Miracle-dz/UniFAR-FTUs huggingface dataset:
The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing

Introduction Determining bacterial community structure in fecal samples through DNA sequencing is an important facet of intestinal health research. The impact of different commercially available DNA extraction kits upon bacterial community structures has received relatively little attention. The aim of this study was to analyze bacterial communities in volunteer and inflammatory bowel disease (IBD) patient fecal samples extracted using widely used DNA extraction kits in established gastrointestinal research laboratories. Methods Fecal samples from two healthy volunteers (H3 and H4) and two relapsing IBD patients (I1 and I2) were investigated. DNA extraction was undertaken using MoBio Powersoil and MP Biomedicals FastDNA SPIN Kit for Soil DNA extraction kits. PCR amplification for pyrosequencing of bacterial 16S rRNA genes was performed in both laboratories on all samples. Hierarchical clustering of sequencing data was done using the Yue and Clayton similarity coefficient. Results DNA extracted using the FastDNA kit and the MoBio kit gave median DNA concentrations of 475 (interquartile range 228-561) and 22 (IQR 9-36) ng/µL respectively (p<0.0001). Hierarchical clustering of sequence data by Yue and Clayton coefficient revealed four clusters. Samples from individuals H3 and I2 clustered by patient; however, samples from patient I1 extracted with the MoBio kit clustered with samples from patient H4 rather than the other I1 samples. Linear modelling on relative abundance of common bacterial families revealed significant differences between kits; samples extracted with MoBio Powersoil showed significantly increased Bacteroidaceae, Ruminococcaceae and Porphyromonadaceae, and lower Enterobacteriaceae, Lachnospiraceae, Clostridiaceae, and Erysipelotrichaceae (p<0.05). Conclusion This study demonstrates significant differences in DNA yield and bacterial DNA composition when comparing DNA extracted from the same fecal sample with different extraction kits. This highlights the importance of ensuring that samples in a study are prepared with the same method, and the need for caution when cross-comparing studies that use different methods.
Remote sensing data for mapping and monitoring African savanna woodlands

Remote sensing data provide unprecedented opportunities for detecting and monitoring forest disturbance and loss. Disturbance and loss have been successfully mapped where cleared land is of sufficient extent to provide discrimination within an image. However, methodologies for mapping and monitoring forest degradation are still lacking, primarily because these features are small in size. In Tanzania, the size and extent of degradation is poorly understood, yet there has been an increase in its drivers, such as shifting cultivation, settlements, logging and charcoal burning of indigenous trees. This study aimed to establish the extent remote sensing can map forest cover and change for REDD+ monitoring in Tanzanian savanna woodlands. A forest baseline for Liwale in south-eastern Tanzania was derived using the Land Cover Classification System (LCCS) from a 2012 RapidEye image, and validated using LiDAR data from 2012. The baseline and a 2014 RapidEye image were then used to perform an object-based change detection, by first identifying potential change features by automatically thresholding the data using a method based on optimising the skewness and kurtosis for distribution of the class of interest, and then classifying, using the random forests algorithm, the true change features. The change results were validated using 2014 LiDAR data. These methods were then scaled out to courser Landsat imagery. The study concluded that both high and low resolution optical RS data have great potential for forest monitoring of the Tanzanian savanna woodlands, even though Landsat does not provide the level of detail to accurately depict small-scale change. Components of a remote sensingbased monitoring system are proposed. However, it was noted that for national monitoring, an integration of both high and low resolution data was best. Being a deciduous environment, it was found that seasonality and persistent cloud cover in the region greatly limit the window for appropriate monitoring data. The developed methodology is robust, and thus can be scaled up to a broader national scale and across similar environments in Africa.
Permutation and phase independent Boolean comparison

The problem of checking the equivalence of two Boolean functions under arbitrary input permutations and/or input plane assignments is considered. This problem has several applications in the synthesis and verification of combinational logic. The approach presented computes a signature for each variable or phase of a variable that will help establish correspondence of variables or phases of variables. The strength of the proposed approach depends on the ability to quickly derive a signature with minimum aliasing. Aliasing refers to two different variables or phases having the same signature, thus rendering this signature useless for the purpose of distinguishing between them. Experimental results on a large number of examples establish the efficacy of this approach. <<ETX>>
Gender Differences When Touching Something Gross: Unpleasant? No. Disgusting? Yes!

ABSTRACT. While many studies find women self-report higher disgust sensitivity than men, few studies have examined gender differences with behavioral tasks in senses other than vision. On a haptic task, we tested the hypothesis that women would report greater disgust but not greater unpleasantness than men. Forty-four undergraduates (29 women) touched 8 out-of-sight stimuli with sensory (unpleasantness) and emotional (disgust) responses recorded. The stimuli consisted of 2 neutral, 2 pleasant, and 4 unpleasant (3 disgust-evoking) objects. No gender differences were found for reporting stimuli unpleasantness. In contrast, women rated their disgust significantly higher than men when touching the high disgust-evoking objects. Unpleasantness of the stimuli correlated with disgust to the objects, but disgust sensitivity (Disgust Scale-Revised) was not a strong predictor of disgust responses. Besides differentiating unpleasantness from disgust, this was also the first study to show gender differences in a disgust-evoking haptic task.
MIRES: an information exchange system for mobile phones

Mobile computing has been studied in the past few years on many respects: adaptive application, mobility model, data access and so on. However, most research aim at a general computing framework but not focus on a specific device, for example, mobile phone. Mobile phones are special due to some constraints compared with other devices and they currently serve as no more than passive terminals to a large extent. At the same time, mobile phones are probably the most popular device today. This paper describes an operative resource sharing model in the context of MIRES - a Mobile Information Resource Exchange System which facilitates convenient resource sharing among mobile phones. Techniques from distributed database systems are combined with such wireless technologies as GPRS and J2ME. With the versatile facilities of MIRES, a mobile phone user can easily share his/her personal resources or get others' resources at his/her own will anytime and anywhere.
Nutrient and carbon loading of black spruce containerized seedlings during nursery culture and early outplanting

Loading conifers seedlings with a maximum level of nutrient and carbonydraie reserves during Vie nursery phase can potentially increase seedling vigor and performance after transplanting to the field. To enhance this integrated practice, black spnice (Picea mariana (Mill.) B.S.P.) seedlings were raised under two fertilizer levels (1 0 mg N seedling-l, representing the conventional regime, and 75 mg N seedling-l, representing exponential loading regirne), and exposed to two levels of CO2 (370 ppm, as ambient, and 800 ppm, as elevated CO2) at the end of the nursery phase for 3 weeks. Compared to the cunventional fertilization regime, exponential loading induced luxury consumption and increased seedling nutrient reserves substantially. Short-terni CO2 enrichment for 3 weeks stimulated photosynthesis and built up carbohydrate reserves in the nutrient-loaded seedlings. However, no significant increase in carbohydrate reserves was observed in the conventional seedlings, due to inadequate nutrient availability. The performance of both nutrientand carbon-loaded seedlings after planting was tested under greenhouse conditions. Results suggested that combined nutrient and carbon loading practices have high potential in building up seedling nutrient and carbon reserves and that may effectively improve early field performance.
The informational architecture of the cell

We compare the informational architecture of biological and random networks to identify informational features that may distinguish biological networks from random. The study presented here focuses on the Boolean network model for regulation of the cell cycle of the fission yeast Schizosaccharomyces pombe. We compare calculated values of local and global information measures for the fission yeast cell cycle to the same measures as applied to two different classes of random networks: Erdös–Rényi and scale-free. We report patterns in local information processing and storage that do indeed distinguish biological from random, associated with control nodes that regulate the function of the fission yeast cell-cycle network. Conversely, we find that integrated information, which serves as a global measure of ‘emergent’ information processing, does not differ from random for the case presented. We discuss implications for our understanding of the informational architecture of the fission yeast cell-cycle network in particular, and more generally for illuminating any distinctive physics that may be operative in life.
Tree‐ring stable isotopes show different ecophysiological strategies in native and invasive woody species of a semiarid riparian ecosystem in the Great Plains of the United States

Persistent shifts in riparian vegetation associated with the invasion of introduced Elaeagnus angustifolia and native nonriparian Juniperus virginiana have been reported in the U.S. Great Plains, with significant impacts on ecosystem services. In Nebraska, these species have been expanding into the native Populus deltoides riparian forests along the Republican River. Using dendrochronological data and stable isotope ratios, we examined the annual growth and acclimation strategies of these three species to climatic and streamflow variability. We hypothesized that the ability of invasive species to grow under a wide range of environmental conditions favour vegetation shifts at the expense of native species. Streamflow was the strongest predictor for performance. When accompanied with above‐average annual precipitation, streamflow resulted in peak tree‐ring widths in P. deltoides. J. virginiana showed less sensitivity, and E. angustifolia showed no response. δ18O values did not differ among species, which indicates that all species compete for the same water source. δ13C ratios and WUEi were higher in J. virginiana than in P. deltoides and E. angustifolia and increased in all species over time. E. angustifolia and P. deltoides exhibit a strong stomatal control and response to relative humidity relative to J. virginiana, which showed anisohydric stomatal behaviour. Our results show that once established, J. virginiana and E. angustifolia thrive in the understory of P. deltoides using different adaptive and acclimation strategies. Based on current water flow management, which prevents high‐flood pulses through the riparian zone, these species will continue to establish and spread throughout the Republican River watershed.
Theoretical studies of the optical properties of photonic crystal and microcavity-based structures

The work reported in this thesis is dedicated to the theoretical study of the certain properties of several types of resonant and nonresonant photonic nanostructures. Negative refraction at the side edge of a Bragg reflector is studied. Analytical theory supported by numerical modelling using finite-difference time-domain (FDTD) simulations shows that the negative refraction in this case is equivalent to −1 order diffraction. Moreover, it is shown that a new effect, spatial oscillation of the Poynting vector of the transmitted radiation, can be observed under certain circumstances. In a separate study the design of a spectral filter for the terahertz frequency range based on a metallic photonic crystal prism has been developed and refined. The theory makes use of the complex band structure method together with FDTD simulations and shows that large angle separation of certain frequency component can be achieved with a prism due to the negative refraction effect. Experimental measurements on a device fabricated with a proposed design are also presented and confirm the theoretical predictions. An optical eigenmode analysis of two organic microcavities separated by a thin metal layer has been carried out, both numerically and analytically. The analytical theory shows that the sharp reflections features observed in experimental reflectivity measurements are caused by the strong coupling of the Tamm plasmon modes present on both sides of the metal film. Analytical theory is developed explaining the experimentally measured reflectivity spectra of a one-dimensional photonic crystal with quantum wells embedded in its layers. The dispersion properties of the eigenmodes of the structure, originating from the strong coupling of quantum well excitons and photonic crystal modes are calculated. It is shown, that a new type of exciton-polariton, defined by the negative group velocity and effective mass can be observed in the structures. A theoretical formalism and corresponding software code have been developed to model the kinetics of polariton lasers. The model is based on a Boltzmann equation approach and accounts for electrical or optical pumping, polariton decay, and polariton-acoustic phonon, polariton-free electron and polariton-polariton scattering. The software code has been used to model the main characteristics of the specific GaN-based polariton lasers using parameters provided by experimental collaborators. It is predicted that the design of electrically driven polariton laser considered would have a threshold current density of 50 Acm−2 at room temperature.
Understanding and managing the off-road vehicle experience: standards of quality

A companion paper in a previous issue of Managing Leisure suggested that crowding, litter, and waiting time to get a use permit were among the variables important in defining a high-quality off-road vehicle (ORV) experience at Cape Cod National Seashore (Cape Cod). Potential standards of quality – the minimum acceptable condition for these indicator variables – are addressed in this paper. Data to help formulate standards were collected during the 2005 summer-use season by asking visitors to evaluate narrative/numeric questions describing a range of visitor-caused impacts or photographic simulations depicting such impacts. Responses to survey questions suggest that between 12.0 and 33.2 ORVs per 0.16 km are appropriate for the ORV route, depending on what evaluative dimension (i.e., ‘preference’, ‘acceptability’, ‘management action’, or ‘displacement’) is considered. Maximum litter densities of 4.0–56.8 pieces of litter per 225 m2 area and a maximum waiting time to receive an ORV-use permit of 58 min to 11 h, 37 min are appropriate, again depending on the evaluative dimension considered. The normative data developed in this study can be used to help formulate standards of quality, enhance understanding of the ORV experience, and guide the management of high-quality ORV recreation.
Dynamic Coding Control in Social Intermittent Connectivity Wireless Networks

In intermittent connectivity wireless networks, packets are always transmitted to their destinations through the cooperation of intermediate nodes, and the limited network resources can be effectively utilized through network coding approaches. However, a large amount of resources will be consumed while all the nodes act as coding nodes simultaneously; meanwhile, redundant coded packets are injected into the network. Therefore, to determine the number of coding nodes and restrain the diffusion of coded packets, a new dynamic coding control mechanism is proposed. In this mechanism, coding nodes are scheduled in a distributed manner based on the network community scale. Moreover, the coding opportunities and forwarding priorities of packets are determined according to the packet redundancy. Simulation results show that the connection opportunities can be exploited, and the utilization of network resources can be optimized.
Activation of neutrophils by soluble and insoluble immunoglobulin aggregates from synovial fluid of patients with rheumatoid arthritis.

OBJECTIVES--Previous work has shown that synovial fluid isolated from patients with active rheumatoid arthritis contains soluble (not sedimented by centrifugation at 11,600 g for two minutes) and insoluble (sedimented by centrifugation at 11,600 g for two minutes) immunoglobulin aggregates that are capable of activating reactive oxidant production by bloodstream neutrophils. The purpose of this study was to determine which of these types of immunoglobulin aggregates activated the secretion of reactive oxygen metabolites and granule enzymes from neutrophils. METHODS--Cell free synovial fluid (from patients with rheumatoid arthritis) was added to neutrophils isolated from blood of healthy controls that had been incubated in the presence and absence of granulocyte-macrophage colony stimulating factor (GM-CSF). Reactive oxidant production was measured by luminol chemiluminescence (which detects both intracellular and extracellular oxidant production) and by cytochrome c reduction (which measures superoxide secretion). RESULTS--The soluble aggregates only activated neutrophils that were previously primed, and activated a rapid and transient burst of reactive oxidant secretion. On the other hand, the insoluble aggregates activated primed and unprimed neutrophils with similar efficacy and most of the oxidants generated (especially in unprimed cells) were intracellular. The soluble aggregates, but not the insoluble aggregates, also activated the secretion of myeloperoxidase from neutrophils that had either been pretreated with cytochalasin B or primed with GM-CSF. CONCLUSION--It is thus proposed that these soluble immunoglobulin aggregates are responsible for activation of the release of tissue damaging granule enzymes and reactive oxidants from primed neutrophils within the rheumatoid joint.
Case Study of Blowing Snow Potential Diagnosis with Dynamical Downscaling

<p>Blowing snow potential is diagnosed for typical cases in roads around Sapporo, Japan, as snow concentration and visibility based on dynamically downscaled data with 1-km resolution. The results are consistent with the blowing-snow records on time and place of traffic disruption, when the dynamical downscaling (DDS) reproduced wind speed well for a case. Moreover, the DDS-based diagnosis had a strength on the onset and cease of blowing snow in the event. The diagnosis with mesoscale model analysis with 5-km resolution does not reproduce the blowing snow events in most area, however. Hence, the DDS potentially, not perfectly, adds the value to estimate blowing snow potential, despite a large scale-gap from an explicit representation of small-scale turbulence related to blowing snow. The meteorological forecast with 1-km resolution might improve the estimate of blowing snow potential. </p>
Formation evaluation challenges in Pliocene gas-bearing reservoirs from the Romanian Western Black Sea shelf

This paper addresses some formation evaluation challenges and petrophysical particularities regarding two gas fields of Early Pliocene age, belonging to the biogenic hydrocarbon system of Western Black Sea Basin - Romanian continental shelf. Although these structures are located at the same depth and only 15 km apart, the wells that intercepted the sands and silts gas-bearing reservoirs indicate an important lateral facies variation and different reservoir qualities. We analyzed and interpreted data from exploration and appraisal wells that targeted these reservoirs, showing that: (1) there is a limited radioactivity contrast between the reservoir and nonreservoir intervals, so a clay volume determination based solely on the gamma ray log is not practical; (2) the reservoirs are characterized by high capillary-bound water contents, leading sometimes to abnormally low resistivity readings; (3) an additional resistivity suppression might be caused by the limited vertical resolution of the electrical logging tools, in the presence of thinly laminated sand - shale intervals; (4) the identification of gas-water contacts based exclusively on pressure gradients may be inaccurate and should be checked against the results of conventional geophysical logs interpretation and of nuclear magnetic resonance logs, for delineating the intervals with bound water or with movable fluids.
Associations of IL6 polymorphisms with lung function decline and COPD

Background: Interleukin-6 (IL6) is a pleiotropic pro-inflammatory and immunomodulatory cytokine which probably plays an important role in the pathogenesis of chronic obstructive pulmonary disease (COPD). There is a functional single nucleotide polymorphism (SNP), -174G/C, in the promoter region of IL6. It was hypothesised that IL6 SNPs influence susceptibility for impaired lung function and COPD in smokers. Methods: Seven and five SNPs in IL6 were genotyped in two nested case-control samples derived from the Lung Health Study (LHS) based on phenotypes of rate of decline of forced expiratory volume in 1 s (FEV1) over 5 years and baseline FEV1 at the beginning of the LHS. Serum IL6 concentrations were measured for all subjects. A partially overlapping panel of nine IL6 SNPs was genotyped in 389 cases of COPD from the National Emphysema Treatment Trial (NETT) and 420 controls from the Normative Aging Study (NAS). Results: In the LHS, three IL6 SNPs were associated with decline in FEV1 (0.023⩽p⩽0.041 in additive models). Among them, the IL6_-174C allele was associated with a rapid decline in lung function. The association was more significant in a genotype-based analysis (p = 0.006). In the NETT-NAS study, IL6_-174G/C and four other IL6 SNPs, all of which are in linkage disequilibrium with IL6_-174G/C, were associated with susceptibility to COPD (0.01⩽p⩽0.04 in additive genetic models). Conclusion: The results suggest that the IL6_-174G/C SNP is associated with a rapid decline in FEV1 and susceptibility to COPD in smokers.