Miracle-dz/UniFAR-FTUs huggingface dataset:
The signaling lipid phosphatidylinositol‐3,5‐bisphosphate targets plant CLC‐a anion/H+ exchange activity

Phosphatidylinositol‐3,5‐bisphosphate (PI(3,5)P2) is a low‐abundance signaling lipid associated with endo‐lysosomal and vacuolar membranes in eukaryotic cells. Recent studies on Arabidopsis indicated a critical role of PI(3,5)P2 in vacuolar acidification and morphology during ABA‐induced stomatal closure, but the molecular targets in plant cells remained unknown. By using patch‐clamp recordings on Arabidopsis vacuoles, we show here that PI(3,5)P2 does not affect the activity of vacuolar H+‐pyrophosphatase or vacuolar H+‐ATPase. Instead, PI(3,5)P2 at low nanomolar concentrations inhibited an inwardly rectifying conductance, which appeared upon vacuolar acidification elicited by prolonged H+ pumping activity. We provide evidence that this novel conductance is mediated by chloride channel a (CLC‐a), a member of the anion/H+ exchanger family formerly implicated in stomatal movements in Arabidopsis. H+‐dependent currents were absent in clc‐a knock‐out vacuoles, and canonical CLC‐a‐dependent nitrate/H+ antiport was inhibited by low concentrations of PI(3,5)P2. Finally, using the pH indicator probe BCECF, we show that CLC‐a inhibition contributes to vacuolar acidification. These data provide a mechanistic explanation for the essential role of PI(3,5)P2 and advance our knowledge about the regulation of vacuolar ion transport.
Landscape Pattern Determines Neighborhood Size and Structure within a Lizard Population

Although defining population structure according to discrete habitat patches is convenient for metapopulation theories, taking this approach may overlook structure within populations continuously distributed across landscapes. For example, landscape features within habitat patches direct the movement of organisms and define the density distribution of individuals, which can generate spatial structure and localized dynamics within populations as well as among them. Here, we use the neighborhood concept, which describes population structure relative to the scale of individual movements, to illustrate how localized dynamics within a population of lizards (Sceloporus arenicolus) arise in response to variation in landscape pattern within a continuous habitat patch. Our results emphasize links between individual movements at small scales and the emergence of spatial structure within populations which resembles metapopulation dynamics at larger scales. We conclude that population dynamics viewed in a landscape context must consider the explicit distribution and movement of individuals within continuous habitat as well as among habitat patches.
UvA-DARE ( Digital Academic Repository ) Are accuracy and reaction time affected via different processes ?

A recent study by van Ede et al. (2012) shows that the accuracy and reaction time in humans of tactile perceptual decisions are affected by an attentional cue via distinct cognitive and neural processes. These results are controversial as they undermine the notion that accuracy and reaction time are influenced by the same latent process that underlie the decision process. Typically, accumulation-to-bound models (like the drift diffusion model) can explain variability in both accuracy and reaction time by a change of a single parameter. To elaborate the findings of van Ede et al., we fitted the drift diffusion model to their behavioral data. Results show that both changes in accuracy and reaction time can be partly explained by an increase in the accumulation of sensory evidence (drift rate). In addition, a change in non-decision time is necessary to account for reaction time changes as well. These results provide a subtle explanation of how the underlying dynamics of the decision process might give rise to differences in both the speed and accuracy of perceptual tactile decisions. Furthermore, our analyses highlight the importance of applying a model-based approach, as the observed changes in the model parameters might be ecologically more valid, since they have an intuitive relationship with the neuronal processes underlying perceptual decision making. Citation: Mulder MJ, van Maanen L (2013) Are Accuracy and Reaction Time Affected via Different Processes? PLoS ONE 8(11): e80222. doi:10.1371/ journal.pone. 0080222 Editor: Daniel Goldreich, McMaster University, Canada Received March 30, 2013; Accepted October 1, 2013; Published November 18, 2013 Copyright: 2013 Mulder and van Maanen. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This study was supported by the Dutch organization for scientific research (NWO). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: m.j.mulder@uva.nl
Health impact assessment on urban development projects in France: finding pathways to fit practice to context

In France, there is increasing interest in health impact assessments (HIAs) and most are performed on urban projects. The field of expertise is still under development and mostly established within the public health sector. To date, in France, all HIAs conducted in urban planning are stand-alone HIAs disconnected from the required environmental impact assessment (EIA). The paper opens with an introduction of the close and complex relationship between health and urban planning, HIA and a description of key elements needed for understanding the French context. Then, the paper analyses the context and the implementation process for four HIAs in progress in order to understand the specific characteristics of urban development, identify the key stages for introducing a health perspective into urban projects, and extract avenues to be explored when adapting HIAs applied to urban planning in France. Using a qualitative multiple case study design, an analysis framework was built to compare several aspects of the four HIAs and made it possible to highlight three pathways for adapting HIA to the urban planning sector: the schedule, links between the EIA and HIA, and the complementarity of the initiatives to involve residents. Legal measures enable a point of contact that brings health institutions and cities closer together. HIA is yet another tool that public authorities now have at their fingertips to work together in strengthening democracy and in reducing social, geographical and environmental health inequalities. More research must be undertaken to develop an understanding of the practice-related context; to judge HIA’s capacity to draw on existing approaches in different fields; and to explore the different avenues leading to increased health, wellbeing and equity.
Evaluation of CVD‐Deposited SiO2 as a Sintering Aid for Cubic Boron Nitride Consolidated with Alumina by Spark Plasma Sintering

A SiO2 nanolayer, 1.0–2.8 mass% in content, was coated on cubic boron nitride (cBN) powder by rotary chemical vapor deposition (RCVD). The morphology of the SiO2 nanolayer changed from isolated islands to a continuous layer with increasing supply rate of the precursor, tetraethyl orthosilicate. The effect of the SiO2 coating on the sinterability and mechanical properties of cBN for machine-tool applications was evaluated. The SiO2-coated cBN (cBN/SiO2) powder was mixed with Al2O3 and consolidated by spark plasma sintering (SPS) at 1473–1873 K. The phase transformation temperature of cBN to hexagonal BN (hBN) in Al2O3–cBN/SiO2 was 1773 K, 100 K higher than that in Al2O3–cBN composites. The highest density of the Al2O3–cBN/SiO2 composites was 99.5% at 30 vol% cBN/SiO2 content, at which the microhardness and fracture toughness were 28 GPa and 4.1 MPa·m1/2, respectively. This indicates that RCVD-deposited SiO2 is a promising sintering aid for cBN and Al2O3–cBN/SiO2 sintered bodies produced by SPS may be applicable as cutting tools.
Influence of Parasitic Wiring on CMOS Logic Gates

in_a in_b out_b out_a in out (a) (b) (c) (d) vdd in out M1 M2 in_a in_b out_a out_b R1 R2 M1 M2 Ibias vdd Abstract—This paper investigates the influence of parasitic interconnections on high speed logic gates. A complementary metal oxide semiconductor logic (CMOS) gate, a high speed source coupled logic (SCL) gate and a low power SCL gate are compared. The circuits are fabricated on commercial 0.25 µm CMOS technology.
A method for analysing small samples of floral pollen for free and protein‐bound amino acids

Pollen provides floral visitors with essential nutrients including proteins, lipids, vitamins and minerals. As an important nutrient resource for pollinators, including honeybees and bumblebees, pollen quality is of growing interest in assessing available nutrition to foraging bees. To date, quantifying the protein‐bound amino acids in pollen has been difficult and methods rely on large amounts of pollen, typically more than 1 g. More usual is to estimate a crude protein value based on the nitrogen content of pollen, however, such methods provide no information on the distribution of essential and non‐essential amino acids constituting the proteins. Here, we describe a method of microwave‐assisted acid hydrolysis using low amounts of pollen that allows exploration of amino acid composition, quantified using ultra high performance liquid chromatography (UHPLC), and a back calculation to estimate the crude protein content of pollen. Reliable analysis of protein‐bound and free amino acids as well as an estimation of crude protein concentration was obtained from pollen samples as low as 1 mg. Greater variation in both protein‐bound and free amino acids was found in pollen sample sizes <1 mg. Due to the variability in recovery of amino acids in smaller sample sizes, we suggest a correction factor to apply to specific sample sizes of pollen in order to estimate total crude protein content. The method described in this paper will allow researchers to explore the composition of amino acids in pollen and will aid research assessing the available nutrition to pollinating animals. This method will be particularly useful in assaying the pollen of wild plants, from which it is difficult to obtain large sample weights.
Safety of high-dose daptomycin in patients with severe renal impairment

Background Treatment options are limited for infections due to multidrug-resistant Gram-positive pathogens. Daptomycin is a lipopeptide antibiotic with concentration-dependent killing characteristic and dose-dependent post-antibiotic effect. To achieve optimized pharma-codynamic effect, some experts advocated using a high dose of daptomycin (≥9 mg/kg) for severe infections. However, the safety of high-dose therapy in patients with renal impairment remains unknown. This study was aimed to evaluate the safety of daptomycin in patients with severe renal impairment. Methods This was a retrospective study performed by reviewing electronic medical records. Patients with severe renal impairment who were treated with daptomycin in a tertiary teaching hospital between January 1, 2013, and June 30, 2016, were included for evaluation. The incidence rates of creatine kinase (CK) elevation between high-dose (≥9 mg/kg) and standard-dose (<9 mg/kg) groups were compared. Results Overall, 164 patients met the inclusion criteria, and 114 (69.5%) of them were on renal replacement therapy. Vancomycin-resistant enterococci were the most common pathogens (61.3%) of the patients with documented pathogens. The treatment success rate was 51.6% in the 91 patients with bacteremia. The average dose of daptomycin was 8.0±2.3 mg/kg, and 37 (22.6%) patients received ≥9 mg/kg. CK levels were followed in 108 (65.9%) patients. Significantly higher incidence of CK elevation was found in the high-dose group compared with that in the standard-dose group (10.8% vs 1.6%, P<0.05). Moreover, patients with elevated CK received a higher dose of daptomycin than those without (9.3±1.2 vs 7.9±2.3 mg/kg, P<0.05). There was no significant difference in the rate of CK elevation between patients treated with different dosing frequency or with the concurrent use of statins, fibrate, or colchicine. Conclusions In patients with severe renal impairment, high-dose (≥9 mg/kg) daptomycin therapy may result in a significantly higher incidence of CK elevation. More frequent CK monitoring is warranted to avoid potential harm in this population.
A Combinational Clustering Based Method for cDNA Microarray Image Segmentation

Microarray technology plays an important role in drawing useful biological conclusions by analyzing thousands of gene expressions simultaneously. Especially, image analysis is a key step in microarray analysis and its accuracy strongly depends on segmentation. The pioneering works of clustering based segmentation have shown that k-means clustering algorithm and moving k-means clustering algorithm are two commonly used methods in microarray image processing. However, they usually face unsatisfactory results because the real microarray image contains noise, artifacts and spots that vary in size, shape and contrast. To improve the segmentation accuracy, in this article we present a combination clustering based segmentation approach that may be more reliable and able to segment spots automatically. First, this new method starts with a very simple but effective contrast enhancement operation to improve the image quality. Then, an automatic gridding based on the maximum between-class variance is applied to separate the spots into independent areas. Next, among each spot region, the moving k-means clustering is first conducted to separate the spot from background and then the k-means clustering algorithms are combined for those spots failing to obtain the entire boundary. Finally, a refinement step is used to replace the false segmentation and the inseparable ones of missing spots. In addition, quantitative comparisons between the improved method and the other four segmentation algorithms--edge detection, thresholding, k-means clustering and moving k-means clustering--are carried out on cDNA microarray images from six different data sets. Experiments on six different data sets, 1) Stanford Microarray Database (SMD), 2) Gene Expression Omnibus (GEO), 3) Baylor College of Medicine (BCM), 4) Swiss Institute of Bioinformatics (SIB), 5) Joe DeRisi’s individual tiff files (DeRisi), and 6) University of California, San Francisco (UCSF), indicate that the improved approach is more robust and sensitive to weak spots. More importantly, it can obtain higher segmentation accuracy in the presence of noise, artifacts and weakly expressed spots compared with the other four methods.
Reducing the oscillations between overlay routing and traffic engineering by repeated game theory

Due to the conflicts existing in the route objectives of overlay routing and traffic engineering, the interaction between the two selfish players may converge to an inefficient Nash equilibrium point, even if the better choice may exist. We formulate the interaction as an infinitely repeated two-player game, where overlay routing aims to minimize the average latency of overlay users and traffic engineering aims to minimize the maximum link utilization of overall network. The whole interaction process could be divided into two stages - learning stage and practice stage. The former collects the historical information and finds the best point with a simple learning algorithm, then the latter uses this point as equilibrium point and converges to it. The simulation results show that both overlay routing and traffic engineering can converge to the win-win results, and the overall network can avoid the performance volatility from endless oscillations.
The role of friction in tow mechanics

Friction plays and important role in the processing of fibrous materials: during production of tow materials, during textile manufacturing and during preforming operations for composite moulding processes. One of the poorly understood phenomena in these processes is the dynamic frictional behaviour of the fibrous tows. This thesis addresses the characterisation of this behaviour during the production of Continuous Fibre Reinforced Polymers (CFRPs). The dynamic frictional behaviour of fibrous tows is studied in a multi-scale context. Both experimental and modelling work were performed to gain insight into the mechanism of fibrous tow friction. Experimental work on carbon, aramid and E-glass tow material provides the relevant parameters that form the basis for contact mechanics modelling approaches of tow friction for tows on metal counterfaces and tows in direct contact with each other. The model is based on the assumption that frictional forces are determined by the the product of the real contact area between the contacting bodies and an interfacial shear strength. The multi-scale nature of friction clearlymanifests itself in the analytical-statisticalmodelling approaches. Surface characteristics down to the sub-microscopic level of asperities on themetal counterfaces and small ridges on carbon filaments were taken into consideration for the determination of the real contact areas. The bottom-up approach of the tow-metal and tow-tow modelling procedures provides the means to predict the experimentally observed frictional behaviour of tows. Finally, this study provides a coupling with the macroscopic ply or laminate scale by linking friction measurements on carbon fabric to those on carbon tows. The main conclusion of this study is that the sub-microscopic friction at the level of contacting asperities and filament ridges determines the final macroscopic behaviour of dry arrangements of fibrous tows to a large extent. This study provides a coupling between the multiple length scales. As such, it forms a basis for further modelling and experimental work.
Application of representational difference analysis to identify genomic differences between Bradyrhizobium elkanii and B. Japonicum species

Bradyrhizobium elkanii is successfully used in the formulation of commercial inoculants and, together with B. japonicum, it fully supplies the plant nitrogen demands. Despite the similarity between B. japonicum and B. elkanii species, several works demonstrated genetic and physiological differences between them. In this work Representational Difference Analysis (RDA) was used for genomic comparison between B. elkanii SEMIA 587, a crop inoculant strain, and B. japonicum USDA 110, a reference strain. Two hundred sequences were obtained. From these, 46 sequences belonged exclusively to the genome of B. elkanii strain, and 154 showed similarity to sequences from B. japonicum genome. From the 46 sequences with no similarity to sequences from B. japonicum, 39 showed no similarity to sequences in public databases and seven showed similarity to sequences of genes coding for known proteins. These seven sequences were divided in three groups: similar to sequences from other Bradyrhizobium strains, similar to sequences from other nitrogen-fixing bacteria, and similar to sequences from non nitrogen-fixing bacteria. These new sequences could be used as DNA markers in order to investigate the rates of genetic material gain and loss in natural Bradyrhizobium strains.
3 . REQUIREMENTS FOR A WORLD-CLASS POKER PLAYER

Poker is an interesting test-bed for artificial intelligence research. It is a game of imperfect knowledge, where multiple competing agents must deal with risk management, opponent modeling, unreliable information, and deception, much like decision-making applications in the real world. Opponent modeling is one of the most difficult problems in decision-making applications and in poker it is essential to achieving high performance. This paper describes and evaluates the implicit and explicit learning in the poker program Lok i. L o k i implicitly “learns” sophisticated strategies by selectively sampling likely cards for the opponents and then simulating the remainder of the game. The program has explicit learning for observing its opponents, constructing opponent models and dynamically adapting its play to exploit patterns in the opponents’ play. The result is a program capable of playing reasonably strong poker, but there remains considerable research to be done to play at a world-class level.
The black soldier fly, Hermetia illucens – a promising source for sustainable production of proteins, lipids and bioactive substances

Abstract The growing demand worldwide for proteins and lipids cannot be met by the intensive use of agricultural land currently available. Insect mass cultures as a source for proteins and lipids have been in focus for various reasons. An insect with many positive properties is the black soldier fly, Hermetia illucens, whose larvae could be used for the sustainable production of proteins and lipids. Furthermore, the larvae produce bioactive substances which could potentially be used for human and animal welfare.
Non-viral nucleic acid delivery methods

ABSTRACT Introduction: Delivery of nucleic acid-based molecules in human cells is a highly studied approach for the treatment of several disorders including monogenic diseases and cancers. Non-viral vectors for DNA and RNA transfer, although in general less efficient than virus-based systems, are particularly well adapted mostly due to the absence of biosafety concerns. Non-viral methods could be classified in two main groups: physical and vector-assisted delivery systems. Both groups comprise several different methods, none of them universally applicable. The choice of the optimal method depends on the predefined objectives and the features of targeted micro-environment. Areas covered: In this review, the authors discuss non-viral techniques and present recent therapeutic achievements in ex vivo and in vivo nucleic acid delivery by most commonly used techniques while emphasizing the role of ‘biological particles’, namely peptide transduction domains, virus like particles, gesicles and exosomes. Expert opinion: The number of available non-viral transfection techniques used for human therapy increased rapidly, followed by still moderate success in efficacy. The prospects are to be found in design of multifunctional hybrid systems that reflect the viral efficiency. In this respect, biological particles are very promising.