Biomass and carbon stocks in two mangrove patches of Chettuva Estuary, south-west coast of India

Mangroves support numerous ecosystem services, including fisheries production and nutrient cycling. The role of mangroves in mitigating climate change is also well known. In the present study, the biomass and carbon sequestration potential of two dense mangrove patches located in the Chettuva estuary, south-west coast of India were assessed

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

Naturally occurring regulatory T (Treg) cells, which specifically express the transcription factor forkhead box P3 (Foxp3), are engaged in the maintenance of immunological self-tolerance and homeostasis. By transcriptional start site cluster analysis, we assessed here how genome-wide patterns of DNA methylation or Foxp3 binding sites were associated with Treg-specific gene expression. We found that Treg-specific DNA hypomethylated regions were closely associated with Treg up-regulated transcriptional start site clusters, whereas Foxp3 binding regions had no significant correlation with either up- or down-regulated clusters in nonactivated Treg cells. However, in activated Treg cells, Foxp3 binding regions showed a strong correlation with down-regulated clusters. In accordance with these findings, the above two features of activation-dependent gene regulation in Treg cells tend to occur at different locations in the genome. The results collectively indicate that Treg-specific DNA hypomethylation is instrumental in gene up-regulation in steady state Treg cells, whereas Foxp3 down-regulates the expression of its target genes in activated Treg cells. Thus, the two events seem to play distinct but complementary roles in Treg-specific gene expression

Elective Cancer Surgery in COVID-19-Free Surgical Pathways During the SARS-CoV-2 Pandemic: An International, Multicenter, Comparative Cohort Study.

PURPOSE: As cancer surgery restarts after the first COVID-19 wave, health care providers urgently require data to determine where elective surgery is best performed. This study aimed to determine whether COVID-19-free surgical pathways were associated with lower postoperative pulmonary complication rates compared with hospitals with no defined pathway. PATIENTS AND METHODS: This international, multicenter cohort study included patients who underwent elective surgery for 10 solid cancer types without preoperative suspicion of SARS-CoV-2. Participating hospitals included patients from local emergence of SARS-CoV-2 until April 19, 2020. At the time of surgery, hospitals were defined as having a COVID-19-free surgical pathway (complete segregation of the operating theater, critical care, and inpatient ward areas) or no defined pathway (incomplete or no segregation, areas shared with patients with COVID-19). The primary outcome was 30-day postoperative pulmonary complications (pneumonia, acute respiratory distress syndrome, unexpected ventilation). RESULTS: Of 9,171 patients from 447 hospitals in 55 countries, 2,481 were operated on in COVID-19-free surgical pathways. Patients who underwent surgery within COVID-19-free surgical pathways were younger with fewer comorbidities than those in hospitals with no defined pathway but with similar proportions of major surgery. After adjustment, pulmonary complication rates were lower with COVID-19-free surgical pathways (2.2% v 4.9%; adjusted odds ratio [aOR], 0.62; 95% CI, 0.44 to 0.86). This was consistent in sensitivity analyses for low-risk patients (American Society of Anesthesiologists grade 1/2), propensity score-matched models, and patients with negative SARS-CoV-2 preoperative tests. The postoperative SARS-CoV-2 infection rate was also lower in COVID-19-free surgical pathways (2.1% v 3.6%; aOR, 0.53; 95% CI, 0.36 to 0.76). CONCLUSION: Within available resources, dedicated COVID-19-free surgical pathways should be established to provide safe elective cancer surgery during current and before future SARS-CoV-2 outbreaks

Elective cancer surgery in COVID-19-free surgical pathways during the SARS-CoV-2 pandemic: An international, multicenter, comparative cohort study

PURPOSE As cancer surgery restarts after the first COVID-19 wave, health care providers urgently require data to determine where elective surgery is best performed. This study aimed to determine whether COVID-19–free surgical pathways were associated with lower postoperative pulmonary complication rates compared with hospitals with no defined pathway. PATIENTS AND METHODS This international, multicenter cohort study included patients who underwent elective surgery for 10 solid cancer types without preoperative suspicion of SARS-CoV-2. Participating hospitals included patients from local emergence of SARS-CoV-2 until April 19, 2020. At the time of surgery, hospitals were defined as having a COVID-19–free surgical pathway (complete segregation of the operating theater, critical care, and inpatient ward areas) or no defined pathway (incomplete or no segregation, areas shared with patients with COVID-19). The primary outcome was 30-day postoperative pulmonary complications (pneumonia, acute respiratory distress syndrome, unexpected ventilation). RESULTS Of 9,171 patients from 447 hospitals in 55 countries, 2,481 were operated on in COVID-19–free surgical pathways. Patients who underwent surgery within COVID-19–free surgical pathways were younger with fewer comorbidities than those in hospitals with no defined pathway but with similar proportions of major surgery. After adjustment, pulmonary complication rates were lower with COVID-19–free surgical pathways (2.2% v 4.9%; adjusted odds ratio [aOR], 0.62; 95% CI, 0.44 to 0.86). This was consistent in sensitivity analyses for low-risk patients (American Society of Anesthesiologists grade 1/2), propensity score–matched models, and patients with negative SARS-CoV-2 preoperative tests. The postoperative SARS-CoV-2 infection rate was also lower in COVID-19–free surgical pathways (2.1% v 3.6%; aOR, 0.53; 95% CI, 0.36 to 0.76). CONCLUSION Within available resources, dedicated COVID-19–free surgical pathways should be established to provide safe elective cancer surgery during current and before future SARS-CoV-2 outbreaks

PROPER: global protein interaction network alignment through percolation matching

Background The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological knowledge between species. Although different PI-network alignment algorithms were introduced during the last decade, developing an accurate and scalable algorithm that can find alignments with high biological and structural similarities among PPI networks is still challenging. Results In this paper, we introduce a new global network alignment algorithm for PPI networks called PROPER. Compared to other global network alignment methods, our algorithm shows higher accuracy and speed over real PPI datasets and synthetic networks. We show that the PROPER algorithm can detect large portions of conserved biological pathways between species. Also, using a simple parsimonious evolutionary model, we explain why PROPER performs well based on several different comparison criteria. Conclusions We highlight that PROPER has high potential in further applications such as detecting biological pathways, finding protein complexes and PPI prediction. The PROPER algorithm is available at http://proper.epfl.ch

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution

CFD simulation for steam distribution in header and tube assemblies

The study of the flow characteristics in manifolds (dividing, combining, parallel or Z-manifold and reverse or U-manifold) is a classic subject of engineering fluid dynamics and hydrodynamics. These manifolds are widely used in chemical processes, electronic cooling equipment, solar collectors, spargers, microchannels, fuel cells, heat exchangers and refrigerant distribution in multi-split type of air conditioner, etc. In the literature extensive work has been done for finding out flow distribution in plate-fin heat exchanger, microchannels and spargers. Present work focuses on the flow and pressure distribution in piping networks, which has gained importance in many areas such as air distribution in diffuser system of aerobic biological treatment, steam distribution in passive decay heat removal systems, etc. The uniformity of flow rates among the parallel tubes of piping manifold is governed by the field of fluid pressure in the system under consideration. In present work, the flow and pressure distribution of pure steam in header and tube assemblies has been investigated with the help of CFD simulations. The effects of design parameters has been investigated over a wide range such as the tube pitch (50 < Dpt < 150 mm), header diameter (50 < Dh < 200 mm), tube diameter (15 < Dt < 32 mm), number of tubes (8 < Nt < 50), inlet or outlet pipe diameter (15 < Din < 65 mm). The sensitivity of inlet mass flow rate (0.033 < m< 0.075kg/s) has been investigated on the extent of non-uniformity (%ENU) in steam distribution. For validating CFD predictions an experiments have been performed on scaled down geometry of header configuration 'C1' using air and water (35,600 < Re < 68,500) as a working fluid. A good agreement was observed between the predicted and the experimental values of %ENU. It is concluded that the tube diameter, number of tubes and their locational arrangement with respect to inlet and/or outlet pipe are most important design parameters affecting the flow and pressure distribution in the pipeline networks

Two phase natural convection: CFD simulations and PIV measurement

Buoyancy induced flow and heat transfer are important phenomena in a wide range of engineering systems e.g. electronics and photovoltaics cooling, thermosiphon heat exchangers, solar-thermal heat absorbers, passive decay heat removal systems, etc. Such systems are subject to thermal stratification. The objective of the present work is to study the single phase and two phase (boiling) natural convection accompanied by thermal stratification. We carried out velocity and temperature measurements in a rectangular tank (0.8×0.6×0.6 m<SUP>3</SUP>) fitted with (a) a central tube, and (b) a 10 tube assembly; which form the heat transfer surface. Flows were measured using Particle Image Velocimetry (PIV). Additionally, computational fluid dynamic (CFD) simulations of these systems were performed: first with an assumption of no-boiling (i.e. no phase change) near the heat transfer surfaces; for which we used the open source CFD code OpenFOAM-1.6. For two phase simulations, we used the boiling model of Ganguli et al. (2010) and carried out simulations using the commercial software FLUENT 6.3. The extent of stratification and mixing has been investigated for a range of Rayleigh numbers from 4.34×10<SUP>11</SUP> to 2.59×10<SUP>14</SUP>. The flow information obtained from PIV was analyzed for insights into the dynamics of turbulent flow structures. We used the signal processing technique of discrete wavelet transform (DWT) for this purpose. From the analysis, we were able to estimate the size, velocity and energy distribution of turbulent structures in our flows. This information was used to estimate wall heat transfer coefficients. A good agreement was observed between the predicted and the experimental values of heat transfer coefficients

Hydrodynamic and heat transfer characteristics of a centrally heated cylindrical enclosure: CFD simulations and experimental measurements

Natural convection in enclosures is of importance in many engineering applications. The stratification arising out of natural convection may be desirable/undesirable depending on applications. In order to control the degree of stratification, understanding of flow pattern and temperature profiles is required. In the present work, transient natural convection in a cylindrical enclosure has been investigated for water with CFD simulations and flow visualization [using particle image velocimetry (PIV) and hot film anemometry (HFA)] over a wide range of parameters namely Rayleigh number (1.08 × 1011 ≤Ra ≤3.76 × 1013) and aspect ratio (1≤H/R≤2). The effect of various parameters like pressure, tube diameter and aspect ratio on the extent of stratification has been studied. PIV measurements have been performed to understand the transient flow behavior. Multiple thermocouples were used to measure the temperature profiles. CFD simulations have been performed using SST k-ω model and the results have been compared with the PIV measurements. The CFD simulations have been carried out for 2D axi-symmetric cases and the effect of boundary conditions (free-slip and no-slip) has been investigated. An excellent agreement was found between the CFD predictions and the experimental measurements of flow and temperature patterns. The extent of stratification has been quantified using dimensionless parameters like stratification number and stratification time. The kinetic energy profiles and kinetic energy dissipation profiles show that almost 75% of the enclosure is stratified (after different times depending on Ra number and the aspect ratio). The turbulence parameters were found to weaken with time in the stratified region and these predictions are corroborated with HFA measurements