Miracle-dz/UniFAR-FTUs huggingface dataset:
Positivity Preservation and Advection Algorithms with Applications to Edge Plasma Turbulence

The unique conditions of edge tokamak plasmas motivate the employment of efficient numerical methods that can robustly handle steep temperature and density gradients. To that end, we compare an Arakawa finite difference technique with some recent high-resolution upwind methods that are designed to minimize nonmonotonic overshoots while preserving the accuracy of solutions at smooth extrema. Versions of these algorithms are able to rigorously preserve positivity when that is physically relevant (such as for the advection of particle density or temperature). We explain in detail the use of these methods for the nonlinear Poisson bracket, an operator applicable to neutral fluid, gyrofluid, gyrokinetic, and general Hamiltonian simulations. For one-dimensional passive advection, the high-resolution upwind techniques maintain monotonicity and approach minimal levels of phase error and dissipation, especially at long wavelengths. In a two-dimensional incompressible Navier--Stokes vortex merging problem we find t.
BMP signalling in early Xenopus development

Bone morphogenetic proteins (BMPs) are typically members of the transforming growth factor β (TGF‐β) family with diverse roles in embryonic development. At least five genes with homology to BMPs are expressed during Xenopus development, along with their receptors and intracellular signalling pathways. The evidence suggests that BMPs have roles to play in both mesoderm induction and dorsoventral patterning. Studies in Xenopus have also identified a number of inhibitory binding proteins for the classical BMPs, encoded by genes such as chordin and noggin. These proteins appear to be responsible for establishing a morphogen gradient of BMP4 activity, which specifies different dorsoventral fates in early gastrulae. An emerging theme is that inhibition of BMP signalling is an important mechanism regulating cell fate decisions in early development. BioEssays 21:751–760, 1999. © 1999 John Wiley & Sons, Inc.
Quantification of Ammonia-Oxidizing Bacteria and Factors Controlling Nitrification in Salt Marsh Sediments

ABSTRACT To elucidate the geomicrobiological factors controlling nitrification in salt marsh sediments, a comprehensive approach involving sediment geochemistry, process rate measurements, and quantification of the genetic potential for nitrification was applied to three contrasting salt marsh habitats: areas colonized by the tall (TS) or short (SS) form of Spartina alterniflora and unvegetated creek banks (CBs). Nitrification and denitrification potential rates were strongly correlated with one another and with macrofaunal burrow abundance, indicating that coupled nitrification-denitrification was enhanced by macrofaunal burrowing activity. Ammonia monooxygenase (amoA) gene copy numbers were used to estimate the ammonia-oxidizing bacterial population size (5.6 × 104 to 1.3 × 106 g of wet sediment−1), which correlated with nitrification potentials and was 1 order of magnitude higher for TS and CB than for SS. TS and CB sediments also had higher Fe(III) content, higher Fe(III)-to-total reduced sulfur ratios, higher Fe(III) reduction rates, and lower dissolved sulfides than SS sediments. Iron(III) content and reduction rates were positively correlated with nitrification and denitrification potential and amoA gene copy number. Laboratory slurry incubations supported field data, confirming that increased amounts of Fe(III) relieved sulfide inhibition of nitrification. We propose that macrofaunal burrowing and high concentrations of Fe(III) stimulate nitrifying bacterial populations, and thus may increase nitrogen removal through coupled nitrification-denitrification in salt marsh sediments.
Second and third-order nonlinear optical effects in ZnO channel waveguides

We demonstrate simultaneous self-phase modulation and second harmonic generation in ZnO channel waveguides. We estimate a value of γ = 13.9 ± 3.0 W<sup>-1</sup> m<sup>-1</sup>, indicating that ZnO offers promise as a platform for nonlinear devices.
Flying capacitor resonant pole inverter applying five voltage levels

Industrial applications, e.g. semiconductor manufacturing equipment, require power amplifiers providing high power with high precision and bandwidth. Due to limitations in system infrastructure, increasing voltage is favorable to increasing current to generate more output power. This research presents a 5-level Flying Capacitor Resonant Pole Inverter (FC RPI) configuration that delivers high output voltage and high switching frequency with reduced switch voltage stress. A multilevel modulation scheme is applied to minimize conduction losses, which, in addition, guarantees Zero-Voltage Switching (ZVS) for the entire operating range to minimize switching losses. Both the flying capacitor voltages and the output current are controlled actively closed-loop, resulting in a high accuracy output signal. The concept is validated by simulation, paving the way for future firmware and hardware implementation.
Periodicity and frequency coding in human auditory cortex

Understanding the neural coding of pitch and frequency is fundamental to the understanding of speech comprehension, music perception and the segregation of concurrent sound sources. Neuroimaging has made important contributions to defining the pattern of frequency sensitivity in humans. However, the precise way in which pitch sensitivity relates to these frequency‐dependent regions remains unclear. Single‐frequency tones also cannot be used to test this hypothesis as their pitch always equals their frequency. Here, temporal pitch (periodicity) and frequency coding were dissociated using stimuli that were bandpassed in different frequency spectra (centre frequencies 800 and 4500 Hz), yet were matched in their pitch characteristics. Cortical responses to both pitch‐evoking stimuli typically occurred within a region that was also responsive to low frequencies. Its location extended across both primary and nonprimary auditory cortex. An additional control experiment demonstrated that this pitch‐related effect was not simply caused by the generation of combination tones. Our findings support recent neurophysiological evidence for a cortical representation of pitch at the lateral border of the primary auditory cortex, while revealing new evidence that additional auditory fields are also likely to play a role in pitch coding.
Early life instruction in foreign language and music and incidence of mild cognitive impairment.

OBJECTIVE To test the hypothesis that foreign language and music instruction in early life are associated with lower incidence of mild cognitive impairment (MCI) and slower rate of cognitive decline in old age. METHOD At enrollment in a longitudinal cohort study, 964 older persons without cognitive impairment estimated years of foreign language and music instruction by age 18. Annually thereafter they completed clinical evaluations that included cognitive testing and clinical classification of MCI. RESULTS There were 264 persons with no foreign language instruction, 576 with 1-4 years, and 124 with > 4 years; 346 persons with no music instruction, 360 with 1-4 years, and 258 with > 4 years. During a mean of 5.8 years of observation, 396 participants (41.1%) developed MCI. In a proportional hazards model adjusted for age, sex, and education, higher levels (> 4 years) of foreign language (hazard ratio [HR] = 0.687, 95% confidence interval [CI] [0.482, 0.961]) and music (HR = 0.708, 95% CI [0.539, 0.930]) instruction by the age of 18 were each associated with reduced risk of MCI. The association persisted after adjustment for other early life indicators of an enriched cognitive environment, and it was stronger for nonamnestic than amnestic MCI. Both foreign language and music instruction were associated with higher initial level of cognitive function, but neither instruction measure was associated with cognitive decline. CONCLUSIONS Higher levels of foreign language and music instruction during childhood and adolescence are associated in old age with lower risk of developing MCI but not with rate of cognitive decline.
Enhancement of motor imagery‐related cortical activation during first‐person observation measured by functional near‐infrared spectroscopy

It is known that activity in secondary motor areas during observation of human limbs performing actions is affected by the observer’s viewpoint, with first‐person views generally leading to stronger activation. However, previous neuroimaging studies have displayed limbs in front of the observer, providing an offset view of the limbs without a truly first‐person viewpoint. It is unknown to what extent these pseudo‐first‐person viewpoints have affected the results published to date. In this experiment, we used a horizontal two‐dimensional mirrored display that places virtual limbs at the correct egocentric position relative to the observer. We compared subjects using the mirrored and conventional displays while recording over the premotor cortex with functional near‐infrared spectroscopy. Subjects watched a first‐person view of virtual arms grasping incoming balls on‐screen; they were instructed to either imagine the virtual arm as their own [motor imagery during observation (MIO)] or to execute the movements [motor execution (ME)]. With repeated‐measures anova, the hemoglobin difference as a direct index of cortical oxygenation revealed significant main effects of the factors hemisphere (P = 0.005) and condition (P ≤ 0.001) with significant post hoc differences between MIO‐mirror and MIO‐conventional (P = 0.024). These results suggest that the horizontal mirrored display provides a more accurate first‐person view, enhancing subjects’ ability to perform motor imagery during observation. Our results may have implications for future experimental designs involving motor imagery, and may also have applications in video gaming and virtual reality therapy, such as for patients following stroke.
Electron microscopic study of bullous pemphigoid.

Blister formation in inflamed lesions of bullous pemphigoid were studied by electron microscopy. Three stages can be distinguished during the development of a blister: (1) There is marked edema in the dermis and epidermis and a rather pronounced cellular infiltrate in the dermis. Projections of basal cells are in contact with infiltrate cells. (2) The basal lamina shows discontinuities. Eosinophilic leukocytes migrate into the epidermis and degranulate. (3) In the fully developed blister the basal lamina is usually absent. Our findings in bullous pemphigoid are indistinguishable from those described in dermatitis herpetiformis.
Aging and Memory for Dreams

This study investigated the influence of aging on memory for home dreams and the extent to which cognitive variables such as visual memory, visuospatial IQ, and verbal IQ could account for possible differences herein. Subjects were 80 men and women of ages 45 to 75 years. Memory for dreams was measured by narrative length and frequency of recall. With respect to both measures no significant age differences were noted. Over-all differences in dream recall seemed best explained by visual memory scores. Partial correlational analyses, however, indicated that the small age differences in dream recall could not be accounted for by differential scores on visual memory or on any of the other cognitive variables. Dream contents were scored for aggression, friendliness, emotion, activities, and the number of characters and objects. The incidence of emotions among women appeared to be lower beyond the age of 60. Comparisons with previous data for young adults indicated that large reductions in aggression, friendliness, and emotion occur before the age of 45.
BRAIN SCANS IN DIAGNOSIS OF CEREBROVASCULAR DISEASE: SCANNING WITH CHLORMERODRIN HG 203.

Twenty-seven patients were studied with a total of 30 brain scans done with chlormerodrin Hg 203 at variable periods of time after cerebrovascular accidents. Infarctions, hemorrhages (both intracerebral and subdural), and insufficiencies were represented in this study. A large percentage of very-high-uptake concentration was demonstrated, except in insufficiencies and in a scan of a lesion of the posterior fossa. Increased uptake was obtained as late as 53 days postinfarction. It is emphasized that in this study the uptake obtained in patients with cerebrovascular disease could not be differentiated from tumors on the basis of scanning alone. Some speculation as to the mechanism of this increased uptake is presented.
EFFECTS OF SUMMER FIRES ON WOODY, SUCCULENT, AND GRAMINOID VEGETATION IN SOUTHERN MIXED-PRAIRIE ECOSYSTEMS: A REVIEW

Interest in the use of summer fires to restore southern Great Plains prairie ecosystems infested with woody plants and cactus is increasing, but information regarding effects on target and nontarget plant species is needed before this practice can be recommended. We review effects of summer and winter fires on mortality and growth of honey mesquite (Prosopis glandulosa), prickly pear (Opuntia phaeacantha), and grasses common to the southern mixed prairie, including C4 midgrass sideoats grama (Bouteloua curtipendula), C4 shortgrass buffalograss (Buchloe dactyloides), and C3 midgrass Texas wintergrass (Nassella leucotricha). Summer fires were more effective than winter fires at top-killing mature mesquite, but plant mortality was 4% in all fire treatments. Prickly pear plant mortality was much greater following summer than winter fires. Sideoats grama, buffalograss, and Texas wintergrass were all tolerant of summer fire, although post-fire recovery rate was slower in sideoats grama than in the other species. Clipping once each spring reduced sideoats grama and Texas wintergrass standing crop in all treatments when measured 1 y after clipping, but effects of clipping summer fire were not negatively additive. The only time fire negatively affected Texas wintergrass was when spring clipping followed winter fire. In contrast, buffalograss standing crop was not reduced by clipping or clipping summer fire at 1 y after treatment. Results suggest that summer fire will not eradicate mesquite and that frequent fires either in summer or winter are necessary to maintain suppression. Grasses studied thus far have demonstrated a tolerance to fire in either season. keywords: cactus, grassland, herbaceous production, mesquite, prescribed fire, southern Great Plains, species composition, summer fire, woody plants. Citation: Ansley, R.J., and M.J. Castellano. 2007. Effects of summer fires on woody, succulent, and graminoid vegetation in southern mixed-prairie ecosystems: a review. Pages 63–70 in R.E. Masters and K.E. M. Galley (eds.). Proceedings of the 23rd Tall Timbers Fire Ecology Conference: Fire in Grassland and Shrubland Ecosystems. Tall Timbers Research Station, Tallahassee, Florida, USA.
Fatigue as a precursor to polymyalgia rheumatica: an explorative retrospective cohort study

Objectives: Polymyalgia rheumatica (PMR) is the commonest inflammatory disorder of older adults. Although not part of the recently published classification criteria, patients with PMR frequently complain of fatigue. We compared consultation for fatigue and sleep problems between individuals with and without PMR. Method: Consulters receiving a Read-coded diagnosis of PMR at nine general practices between 2000 and 2009 were matched by age, gender, general practice, and year of consultation to four patients without PMR. Fatigue and sleep problems were defined using Read codes. Cox regression was used to determine the association between PMR diagnosis and consultation for a fatigue/sleep problem. Results: In total, 549 PMR patients were identified. Their mean (SD) age was 73.9 (8.6) years and 71% of the participants were female. Prior to the index date, 33 PMR patients and 80 matched non-PMR patients consulted with fatigue (0.43 vs. 0.25 consultations per 10 000 person-years, p = 0.006). PMR was associated with significantly more multiple fatigue consultations in the 12 months before PMR diagnosis [hazard ratio (HR) 1.95, 95% confidence interval (CI) 1.23–3.08]; no significant difference was seen in rates of consultations for sleep problems between patients with and without PMR. Conclusions: PMR patients were significantly more likely to have had multiple fatigue consultations before being diagnosed with PMR. Given the overproduction of inflammatory cytokines seen in PMR, this fatigue may represent a prodromal phase prior to consulting with more classical musculoskeletal symptoms. This suggests that clinicians should consider PMR as a potential diagnosis in older patients consulting with fatigue.
Chapter 9 COTTON SEED DEVELOPMENT : OPPORTUNITIES TO ADD VALUE TO A BYPRODUCT OF FIBER PRODUCTION

Unlike other major crops in which seeds provide most of the economic value, cotton seed is largely a by-product of more valuable fiber production and represents only approximately 15% of the farm gate value of the cotton crop. A cotton plant normally produces about 1.6 kg of seed for every kg of lint. Following ginning to remove the lint fiber, fuzzy cotton seed is either used directly as animal feed, or processed into four major products including oil, meal, hull and short linter fibers (Cherry and Leffler, 1984; O’Brien et al., 2005). With about 21% oil and 23% protein by weight in the seed, however, this makes cotton the fifth largest oil crop in the world and the second most important potential source of plant proteins. As a by-product of fiber production, the continued large scale production of cotton seeds is assured because of the on-going demand for the fiber by the textile industry. Until recently, the quality of cotton seed has been relatively neglected as the main research priority has been devoted to enhancing fiber quality and fiber yield. This continual human selection for high yield and better quality of fiber has narrowed the genetic variation available for cotton seed quality improvement through breeding. An in-depth understanding of metabolic events that determine the overall components of the storage reserves in cotton seeds is therefore of vital importance for improving the yield, quality and ultimately the value of seed products and opens the possibility for significant value-adding by engineering novel attributes into the seed. While in this review we have focused primarily on the development of the cotton seed, other more studied species such as Arabidopsis thaliana can serve as a model for cotton and for completeness those other species are mentioned where data for cotton are limited.
The distribution of haemoglobin and blood potassium types in British breeds of sheep

The incidence of the haemoglobin types, A, B and AB, and of the high- and low-potassium blood types has been determined in thirty-three British breeds of sheep. There is no correlation between the haemoglobin types and the potassium types within the breeds. The gene frequencies at the two loci associated with these characters have been estimated for each breed; there is considerable variation at both loci from breed to breed. The hill breeds of sheep have relatively greater frequencies of the gene for haemoglobin A and the high-potassium gene, while low land breeds have relatively greater frequencies for the haemoglobin B gene and the low-potassium gene. When different breeds are compared, a marked correlation is found between the haemoglobin A gene frequency and the high-potassium gene frequency. The possible biological significance of these findings is discussed.
Boundaries in the Study of Organization

The concept of boundaries as relational processes has been central and ubiquitous in the social sciences, especially in areas such as the formation of individual, group or national identities, the creation of class, ethnic or gender inequalities, or the social construction of professions, knowledge and science itself. A key theme running through these literatures is how symbolic resources are used to create, perpetuate, or challenge institutionalized differences or inequalities by creating distinctions between ‘us’ and ‘them’, the legitimate or illegitimate, the acceptable or unacceptable, the in or out (Lamont & Molnar, 2002). A central focus of study has thus been how ‘symbolic boundaries’ (Lamont, 2001), particular classification systems enshrined in cognitive schemata have very real consequences in forming and sustaining corresponding social boundaries. In the management literature, however, there has been little serious and concerted study of the formation, properties and consequences of boundaries per se as complex, shifting, socially constructed entities. Organizational boundaries are often treated as socially and organizationally unproblematic, to be determined by considerations of economic efficiency, as, for example, in the case of transaction cost economics (Williamson, 1985), advancing a perspective originally proposed by Coase (1937). From a transaction cost perspective, for example, new technologies such as the internet can either enlarge or shrink firm boundaries through their effects on production costs that influence whether a productive task is outsourced or carried out internally (Afuah, 2003). The property rights approach (Grossman & Hart, 1986) has also been very influential in the theorizing of boundaries. In this approach, the boundaries of the firm are determined by the common ownership of assets that grants the owner bargaining power when issues of incomplete contracting, opportunism or hold-up problems emerge.
Predictors of diabetes-related quality of life after transitioning to the insulin pump.

OBJECTIVE To examine family and individual psychosocial, medical, and demographic factors associated with improved diabetes-related quality of life (QOL) after transitioning to the insulin pump among youth with type 1 diabetes. METHOD Fifty-three parent-child dyads completed questionnaires on four occasions prior to and following this medical regimen change, assessing QOL, family environment, depressive and anxiety symptoms, and medical and demographic information. Trajectories of change in QOL were analyzed using multilevel modeling. RESULT Psychosocial, medical, and demographic characteristics were associated with QOL prior to pump-start. Elements of children's QOL significantly improved after the transition, and improvement was predicted by psychosocial, medical, and demographic characteristics. CONCLUSION Results indicate that individual and contextual factors may play a role in QOL as children transition to the insulin pump. Findings may guide efforts to support families through this challenging time and potentially inform candidacy for transition to the pump.
What is the relation between cultural orientation and socially desirable responding?

Research suggests that collectivists are more likely to engage in deception and socially desirable responding to maintain good relationships with others. In contrast, individualists are portrayed as candid and sincere because individualism encourages people to "be yourself. " The authors propose that people with both types of cultural orientations or backgrounds engage in desirable responding, albeit in distinct ways. In Study 1, respondents from the United States compared with those from Singapore, and European Americans compared with Asian Americans, scored higher on self-deceptive enhancement (SDE)-the tendency to see oneself in a positive light and to give inflated assessment of one's skills and abilities- but lower on impression management (IM) by misrepresenting their self-reported actions to appear more normatively appropriate. In Studies 2 to 4, horizontal individualism as a cultural orientation correlated with SDE but not with IM, whereas horizontal collectivism correlated with IM but not with SDE. Further analyses examining (a) individual differences in the tendency to answer deceptively and (b) responses to behavioral scenarios shed additional light on the culturally relevant goals served by these distinct types of socially desirable responding.