo approaches; (iv) the sources of potential genotyping errors of the library preparation/bioinformatics protocol, by comparing technical replicates. Our results showed use of a reference genome and a posteriori genotype correction improved genotyping precision. Individual read coverage was a key variable for reproducibility; variance in sequencing depth between loci in the same individual was also identified as an important factor and found to correlate to tag length. A comparison of downstream analysis carried out with ddRAD vs single SNP allele specific assay genotypes provided information about the levels of genotyping imprecision that can have a significant impact on allele frequency estimations and population assignment. The results and insights presented here will help to select and improve approaches to the analysis of large datasets based on RAD-like methodologies.

Where technology does not go: specialised neonatal care in resource-poor and conflict-affected contexts

Setting: Although neonatal mortality is gradually decreasing worldwide, 98% of neonatal deaths occur in low- and middle-income countries, where hospital care for sick and premature neonates is often unavailable. Médecins Sans Frontières Operational Centre Brussels (MSF-OCB) managed eight specialised neonatal care units (SNCUs) at district level in low-resource and conflict-affected settings in seven countries. Objective: To assess the performance of the MSF SNCU model across different settings in Africa and Southern Asia, and to describe the set-up of eight SNCUs, neonate characteristics and clinical outcomes among neonates from 2012 to 2015. Design: Multicentric descriptive study. Results: The MSF SNCU model was characterised by an absence of high-tech equipment and an emphasis on dedicated nursing and medical care. Focus was on the management of hypothermia, hypoglycaemia, feeding support and early identification/treatment of infection. Overall, 11 970 neonates were admitted, 41% of whom had low birthweight (<2500 g). The main diagnoses were low birthweight, asphyxia and neonatal infections. Overall mortality was 17%, with consistency across the sites. Chances of survival increased with higher birthweight. Conclusion: The standardised SNCU model was implemented across different contexts and showed in-patient outcomes within acceptable limits. Low-tech medical care for sick and premature neonates can and should be implemented at district hospital level in low-resource settings.

The impact of education, country, race and ethnicity on the self-report of postpartum depression using the Edinburgh Postnatal Depression Scale

BACKGROUND

Universal screening for postpartum depression is recommended in many countries. Knowledge of whether the disclosure of depressive symptoms in the postpartum period differs across cultures could improve detection and provide new insights into the pathogenesis. Moreover, it is a necessary step to evaluate the universal use of screening instruments in research and clinical practice. In the current study we sought to assess whether the Edinburgh Postnatal Depression Scale (EPDS), the most widely used screening tool for postpartum depression, measures the same underlying construct across cultural groups in a large international dataset.

METHOD

Ordinal regression and measurement invariance were used to explore the association between culture, operationalized as education, ethnicity/race and continent, and endorsement of depressive symptoms using the EPDS on 8209 new mothers from Europe and the USA.

RESULTS

Education, but not ethnicity/race, influenced the reporting of postpartum depression [difference between robust comparative fit indexes (∆*CFI) 0.01), but not between European countries (∆*CFI < 0.01).

CONCLUSIONS

Investigators and clinicians should be aware of the potential differences in expression of phenotype of postpartum depression that women of different educational backgrounds may manifest. The increasing cultural heterogeneity of societies together with the tendency towards globalization requires a culturally sensitive approach to patients, research and policies, that takes into account, beyond rhetoric, the context of a person's experiences and the context in which the research is conducted.

Orthodontic camouflage versus orthognathic surgery for class III deformity: comparative cephalometric analysis

The objective of this study was to compare different cephalometric variables in adult patients with class III malocclusions before and after treatment, in order to determine which variables are indicative of orthodontic camouflage or orthognathic surgery. The cases of 156 adult patients were assessed: 77 treated with orthodontic camouflage and 79 treated with orthodontics and orthognathic surgery. The following cephalometric variables were measured on pre-treatment (T1) and post-treatment (T2) lateral cephalograms: sella-nasion-A-point (SNA), sella-nasion-B-point (SNB), and A-point-nasion-B-point (ANB) angles, Wits appraisal, facial axis angle, mandibular plane angle, upper and lower incisor inclination, and inter-incisal angle. There were statistically significant differences in cephalometric variables before and after treatment between the two groups. The percentage of normal pre-treatment measurements in the camouflage orthodontics group was 30.7%, which worsened slightly to 28.4% post-treatment. However in the group receiving surgery, this was 24.5% pre-treatment, improving to 33.5% after surgery. SNA, SNB, Wits appraisal, lower incisor inclination, and inter-incisal angle showed differences between the two groups before and after treatment. Wits appraisal, lower incisor inclination, and inter-incisal angle were indicative of one or other treatment. Upper and lower incisor decompensation in both groups did not reach ideal values, which impeded complete skeletal correction in 52% of surgical cases.

SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair

Defining mechanisms that generate intratumour heterogeneity and branched evolution may inspire novel therapeutic approaches to limit tumour diversity and adaptation. SETD2 (Su(var), Enhancer of zeste, Trithorax-domain containing 2) trimethylates histone-3 lysine-36 (H3K36me3) at sites of active transcription and is mutated in diverse tumour types, including clear cell renal carcinomas (ccRCCs). Distinct SETD2 mutations have been identified in spatially separated regions in ccRCC, indicative of intratumour heterogeneity. In this study, we have addressed the consequences of SETD2 loss-of-function through an integrated bioinformatics and functional genomics approach. We find that bi-allelic SETD2 aberrations are not associated with microsatellite instability in ccRCC. SETD2 depletion in ccRCC cells revealed aberrant and reduced nucleosome compaction and chromatin association of the key replication proteins minichromosome maintenance complex component (MCM7) and DNA polymerase δ hindering replication fork progression, and failure to load lens epithelium-derived growth factor and the Rad51 homologous recombination repair factor at DNA breaks. Consistent with these data, we observe chromosomal breakpoint locations are biased away from H3K36me3 sites in SETD2 wild-type ccRCCs relative to tumours with bi-allelic SETD2 aberrations and that H3K36me3-negative ccRCCs display elevated DNA damage in vivo. These data suggest a role for SETD2 in maintaining genome integrity through nucleosome stabilization, suppression of replication stress and the coordination of DNA repair.

Benefit to neoadjuvant anti-human epidermal growth factor receptor 2 (HER2)-targeted therapies in HER2-positive primary breast cancer is independent of phosphatase and tensin homolog deleted from chromosome 10 (PTEN) status

BACKGROUND

Assessment of phosphatase and tensin homolog deleted from chromosome 10 (PTEN) might be an important tool in identifying human epidermal growth factor receptor 2 (HER2)-positive breast cancer patients unlikely to derive benefit from anti-HER2 therapies. However, studies to date have failed to demonstrate its predictive role in any treatment setting.

PATIENTS AND METHODS

Prospectively collected baseline core biopsies from 429 early-stage HER2-positive breast cancer patients treated with trastuzumab, lapatinib, or their combination in the Neo-ALTTO study were stained using two anti-PTEN monoclonal antibodies (CST and DAKO). The association of PTEN status and PI3K pathway activation (defined as either PTEN loss and/or PIK3CA mutation) with total pathological complete response (tpCR) at surgery, event-free survival (EFS), and overall survival (OS) was evaluated.

RESULTS

PTEN loss was observed in 27% and 29% of patients (all arms, n = 361 and n = 363) for CST and DAKO, respectively. PTEN loss was more frequently observed in hormone receptor (HR)-negative (33% and 36% with CST and DAKO, respectively) compared with HR-positive tumours (20% and 22% with CST and DAKO, respectively). No significant differences in tpCR rates were observed according to PTEN status. PI3K pathway activation was found in 47% and 48% of patients (all arms, n = 302 and n = 301) for CST and DAKO, respectively. Similarly, tpCR rates were not significantly different for those with or without PI3K pathway activation. Neither PTEN status nor PI3K pathway activation were predictive of tpCR, EFS, or OS, independently of treatment arm or HR status. High inter-antibody and inter-observer agreements were found (>90%). Modification of scoring variables significantly affected the correlation between PTEN and HR status but not with tpCR.

CONCLUSION

These data show that PTEN status determination is not a useful biomarker to predict resistance to trastuzumab and lapatinib-based therapies. The lack of standardization of PTEN status determination may influence correlations between expression and relevant clinical end points.

CLINICAL TRIALS

This trial is registered with ClinicalTrials.gov: NCT00553358.