On the relationships among cloud cover, mixed-phase partitioning, and planetary albedo in GCMs

In this study, it is shown that CMIP5 global climate models (GCMs) that convert supercooled water to ice at relatively warm temperatures tend to have a greater mean-state cloud fraction and more negative cloud feedback in the middle and high latitude Southern Hemisphere. We investigate possible reasons for these relationships by analyzing the mixed-phase parameterizations in 26 GCMs. The atmospheric temperature where ice and liquid are equally prevalent (T5050) is used to characterize the mixed-phase parameterization in each GCM. Liquid clouds have a higher albedo than ice clouds, so, all else being equal, models with more supercooled liquid water would also have a higher planetary albedo. The lower cloud fraction in these models compensates the higher cloud reflectivity and results in clouds that reflect shortwave radiation (SW) in reasonable agreement with observations, but gives clouds that are too bright and too few. The temperature at which supercooled liquid can remain unfrozen is strongly anti-correlated with cloud fraction in the climate mean state across the model ensemble, but we know of no robust physical mechanism to explain this behavior, especially because this anti-correlation extends through the subtropics. A set of perturbed physics simulations with the Community Atmospheric Model Version 4 (CAM4) shows that, if its temperature-dependent phase partitioning is varied and the critical relative humidity for cloud formation in each model run is also tuned to bring reflected SW into agreement with observations, then cloud fraction increases and liquid water path (LWP) decreases with T5050, as in the CMIP5 ensemble

Local Volatility Calibration by Optimal Transport

The calibration of volatility models from observable option prices is a fundamental problem in quantitative finance. The most common approach among industry practitioners is based on the celebrated Dupire's formula [6], which requires the knowledge of vanilla option prices for a continuum of strikes and maturities that can only be obtained via some form of price interpolation. In this paper, we propose a new local volatility calibration technique using the theory of optimal transport. We formulate a time continuous martingale optimal transport problem, which seeks a martingale diffusion process that matches the known densities of an asset price at two different dates, while minimizing a chosen cost function. Inspired by the seminal work of Benamou and Brenier [1], we formulate the problem as a convex optimization problem, derive its dual formulation, and solve it numerically via an augmented Lagrangian method and the alternative direction method of multipliers (ADMM) algorithm. The solution effectively reconstructs the dynamic of the asset price between the two dates by recovering the optimal local volatility function, without requiring any time interpolation of the option prices

Sustainable construction and the versatility of the quantity surveying profession in Singapore

Purpose The changing role of quantity surveyors in the new paradigm of sustainable construction requires studies into new competencies and skills for the profession. The impact of sustainable construction on quantity surveying services, engagement and how they manage challenges provided an indication of the success indicators of the quantity surveying profession in meeting the sustainable construction needs. Design/methodology/approach A five-point Likert scale was developed from the list of quantity surveying firms in Singapore. An 85% response rate from 60 quantity surveying firms contacted in this study provided 51 responses. Descriptive statistics and factor analysis were employed to evaluate the findings. Findings The factor analysis categorised the drivers derived from the literature into awareness of sustainable construction, adversarial role on green costing; carbon cost planning; valuing a sustainable property; common knowledge of sustainable construction; and lack of experience in sustainable construction. Social implications The research findings supported the idea of increased sustainable construction skills in quantity surveying education, research and training. Originality/value The dearth of quantity surveyors with sustainable construction experience must focus on quantity surveying professional bodies and higher education. The quantity surveying profession needs reskilling in green costing and carbon cost planning to meet the needs of sustainable construction

Discovering Spatio-Temporal Patterns in Precision Agriculture Based on Triclustering

Agriculture has undergone some very important changes over the last few decades. The emergence and evolution of precision agri culture has allowed to move from the uniform site management to the site-specific management, with both economic and environmental advan tages. However, to be implemented effectively, site-specific management requires within-field spatial variability to be well-known and character ized. In this paper, an algorithm that delineates within-field management zones in a maize plantation is introduced. The algorithm, based on tri clustering, mines clusters from temporal remote sensing data. Data from maize crops in Alentejo, Portugal, have been used to assess the suit ability of applying triclustering to discover patterns over time, that may eventually help farmers to improve their harvests.Ministerio de Economía y Competitividad TIN2017-88209-C2Fundaçao para a Ciéncia e a Tecnologia (FCT) UIDB/04561/202

Site-specific incorporation of phosphotyrosine using an expanded genetic code.

Access to phosphoproteins with stoichiometric and site-specific phosphorylation status is key to understanding the role of protein phosphorylation. Here we report an efficient method to generate pure, active phosphotyrosine-containing proteins by genetically encoding a stable phosphotyrosine analog that is convertible to native phosphotyrosine. We demonstrate its general compatibility with proteins of various sizes, phosphotyrosine sites and functions, and reveal a possible role of tyrosine phosphorylation in negative regulation of ubiquitination

Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction

Background: We present a novel method of protein fold decoy discrimination using machine learning, more specifically using neural networks. Here, decoy discrimination is represented as a machine learning problem, where neural networks are used to learn the native-like features of protein structures using a set of positive and negative training examples. A set of native protein structures provides the positive training examples, while negative training examples are simulated decoy structures obtained by reversing the sequences of native structures. Various features are extracted from the training dataset of positive and negative examples and used as inputs to the neural networks.Results: Results have shown that the best performing neural network is the one that uses input information comprising of PSI-BLAST [1] profiles of residue pairs, pairwise distance and the relative solvent accessibilities of the residues. This neural network is the best among all methods tested in discriminating the native structure from a set of decoys for all decoy datasets tested. Conclusion: This method is demonstrated to be viable, and furthermore evolutionary information is successfully used in the neural networks to improve decoy discrimination

Distinct gene subsets in pterygia formation and recurrence: dissecting complex biological phenomenon using genome wide expression data

<p>Abstract</p> <p>Background</p> <p>Pterygium is a common ocular surface disease characterized by fibrovascular invasion of the cornea and is sight-threatening due to astigmatism, tear film disturbance, or occlusion of the visual axis. However, the mechanisms for formation and post-surgical recurrence of pterygium are not understood, and a valid animal model does not exist. Here, we investigated the possible mechanisms of pterygium pathogenesis and recurrence.</p> <p>Methods</p> <p>First we performed a genome wide expression analysis (human Affymetrix Genechip, >22000 genes) with principal component analysis and clustering techniques, and validated expression of key molecules with PCR. The controls for this study were the un-involved conjunctival tissue of the same eye obtained during the surgical resection of the lesions. Interesting molecules were further investigated with immunohistochemistry, Western blots, and comparison with tear proteins from pterygium patients.</p> <p>Results</p> <p>Principal component analysis in pterygium indicated a signature of matrix-related structural proteins, including fibronectin-1 (both splice-forms), collagen-1A2, keratin-12 and small proline rich protein-1. Immunofluorescence showed strong expression of keratin-6A in all layers, especially the superficial layers, of pterygium epithelium, but absent in the control, with up-regulation and nuclear accumulation of the cell adhesion molecule CD24 in the pterygium epithelium. Western blot shows increased protein expression of beta-microseminoprotein, a protein up-regulated in human cutaneous squamous cell carcinoma. Gene products of 22 up-regulated genes in pterygium have also been found by us in human tears using nano-electrospray-liquid chromatography/mass spectrometry after pterygium surgery. Recurrent disease was associated with up-regulation of sialophorin, a negative regulator of cell adhesion, and <it>never in mitosis a</it>-5, known to be involved in cell motility.</p> <p>Conclusion</p> <p>Aberrant wound healing is therefore a key process in this disease, and strategies in wound remodeling may be appropriate in halting pterygium or its recurrence. For patients demonstrating a profile of 'recurrence', it may be necessary to manage as a poorer prognostic case and perhaps, more adjunctive treatment after resection of the primary lesion.</p

How early can myocardial iron overload occur in Beta thalassemia major?

BACKGROUND: Myocardial siderosis is the most common cause of death in patients with beta thalassemia major(TM). This study aimed at investigating the occurrence, prevalence and severity of cardiac iron overload in a young Chinese population with beta TM. METHODS AND RESULTS: We analyzed T2* cardiac magnetic resonance (CMR), left ventricular ejection fraction (LVEF) and serum ferritin (SF) in 201 beta TM patients. The median age was 9 years old. Patients received an average of 13 units of blood per year. The median SF level was 4536 ng/ml and 165 patients (82.1%) had SF>2500 ng/ml. Myocardial iron overload was detected in 68 patients (33.8%) and severe myocardial iron overload was detected in 26 patients (12.6%). Twenty-two patients ≤10 years old had myocardial iron overload, three of whom were only 6 years old. No myocardial iron overload was detected under the age of 6 years. Median LVEF was 64% (measured by CMR in 175 patients). Five of 6 patients with a LVEF<56% and 8 of 10 patients with cardiac disease had myocardial iron overload. CONCLUSIONS: The TM patients under follow-up at this regional centre in China patients are younger than other reported cohorts, more poorly-chelated, and have a high burden of iron overload. Myocardial siderosis occurred in patients younger than previously reported, and was strongly associated with impaired LVEF and cardiac disease. For such poorly-chelated TM patients, our data shows that the first assessment of cardiac T2* should be performed as early as 6 years old

Persistent viral shedding of SARS‐CoV‐2 in faeces – a rapid review

Aim In addition to respiratory symptoms, COVID‐19 can present with gastrointestinal complaints suggesting possible faeco‐oral transmission. The primary aim of this review was to establish the incidence and timing of positive faecal samples for SARS‐CoV‐2 in patients with COVID‐19. Methods A systematic literature review identified studies describing COVID‐19 patients tested for faecal virus. Search terms for MEDLINE included ‘clinical’, ‘faeces’, ‘gastrointestinal secretions’, ‘stool’, ‘COVID‐19’, ‘SARS‐CoV‐2’ and ‘2019‐nCoV’. Additional searches were done in the American Journal of Gastroenterology , Gastroenterology , Gut , Lancet Gastroenterology and Hepatology , the World Health Organization Database, the Centre for Evidence‐Based Medicine, New England Journal of Medicine , social media and the National Institute for Health and Care Excellence, bioRxiv and medRxiv preprints. Data were extracted concerning the type of test, number and timing of positive samples, incidence of positive faecal tests after negative nasopharyngeal swabs and evidence of viable faecal virus or faeco‐oral transmission of the virus. Results Twenty‐six relevant articles were identified. Combining study results demonstrated that 53.9% of those tested for faecal RNA were positive. The duration of faecal viral shedding ranged from 1 to 33 days after a negative nasopharyngeal swab with one result remaining positive 47 days after onset of symptoms. There is insufficient evidence to suggest that COVID‐19 is transmitted via faecally shed virus. Conclusion There is a high rate of positive polymerase chain reaction tests with persistence of SARS‐CoV‐2 in faecal samples of patients with COVID‐19. Further research is needed to confirm if this virus is viable and the degree of transmission through the faeco‐oral route. This may have important implications on isolation, recommended precautions and protective equipment for interventional procedures involving the gastrointestinal tract

Serum microRNA array analysis identifies miR-140-3p, miR-33b-3p and miR-671-3p as potential osteoarthritis biomarkers involved in metabolic processes.

Background: MicroRNAs (miRNAs) in circulation have emerged as promising biomarkers. In this study, we aimed to identify a circulating miRNA signature for osteoarthritis (OA) patients and in combination with bioinformatics analysis to evaluate the utility of selected differentially expressed miRNAs in the serum as potential OA biomarkers. Methods: Serum samples were collected from 12 primary OA patients, and 12 healthy individuals were screened using the Agilent Human miRNA Microarray platform interrogating 2549 miRNAs. Receiver Operating Characteristic (ROC) curves were constructed to evaluate the diagnostic performance of the deregulated miRNAs. Expression levels of selected miRNAs were validated by quantitative real-time PCR (qRT-PCR) in all serum and in articular cartilage samples from OA patients (n = 12) and healthy individuals (n = 7). Bioinformatics analysis was used to investigate the involved pathways and target genes for the above miRNAs. Results: We identified 279 differentially expressed miRNAs in the serum of OA patients compared to controls. Two hundred and five miRNAs (73.5%) were upregulated and 74 (26.5%) downregulated. ROC analysis revealed that 77 miRNAs had area under the curve (AUC) > 0.8 and p < 0.05. Bioinformatics analysis in the 77 miRNAs revealed that their target genes were involved in multiple signaling pathways associated with OA, among which FoxO, mTOR, Wnt, pI3K/akt, TGF-β signaling pathways, ECM-receptor interaction, and fatty acid biosynthesis. qRT-PCR validation in seven selected out of the 77 miRNAs revealed 3 significantly downregulated miRNAs (hsa-miR-33b-3p, hsa-miR-671-3p, and hsa-miR-140-3p) in the serum of OA patients, which were in silico predicted to be enriched in pathways involved in metabolic processes. Target-gene analysis of hsa-miR-140-3p, hsa-miR-33b-3p, and hsa-miR-671-3p revealed that InsR and IGFR1 were common targets of all three miRNAs, highlighting their involvement in regulation of metabolic processes that contribute to OA pathology. Hsa-miR-140-3p and hsa-miR-671-3p expression levels were consistently downregulated in articular cartilage of OA patients compared to healthy individuals. Conclusions: A serum miRNA signature was established for the first time using high density resolution miR-arrays in OA patients. We identified a three-miRNA signature, hsa-miR-140-3p, hsa-miR-671-3p, and hsa-miR-33b-3p, in the serum of OA patients, predicted to regulate metabolic processes, which could serve as a potential biomarker for the evaluation of OA risk and progression.Peer reviewedFinal Published versio