Developing composite indicators for ecological water quality assessment based on network interactions and expert judgment

Increasingly, composite indicators and multi-criteria approaches are applied in environmental assessment and decision-making, including the EU Water Framework Directive. For example, integrated evaluation of aquatic ecosystem conditions and functioning usually involves a group of criteria, such as biological organisms and communities, physicochemical and hydromorphological variables, which are measured individually and combined by a weighted linear function into an overall 'score’. We argue that the network interactions of evaluation components are useful information for expert judgments, which have not been sufficiently considered in existing multi-criteria combination strategies in environmental assessment and management. Built upon the Analytic Network Process and demonstrated with the Chishui River Basin in China, this paper introduces a network-based expert judgment approach to construct ecological water quality indicators, and to determine and adjust their variable weight settings with information of interaction networks. This approach has potential to construct composite indicators for a broad environmental context.</p

Scalable and physiologically relevant microenvironments for human pluripotent stem cell expansion and differentiation

Human pluripotent stem cells (hPSCs), including human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs), are attractive cell sources for various biomedical applications including cell therapies, tissue biofabrication, drug screening and toxicity tests. These applications require large numbers of high quality cells. However, the scalable and cost-effective culturing of high quality hPSCs and their derivatives, especially for clinical applications, remains a challenge. In vivo, majority of human cells including the hESCs reside in 3D microenvironments that have plenty of cell-cell and cell-ECM (extracellular matrix) interactions, sufficient supply of nutrients, oxygen and growth factors, and no or minimal hydrodynamic stresses. The current hPSC culturing methods, however, provide culturing conditions that are very different from these physiological microenvironments, leading to low culture efficiency and difficulty to culture cells at large scales. For instance, we and others showed hPSCs typically expanded 4-fold in 4 days to yield around 2.0x10^6 cells/mL with current 3D suspension culturing. These cells occupy ~0.4% of the bioreactor volume. To our best knowledge, the largest 3D suspension culture volume demonstrated to date for hPSCs is less than 10 liters. Please click Additional Files below to see the full abstract

A quantum coherent spin in a two-dimensional material at room temperature

Quantum networks and sensing require solid-state spin-photon interfaces that combine single-photon generation and long-lived spin coherence with scalable device integration, ideally at ambient conditions. Despite rapid progress reported across several candidate systems, those possessing quantum coherent single spins at room temperature remain extremely rare. Here, we report quantum coherent control under ambient conditions of a single-photon emitting defect spin in a a two-dimensional material, hexagonal boron nitride. We identify that the carbon-related defect has a spin-triplet electronic ground-state manifold. We demonstrate that the spin coherence is governed predominantly by coupling to only a few proximal nuclei and is prolonged by decoupling protocols. Our results allow for a room-temperature spin qubit coupled to a multi-qubit quantum register or quantum sensor with nanoscale sample proximity

Preference versus performance: Investigating the dissociation between objective measures and subjective ratings of usability for schematic metro maps and intuitive theories of design

Three experiments are reported in which objective measures and subjective ratings of schematic metro map usability were investigated. Experiment 1 used a within-subjects design to compare octolinear and curvilinear Paris Metro maps. This replicated and extended Roberts et al. (2013); the curvilinear map was associated with faster journey planning times, and yet preference between the two was unrelated to this measure. In Experiment 2, nine matched versions of the London Underground map were rated for usability and attractiveness, and a clear octolinear bias was displayed. It was also possible to identify individuals who held a simplicity theory of effective design, versus an octolinearity theory. Experiment 3 investigated the relationship between usability ratings and journey planning times for three Berlin network maps, all optimized for simplicity of line trajectories. No differences in times were found, and yet usability ratings after experience at using the maps differed significantly, in line with the findings for the London designs in Experiment 2. Overall, the dissociation between objective measures of performance and subjective ratings of usability is robust, and appears to reflect expectations and prejudices concerning effective design. The octolinearity as a gold standard conjecture for achieving optimum usability continues to be refuted

High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.

Here, we report the high-quality draft genome sequences of four phylogenetically diverse lignocellulose-degrading bacteria isolated from tropical soil (Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.) to elucidate the genetic basis of their ability to degrade lignocellulose. These isolates may provide novel enzymes for biofuel production

Analyses of the yeast Rad51 recombinase A265V mutant reveal different in vivo roles of Swi2-like factors

The Saccharomyces cerevisiae Swi2-like factors Rad54 and Rdh54 play multifaceted roles in homologous recombination via their DNA translocase activity. Aside from promoting Rad51-mediated DNA strand invasion of a partner chromatid, Rad54 and Rdh54 can remove Rad51 from duplex DNA for intracellular recycling. Although the in vitro properties of the two proteins are similar, differences between the phenotypes of the null allele mutants suggest that they play different roles in vivo. Through the isolation of a novel RAD51 allele encoding a protein with reduced affinity for DNA, we provide evidence that Rad54 and Rdh54 have different in vivo interactions with Rad51. The mutant Rad51 forms a complex on duplex DNA that is more susceptible to dissociation by Rdh54. This Rad51 variant distinguishes the in vivo functions of Rad54 and Rdh54, leading to the conclusion that two translocases remove Rad51 from different substrates in vivo. Additionally, we show that a third Swi2-like factor, Uls1, contributes toward Rad51 clearance from chromatin in the absence of Rad54 and Rdh54, and define a hierarchy of action of the Swi2-like translocases for chromosome damage repair

Enzyme kinetics and inhibition of histone acetyltransferase KAT8

Lysine acetyltransferase 8 (KAT8) is a histone acetyltransferase (HAT) responsible for acetylating lysine 16 on histone H4 (H4K16) and plays a role in cell cycle progression as well as acetylation of the tumor suppressor protein p53. Further studies on its biological function and drug discovery initiatives will benefit from the development of small molecule inhibitors for this enzyme. As a first step towards this aim we investigated the enzyme kinetics of this bi-substrate enzyme. The kinetic experiments indicate a ping-pong mechanism in which the enzyme binds Ac-CoA first, followed by binding of the histone substrate. This mechanism is supported by affinity measurements of both substrates using isothermal titration calorimetry (ITC). Using this information, the KAT8 inhibition of a focused compound collection around the non-selective HAT inhibitor anacardic acid has been investigated. Kinetic studies with anacardic acid were performed, based on which a model for the catalytic activity of KAT8 and the inhibitory action of anacardic acid (AA) was proposed. This enabled the calculation of the inhibition constant Ki of anacardic acid derivatives using an adaptation of the Cheng-Prusoff equation. The results described in this study give insight into the catalytic mechanism of KAT8 and present the first well-characterized small-molecule inhibitors for this HAT

Smc5/6 coordinates formation and resolution of joint molecules with chromosome morphology to ensure meiotic divisions

During meiosis, Structural Maintenance of Chromosome (SMC) complexes underpin two fundamental features of meiosis: homologous recombination and chromosome segregation. While meiotic functions of the cohesin and condensin complexes have been delineated, the role of the third SMC complex, Smc5/6, remains enigmatic. Here we identify specific, essential meiotic functions for the Smc5/6 complex in homologous recombination and the regulation of cohesin. We show that Smc5/6 is enriched at centromeres and cohesin-association sites where it regulates sister-chromatid cohesion and the timely removal of cohesin from chromosomal arms, respectively. Smc5/6 also localizes to recombination hotspots, where it promotes normal formation and resolution of a subset of joint-molecule intermediates. In this regard, Smc5/6 functions independently of the major crossover pathway defined by the MutLγ complex. Furthermore, we show that Smc5/6 is required for stable chromosomal localization of the XPF-family endonuclease, Mus81-Mms4Eme1. Our data suggest that the Smc5/6 complex is required for specific recombination and chromosomal processes throughout meiosis and that in its absence, attempts at cell division with unresolved joint molecules and residual cohesin lead to severe recombination-induced meiotic catastroph

Maternal autoimmunity and inflammation are associated with childhood tics and obsessive-compulsive disorder: Transcriptomic data show common enriched innate immune pathways.

Although genetic variation is a major risk factor of neurodevelopmental disorders, environmental factors during pregnancy and early life are also important in disease expression. Animal models demonstrate that maternal inflammation causes fetal neuroinflammation and neurodevelopmental deficits, and brain transcriptomics of neurodevelopmental disorders in humans show upregulated differentially expressed genes are enriched in immune pathways. We prospectively recruited 200 sequentially referred children with tic disorders/obsessive-compulsive disorder (OCD), 100 autoimmune neurological controls, and 100 age-matched healthy controls. A structured interview captured the maternal and family history of autoimmune disease and other pro-inflammatory states. Maternal blood and published Tourette brain transcriptomes were analysed for overlapping enriched pathways. Mothers of children with tics/OCD had a higher rate of autoimmune disease compared with mothers of children with autoimmune neurological conditions (p = 0.054), and mothers of healthy controls (p = 0.0004). Autoimmunity was similarly elevated in first- and second-degree maternal relatives of children with tics/OCD (p 0.0001 and p = 0.014 respectively). Other pro-inflammatory states were also more common in mothers of children with tics/OCD than controls (p 0.0001). Upregulated differentially expressed genes in maternal autoimmune disease and Tourette brain transcriptomes were commonly enriched in innate immune processes. Pro-inflammatory states, including autoimmune disease, are more common in the mothers and families of children with tics/OCD. Exploratory transcriptome analysis indicates innate immune signalling may link maternal inflammation and childhood tics/OCD. Targeting inflammation may represent preventative strategies in pregnancy and treatment opportunities for children with neurodevelopmental disorders

Laparoscopy to predict the result of primary cytoreductive surgery in advanced ovarian cancer patients (LapOvCa-trial): a multicentre randomized controlled study

Contains fulltext : 108486.pdf (publisher's version ) (Open Access)BACKGROUND: Standard treatment of advanced ovarian cancer is surgery and chemotherapy. The goal of surgery is to remove all macroscopic tumour, as the amount of residual tumour is the most important prognostic factor for survival. When removal off all tumour is considered not feasible, neoadjuvant chemotherapy (NACT) in combination with interval debulking surgery (IDS) is performed. Current methods of staging are not always accurate in predicting surgical outcome, since approximately 40% of patients will have more than 1 cm residual tumour after primary debulking surgery (PDS). In this study we aim to assess whether adding laparoscopy to the diagnostic work-up of patients suspected of advanced ovarian carcinoma may prevent unsuccessful primary debulking surgery for ovarian cancer. METHODS: Multicentre randomized controlled trial, including all gynaecologic oncologic centres in the Netherlands and their affiliated hospitals. Patients are eligible when they are planned for PDS after conventional staging. Participants are randomized between direct PDS or additional diagnostic laparoscopy. Depending on the result of laparoscopy patients are treated by PDS within three weeks, followed by six courses of platinum based chemotherapy or with NACT and IDS 3-4 weeks after three courses of chemotherapy, followed by another three courses of chemotherapy. Primary outcome measure is the proportion of PDS's leaving more than one centimetre tumour residual in each arm. In total 200 patients will be randomized. Data will be analysed according to intention to treat. DISCUSSION: Patients who have disease considered to be resectable to less than one centimetre should undergo PDS to improve prognosis. However, there is a need for better diagnostic procedures because the current number of debulking surgeries leaving more than one centimetre residual tumour is still high. Laparoscopy before starting treatment for ovarian cancer can be an additional diagnostic tool to predict the outcome of PDS. Despite the absence of strong evidence and despite the possible complications, laparoscopy is already implemented in many countries. We propose a randomized multicentre trial to provide evidence on the effectiveness of laparoscopy before primary surgery for advanced stage ovarian cancer patients. TRIAL REGISTRATION: Netherlands Trial Register number NTR2644