Miracle-dz/UniFAR-FTUs huggingface dataset:
PERTUMBUHAN RUMPUT LAUT KAPPAPHYCUS ALVAREZII HASIL KULTUR JARINGAN

The purpose of this study is to determine the right planting point and seed weight to produce optimal growth Kappaphycus alvarezii. Seaweed cultivation method used is bottom off method and seed used is tissue culture seaweed. This research was conducted from February to April 2016 at Nambung beach, Sekotong Subdistrict, West Lombok regency, West Nusa Tenggara Province. This research used experimental method in field with experimental design that used is Factorial Random Design (Factorial RAL). Treatment consists of 2 factors, where the first factor is 3 different planting point (10 meters from coastline, 20 meter from coastline and 30 meters from the coastline) and the second factor is the weight of different seeds (1.5 gram and 50 gram seed weight). The results showed that the planting position of seaweed and the weight of the seeds used gave effect to absolute growth. The interaction between planting position and seed weight also gives Kappaphycus alvarezii a significantly different growth. The conclusion of this research is the use of planting point and seed weight give interaction to each other.Keywords: growth, tissue culture, bottom off method, weight, cultivated
Multiscale modeling of polystyrene dynamics in different environments

In troduction Polystyrene is an abundant and industrially important polymer. We are modeling its behavior on multiple length scales and different environments. Here we focus on the behavior in blends with polysioprene and brushes with and without solvent. Co mputer simulations cannot only address average properties of the system under study but also the distribution over any observable of interest so in our study of mixtures of polystyrene and polyisoprene by atomistic molecular dynamics we calculate correlati on times for all segments in the system [1 -3]. We can then identify fast and slow segments and can correlate the segment speed with the local neighborhood and obtain that fast segments have a surplus of the faster component in their neighborhood and vice v ersa. We present a coarse grained model for the blend which is capable of showing phase separation [4, 5]. Finally we also present some recent data on polymer brushes. All atomistic simulations were performed using the GROMACS simulation package [6] . The p olystyrene and polyisoprene simulation model s were tak en from our earlier work [7,8]. Dynamics in Blends Mixtures of cis -1,4 polyisoprene and atactic polystyrene have been studied using atomistic molecular dynamic simulations over a wide range of concent rations at temperatures from slightly above the glass transition of PS (380 K) to deep in the melt (450 K). Static and dynamic properties together with their heterogeneities were elucidated. Such properties include reorientation correlation times of carbon -hydrogen segments, density profiles, and diffusion coefficients. We find semi -quantitative agreement with experimental NMR measurements. We especially focus on the correlation of static and dynamic heterogeneities showing that a distribution of local neig hborhoods is crucial for understanding the local dynamics. Generally, polyisoprene has faster dynamics than polystyrene. Both polymers exhibit distinct dynamic heterogeneities, which correlate with static heterogeneities in local concentrations. With our a tomistic simulations we may be close to seeing the onset of phase separation. ESAT 2008ESAT 2008 593 Cannes, ranceF
Multi-scale approach to disentangle the small mammal composition in a fragmented landscape in central Brazil

Habitat quality and its availability affect the structure of communities at a variety of different spatial and environmental scales, including habitat and landscape levels. Analyses conducted at multiple scales have demonstrated the importance of landscape patterns with regard to community structure. We used a multi-scale approach to better understand the composition of small mammal communities in central Brazil. We delimited 24 sampling units for the purpose of investigating the response of small mammal composition at the habitat, patch, and landscape scales, while evaluating quality and availability of habitat in each patch, as well as landscape configuration and landscape composition. We used a Mantel correlogram to check for spatial autocorrelation, and partial redundancy analysis to correlate the matrix of species composition with the matrix of environmental variables. Small mammal composition was spatially structured and correlated with variables at all environmental scales: vegetation structure (fallen logs, lianas, and canopy cover), habitat patch (normalized difference vegetation index [NDVI]), and landscape composition (total core area—a forest cover metric). Our findings show evidence of the limited dispersal capacity of small mammals and the importance of habitat quality at habitat and patch scales, and habitat availability at the landscape scale, for small mammal composition. This study highlights the importance of a multi-scale approach for understanding community structure in a human-altered landscape.
The shape of density dependence and the relationship between population growth, intraspecific competition and equilibrium population density

Many ecologists and evolutionary biologists use the logistic growth model to capture density dependence. However, assumptions and limitations of this popular model are not well appreciated. Here, we derive population growth models from underlying consumer-resource dynamics and show that the logistic is likely not applicable to many biological systems. We first validate that filter feeders (type I functional response) using abiotic resources generally follow a convex density-regulation function, fully described by the continuous-time Beverton-Holt model. Furthermore, we show that saturating consumers (type II functional response) exhibit density-regulation functions that can switch from concave to convex. We derive a density-regulation function for saturating feeders on abiotic resources and show that more complex consumer dynamics can be well approximated with a continuous-time Maynard Smith-Slatkin model. Importantly, we show how population level parameters, such as intrinsic rates of increase and equilibrium population densities are not independent, but are functions of the same underlying parameters. Our work highlights that the commonly assumed positive relationship between equilibrium population density and competitive ability is typically invalid. Alternatively, we propose simple and general relationships between intrinsic rates of increase and equilibrium population densities that capture the essence of different consumer-resource systems. Finally, we expand our considerations to include multiple consumer and resource species. Relating population level models to underlying mechanisms allows us to discuss applications to evolutionary outcomes and how these models depend on environmental conditions, like temperature via metabolic scaling. Finally, we use time-series from microbial food chains to fit population growth models and validate theoretical predictions. Density-regulation functions need to be chosen carefully as their shapes will depend on the study system’s biology. Importantly, we provide a mechanistic understanding of correlations between model parameters, which has implications for theory and for formulating biologically sound and empirically testable predictions.
Sex differences in longitudinal personality stability in chimpanzees

Abstract Abstract Personality factors analogous to the Big Five observed in humans are present in the great apes. However, few studies have examined the long-term stability of great ape personality, particularly using factor-based personality instruments. Here, we assessed overall group, and individual-level, stability of chimpanzee personality by collecting ratings for chimpanzees (N = 50) and comparing them with ratings collected approximately 10 years previously, using the same personality scale. The overall mean scores of three of the six factors differed across the two time points. Sex differences in personality were also observed, with overall sex differences found for three traits, and males and females showing different trajectories for two further traits over the 10 year period. Regardless of sex, rank-order stability analysis revealed strong stability for dominance; individuals who were dominant at the first time point were also dominant 10 years later. The other personality factors exhibited poor to moderate rank-order stability, indicating that individuals were variable in their rank-position consistency over time. As many studies assessing chimpanzee cognition rely on personality data collected several years prior to testing, these data highlight the importance of collecting current personality data when correlating them with cognitive performance.
Environmental Noise Cancellation Technique for the Compensation Interferometer in Fiber-Optic PMDI-Based Sensor Arrays

A path matched differential interferometry (PMDI) is one of the most common architectures for fiber-optic sensor arrays. It allows to interrogate many fiber-optic sensors time-multiplexed at a single fiber by using an auxiliary compensation interferometer (CIF). The CIF is typically based on an unbalanced Michelson or Mach-Zehnder interferometer. Therefore, it may be affected by different acoustic and vibration environmental noises. Any vibroacoustic impacts on the CIF might produce undesirable noises in the sensor signals and the noise performance of the measuring system will degrade. An environmental noise cancellation technique for the CIF in fiber-optic PMDI-based sensor arrays is presented in this paper. The proposed approach is based on the separate interrogation of the CIF by the additional fiber laser together with using polarization-division multiplexing. The noise cancellation is performing by the subtraction of the independent CIF’s signal from measured signals from the sensors array. In this paper, the main parameters of the noise cancellation system, which are critical for its performance, are discussed in detail. The experimental efficiency estimation of the proposed technique was performed in situ under open water conditions. It was shown, that for the measured signal with the standard deviation of 0.059 rad and the environmental impact on the CIF with the standard deviation of 0.61 rad the noise cancellation efficiency was −24.9 dB. The proposed technique might be easily integrated to large-scale PMDI-based fiber-optic sensors arrays and it’s compatible with PMDI-based Fiber Bragg Grating arrays in combination with the wavelength division multiplexing.
Real-Time Optimal Torque Control of Interior Permanent Magnet Synchronous Motors Based on a Numerical Optimization Technique

This study presents a real-time optimal torque control scheme for interior permanent magnet synchronous motors (IPMSMs). The proposed scheme enables computation of optimal current reference for a torque reference under all operating regions, including the maximum torque per ampere (MTPA), flux weakening (FW), maximum current (MC), and maximum torque per voltage (MTPV), using numerical optimization techniques to simplify the problems and obtain the corresponding solutions with reduced computation burden. Linearizing the torque equation of IPMSM is utilized to derive solutions for the MTPA and FW. These solutions are proved to converge to their optimum with the aid of the reference smoother. Numerical solutions for the MC and MTPV are derived based on the assumption that the resistive voltage drop is small enough but not zero. These solutions differ from the existing solutions that ignore the resistive voltage drop. The effectiveness of the proposed method is numerically and experimentally verified using a 7.5-kW IPMSM with a considerable reduction in computational time of approximately 90% in the simulation compared with the analytic solution.
Celiac disease: From genetic variation to molecular culprits

Coeliakie (CeD) is een auto-immuunziekte die veroorzaakt door gluten bij genetisch gevoelige individuen. Het doel van dit proefschrift was om meer inzicht te krijgen in de functie van enkele van de CeD-kandidaat genen en de biologische mechanismen waar deze genen bij betrokken zijn. Hoofdstuk 1 geeft een overzicht van de voornaamste celtypes, cytokines, immuun moleculen en genetische- en omgevingsfactoren die zouden kunnen bijdragen aan CeD. In hoofdstuk 2 bestuderen we de rol die LPP, een slecht gekenmerkt eiwit in darmepitheelcellen. We vonden dat LPP bijdraagt aan de ziekte via zowel non-immuun als immuun functies van darmepitheelcellen. In hoofdstuk 3 hebben we 118 CeD-geassocieerde kandidaat genen geidentificeerd door middel van expression quantitative trait loci (eQTL) analyse en statistische om eQTL genen aan een genetisch risico op CeD te koppelen. In hoofdstuk 4 hebben we onderzocht hoe cytokines, die verhoogd zijn in weefsels die door auto-immuunziektes zijn aangedaan (IFNb, Il-15 en IL-21), de genexpressie profiel van Intra-epitheliale cytotoxische lymfocyten (IE-CTLs) veranderen. In een poging om de rol van lncRNAs in het aangeboren immuunsysteem beter te begrijpen, hebben we lncRNAs (RP11-291B21.2) gekarakteriseerd in IEL-CTLs (hoofdstuk 6). We vonden dat deze lncRNA een rol zou kunnen spelen in T-cel activatie. Tenslotte heb ik In hoofdstuk 7 de belangrijkste bevindingen van dit proefschrift samengevat. Verder bespreek ik enkele tekortkomingen in het vaststellen van kandidaat genen en biologische mechanismen geassocieerd met CeD. Daarnaast bespreek ik hoe nieuwe technologieen kunnen worden gebruikt om deze tekortkomingen te overkome.
Application of advanced reproductive biotechnologies for buffalo improvement with focusing on Egyptian buffaloes

Many countries in the world consider the buffalo as a priority animal for the future, since it plays a pivotal role in human food sustainability. Even though Food and Agriculture Organization has termed the buffalo as an important undervalued asset, this species has yet to drive the same attention as cattle. Egypt has a wealth of buffaloes dispersed in small herds all over the country, so the efforts that have been made to improve their genetic background show little return. Contrarily, other countries concerned with buffalo improvement have already used a data recording system in buffalo herds, allowing to achieve a much faster improvement progress. This review intends to survey the existing information on the application of assisted reproduction techniques to improve buffalo productivity. The strength points that may help to improve buffalo production are identified, and the obstacles hindering the genetic improvement of Egyptian buffalo are characterized. Therefore, this work will gather information related to buffalo and compile it for an audience of researchers and specialists to enforce international collaboration for the development of buffalo production. Also, it will open the way for people interested in developing a future vision for buffalo potential, which will be helpful to close or minimize the biological gaps of buffaloes’ researches.
Bicatalytic conversion of glycerol to value-added products

The objective of this study was to develop a tandem bio- chemical transformation of a feedstock material to value-added products. The chosen example is microbial fermentation of glycerol with subsequent esterification of the intermediate 1,3-propanediol with fatty acids. The use of biphasic aqueous/organic medium for the bi-catalytic system is the key feature of this study. In the first part of this work, batch and continuous fermentations of glycerol by Clostridium Butyricum bacteria were optimized to increase productivity of 1,3-propanediol. In the second part, several catalysts were screened for mono- and biphasic transformation of 1,3- propanediol. It was discovered that enzymes are the most suitable catalysts for the tandem reactions of glycerol to 1,3-propanediol derivatives compared to chemical catalysts. Biphasic enzymatic esterification of 1,3-propanediol was further optimized using Rhizomucor miehei lipase. Finally, a segmented flow tubular reactor and hollow fiber membrane contactors were designed and tested as a concept tandem reactor. The hollow fiber reactor with Rhizomucor miehei lipase immobilized onto polypropylene membrane was found to be the most effective in the biphasic linoleic acid/aqueous esterification of 1,3-propanediol. In general, the demonstrated approach and the developed system can be easily utilized in the biorefinery processes to avoid extraction and purification of the intermediate products, thus reducing time, energy and emissions.
Evolution of size‐dependent intraspecific competition predicts body size scaling of metabolic rate

Abstract Growth in body size is accompanied by changes in foraging capacity and metabolic costs, which lead to changes in competitive ability during ontogeny. The resulting size‐dependent competitive asymmetry influences population dynamics and community structure, but it is not clear whether natural selection leads to asymmetry in intraspecific competition. We address this question by using a size‐structured consumer–resource model, in which the strength and direction of competitive asymmetry between different consumer individuals depends on the scaling of maximum ingestion and maintenance metabolism with consumer body size. We use adaptive dynamics to study selection on the scaling exponents of these processes. Selection leads to an identical scaling of maximum ingestion and maintenance metabolism with consumer body size. Equal scaling exponents neutralize strong competitive differences within the consumer population, because all consumer individuals require the same amount of resources to cover maintenance requirements. Furthermore, the scaling exponents respond adaptively to changes in mortality such that biomass production through growth or reproduction increases in the life stage that is subject to increased mortality. Also, decreasing size at birth leads to increased investment in juvenile growth, while increasing maximum size leads to increased investment in post‐maturation growth and reproduction. These results provide an explanation for observed variation in the ontogenetic scaling of metabolic rate with body size. Data of teleost fish are presented that support these predictions. However, selection towards equal scaling exponents is contradicted by empirical findings, which suggests that additional ecological complexity beyond this basic consumer–resource interaction is required to understand the evolution of size‐dependent asymmetry in intraspecific competition. A plain language summary is available for this article.
Fabrication of fiber grating by phase mask and its sensing application

This paper reports an investigation of a fabricated fiber grating device characteristics and its applications, using a phase mask writing technique. The phase mask technique used for writing fiber gratings has the advantages over the traditional holographic method because of its simpler writing setup and more reproducible characteristics. Specifically, the utilization of phase mask relaxes the strict requirement on the coherence of a UV light source. On the other hand, to photo induce an index change in the fiber core, light absorption must somehow occur. Alkins measured the absorption spectrum in a standard germanium doped mono mode telecommunication fiber to the wavelength as short as 200 nm. The results show that a light source in the UV spectral region 228 to 253 nm is most effective in photo inducing refractive index changes in such optical fibers. Therefore, we used a KrF excimer laser with wavelength âˆ¼248 nm as light source, and applied the phase mask technique to writing fiber grating. This method has the significant advantage for its much less relaxed requirement on the spatial coherence of exposure light source. The device (i-e grating) characteristics especially, in sensing application, were investigated. In addition, the possibility of using such device as a temperature and strain sensors is also discussed in detail.
Enteric Human Pathogens of Wild Boar, Feral Swine, and Javelina (Order: Artiodactyla)

Artiodactyls are even-toed ungulates that include domestic and wild ruminant herbivores (cattle, sheep, goat, deer, elk), pigs, and javelinas. There is increasing evidence that some wild ungulate species are important reservoirs of enteric human pathogens, and they may contribute to foodborne disease transmission directly through ingestion of undercooked game meat or indirectly via fecal contamination of fresh fruit and vegetable crops or agricultural water sources. To better understand zoonotic risks from feral swine and javelina in the U.S. southwestern desert, we conducted a prevalence survey of Shiga toxin-producing Escherichia coli (STEC) and Salmonella in colonic-fecal samples from animals collected through hunter-harvest or depredation. STEC O157:H7 was detected in feral swine, but not in javelina samples. Salmonella and non-O157 STEC serotypes of potential public health importance were found in both species. The findings underscore the importance of continued public health education efforts to protect hunters from exposure to these pathogens when handling game animals. Fresh fruit and vegetable growers should continue to prevent intrusions by wild and feral animals in the produce production environment to minimize transport of fecal-borne pathogens to crops intended for human consumption.
Improved Analysis of Large Genetic Association Studies Using Summary Statistics

xiv Chapter 1: Introduction 1 An Overview of Meta-Analysis Methods for GWAS . 2 Prioritizing Variants for Follow-up . 4 Overlapping Samples in Meta-Analysis Studies . 6 Thesis Overview . 7 Chapter 2 : Discovery and Refinement of Loci Associated with Lipid Levels 9 Introduction . 9 Results . 10 Novel loci associated with blood lipid levels . 10 Overlap of genetic discoveries and prior knowledge . 11 Pathway analyses . 12 Protein-protein interactions . 13 Regulation of gene expression by associated variants . 13 Coding variation . 14 Overlap between association signals and regulators of transcription in liver . 14 Initial fine-mapping of 65 lipid-associated loci . 15 Association of lipid loci with metabolic and cardiovascular traits . 17 Association of individual lipids with coronary artery disease. 18 Evidence for additional loci, not yet reaching genome-wide significance . 19 Discussion . 20 Online Methods . 29 Supplementary Tables. 35 Supplementary Figures . 71