Miracle-dz/UniFAR-FTUs huggingface dataset:
Summary of significant positive studies for each type of model and protocol : effect of light exposure during biological darkness and the circadian disruption on cancer incidence and growth

Introduction The regular alternation of light and darkness over 24 hours synchronizes the endogenous circadian timing system of mammals through multiple pathways that involve (a) the elicitation of multiple gene transcription responses to glutamate and pituitary adenylcyclase activating peptide, the neuromediators that convey light messages to the suprachiasmatic nuclei (SCN) in the hypothalamus (Harmar et al., 2002); the SCN are the main circadian pacemakers that coordinate the rhythmic organization of biological functions over 24 hours (Hastings et al., 2003); and (b) the elicitation of multiple hormonal responses, including melatonin and corticosterone, in response to light. These neuroendocrine or endocrine effects seem to require SCN mediation and their extent depends upon the endogenous circadian time of exposure (Ishida et al., 2005; Schibler & Brown, 2005); glucocorticoids, including corticosterone, can reset both the molecular clock and downstream clock-controlled genes in peripheral tissues, such as liver (Balsalobre et al., 2000). In experimental systems, light exposure plays a key role in the resetting of the circadian timing system, that can involve, but does not require, melatonin signalling (Skene et al., 1999). The relevance of environmental light-dark schedules for cancer development or growth has been studied (see Table 3.1) with regard to the respective effects of (a) circadian time of carcinogen exposure in rodents kept in 24-hour light-dark regimens; (b) constant exposure to light or constant darkness; (c) experimental jet lag or other alterations of photoperiodic regimens; and (d) experimental mutations of clock genes. The intrication between carcinogen effects and circadian disruption was obvious in most reports. Conversely, circadian disruption, through experimental jet lag exposure, as well as clock genes mutations or SCN ablation, also leads to malignant processes taking place. The influence of circadian time on carcinogen or promoter exposure and malignant growth was studied in intact mice or rats kept in a regular alternation of 12 hours of light and 12 hours of darkness (LD12:12) before exposure to carcinogens. Modifications to the regular alteration of light and darkness over 24 hours can disrupt both the circadian timing system at one or several levels of its hierarchical organization and the clock-controlled rhythms in mammals. The multifaceted changes that can occur range from clear whole organism response such as significant modifications in rest–activity rhythms and inability to rhythmically control core body temperature, to more subtle changes such as altered SHIFTWORK 635 Table 3.1. Summary of significant positive studies for each type of model and protocol: …
Macular Ganglion Cell Imaging Study: Covariate Effects on the Spectral Domain Optical Coherence Tomography for Glaucoma Diagnosis

Purpose To evaluate the effect of multiple covariates on the diagnostic performance of the Cirrus high-definition optical coherence tomography (HD-OCT) for glaucoma detection. Methods A prospective case-control study was performed and included 173 recently diagnosed glaucoma patients and 63 unaffected individuals from the Macular Ganglion Cell Imaging Study. Regression analysis of receiver operating characteristic were conducted to evaluate the influence of age, spherical equivalent, axial length, optic disc size, and visual field index on the macular ganglion cell-inner plexiform layer (GCIPL) and peripapillary retinal nerve fiber layer (RNFL) measurements. Results Disease severity, as measured by visual field index, had a significant effect on the diagnostic performance of all Cirrus HD-OCT parameters. Age, axial length and optic disc size were significantly associated with diagnostic accuracy of average peripapillary RNFL thickness, whereas axial length had a significant effect on the diagnostic accuracy of average GCIPL thickness. Conclusions Diagnostic performance of the Cirrus HD-OCT may be more accurate in the advanced stages of glaucoma than at earlier stages. A smaller optic disc size was significantly associated with improved the diagnostic ability of average RNFL thickness measurements; however, GCIPL thickness may be less affected by age and optic disc size.
Identifying Power-Efficient Multicore Cache Hierarchies via Reuse Distance Analysis

To enable performance improvements in a power-efficient manner, computer architects have been building CPUs that exploit greater amounts of thread-level parallelism. A key consideration in such CPUs is properly designing the on-chip cache hierarchy. Unfortunately, this can be hard to do, especially for CPUs with high core counts and large amounts of cache. The enormous design space formed by the combinatorial number of ways in which to organize the cache hierarchy makes it difficult to identify power-efficient configurations. Moreover, the problem is exacerbated by the slow speed of architectural simulation, which is the primary means for conducting such design space studies. A powerful tool that can help architects optimize CPU cache hierarchies is reuse distance (RD) analysis. Recent work has extended uniprocessor RD techniques-i.e., by introducing concurrent RD and private-stack RD profiling—to enable analysis of different types of caches in multicore CPUs. Once acquired, parallel locality profiles can predict the performance of numerous cache configurations, permitting highly efficient design space exploration. To date, existing work on multicore RD analysis has focused on developing the profiling techniques and assessing their accuracy. Unfortunately, there has been no work on using RD analysis to optimize CPU performance or power consumption. This article investigates applying multicore RD analysis to identify the most power efficient cache configurations for a multicore CPU. First, we develop analytical models that use the cache-miss counts from parallel locality profiles to estimate CPU performance and power consumption. Although future scalable CPUs will likely employ multithreaded (and even out-of-order) cores, our current study assumes single-threaded in-order cores to simplify the models, allowing us to focus on the cache hierarchy and our RD-based techniques. Second, to demonstrate the utility of our techniques, we apply our models to optimize a large-scale tiled CPU architecture with a two-level cache hierarchy. We show that the most power efficient configuration varies considerably across different benchmarks, and that our locality profiles provide deep insights into why certain configurations are power efficient. We also show that picking the best configuration can provide significant gains, as there is a 2.01x power efficiency spread across our tiled CPU design space. Finally, we validate the accuracy of our techniques using detailed simulation. Among several simulated configurations, our techniques can usually pick the most power efficient configuration, or one that is very close to the best. In addition, across all simulated configurations, we can predict power efficiency with 15.2% error.
Reflections from teachers and students on speaking anxiety in an EFL classroom

Abstract This paper reports on part of the research project in which instructor perspectives on the role of anxiety in an EFL speaking classroom and anxiety-coping strategies students employ when speaking English have been investigated. The existence of students’ speaking anxiety was revealed via a teacher interview. A total of 88 students from the intact classes also responded to an interview form for an analysis of anxiety-coping strategies they utilised when speaking English in class. The qualitative data from both instruments was analysed using the content analysis. The findings of the teacher interview data put forward that students of this study have experienced speaking-in-class anxiety. This anxiety may influence their grades, to some extent. Three factors that may hinder students’ development of oral skills emerge, including their lack of self-confidence, having poor English background and having neither intrinsic nor extrinsic motivation to use English. Using the target language as the medium of communication in class is viewed by the teachers as a must in theory, but flexibility is allowed in practice. Moreover, the results of the student interview data show a wide range of strategies employed to deal with anxiety (ie social, affective, meta-cognitive, compensatory, cognitive and memory-related strategies). Social strategies are the most frequently-used techniques. Suggestions for improvement in the overall oral English (ie vocabulary focus, audiovisual focus, self-practice, social focus, auditory focus, meta-cognitive focus, compensatory focus and affective focus) have also been given by the student participants. An increased repertoire of vocabulary is viewed as the most effective tool for such improvement.
Importance of nurse logs as a substrate for the regeneration of pioneer tree species on Barro Colorado Island, Panama

Abstract: Fallen tree trunks (‘nurse logs’) are important recruitment sites for trees in temperate forest, however nurse log use is seldom reported in tropical forests. We predicted that logs should be important for the regeneration of small-seeded tropical pioneer species because surface leaf litter and competition with established vegetation reduces the establishment success of these species from soil seed banks. In a survey on Barro Colorado Island, Panama, we found that pioneer seedlings were present on logs in 40 of 95 recent treefall gaps. In gaps where seedlings were present on logs, seedling density was not significantly different from adjacent areas of soil. However, species composition was significantly different; logs were disproportionately colonized by smaller-seeded and wind-dispersed species. In growing-house experiments using 12 species, we found that wood substrate had little effect on seed germination. In contrast, seedling growth was 50% lower on decayed wood than soil. Furthermore, species growth rates on wood were not significantly correlated with growth rates in soil (df = 10, r = 0.48). If establishment on logs eventually leads to recruitment to the forest canopy, then logs may promote the maintenance of diversity by favouring a different group of species from those that recruit in soil.
Curiosity, Motivation, Attitude, Gender, and Mathematics Performance

This study sought to determine the curiosity, motivation, and attitudes of fourth year students of a government-owned secondary school in Bulacan in relation to their performance in Mathematics. It utilized the descriptive-correlation method of research. It was revealed by the randomly selected 321 Grade 10 respondents that in terms of curiosity, they felt that they have the ability to seek out opportunities to challenge themselves and grow as a person resulting in higher motivation and higher effect on mathematical performance. Motivation directly affected the respondents' perception about performance while attitude contributed a lot to performance in mathematics. Furthermore, the male students differed from their female counterparts in their mathematical performance. Female students were more curious, motivated, and have positive attitude towards mathematics than the males. However, there was no significant difference between the means of the male and females in all the variables. The study also showed that motivation is a significant predictor of mathematics performance.
The Roots of Latin American Protectionism: Looking Before the Great Depression

This paper uncovers a fact that has not been well appreciated: tariffs in Latin America were far higher than anywhere else in the century before the Great Depression. This is a surprising fact given that this region has been said to have exploited globalization forces better than most during the pre-1914 belle epoque and for which the Great Depression has always been viewed as a critical policy turning point towards protection and de-linking from the world economy. This paper shows that the explanation cannot lie with output gains from protection, since, while such gains were present in Europe and its non-Latin offshoots, they were not present in Latin America. The paper then explores Latin American tariffs as a revenue source, as a protective device for special interests, and as the result of other political economy struggles. We conclude by asking whether the same pro-protection conditions exist today as those which existed more than a century ago.
Evaluating the Effect of Customers' Trust and Attraction in Electronic Banking: Examining the Trust- Relationship Commitment Model (TRC)

The main aim of the research is to determine the factors which affect the electronic banking customers' commitment. Accordingly, a model of Commitment- Relation-Trust (TRC) has been fitted with the data accumulated from the subject statistical population. The main approach of this research is the applied approach with the causal strategy. To accumulate the data, standardized questionnaires have been used. The Agricultural Banks of Tabriz are the statistical population of the research in which a sample of 185 customers from these banks, who were chosen in clusters, was studied. After analyzing the confirmed cause and drawing the route diagram by LISREL Software, it was realized that the following variables had direct and meaningful effects: Relation on trust, relation on attraction, common value on the commitment, attraction on commitment and trust on commitment. But according to the accumulated data from the statistical population, the direct effect of common value on the customers' trust and the direct effect of the opportunistic behavior on the customers' trust were not conformed.
A Critical Role of Luteolin-Induced Reactive Oxygen Species in Blockage of Tumor Necrosis Factor-Activated Nuclear Factor-κB Pathway and Sensitization of Apoptosis in Lung Cancer Cells

Nuclear factor κB (NF-κB) activated by tumor necrosis factor (TNF) attenuates the TNF-induced apoptosis pathway. Therefore, blockage of NF-κB should improve the anticancer activity of TNF. Luteolin, a naturally occurring polyphenol flavonoid, has been reported to sensitize colorectal cancer cells to TNF-induced apoptosis through suppression of NF-κB; however, the mechanisms of this effect have not been well elucidated. In this article, we provide evidence showing a critical role of reactive oxygen species (ROS) accumulation induced by luteolin in modulating TNF-activated pathways in lung cancer cells. Luteolin effectively suppressed NF-κB, whereas it potentiated the c-Jun N-terminal kinase (JNK) to increase apoptosis induced by TNF in lung cancer cells. Our results further demonstrate that luteolin induced an early phase ROS accumulation via suppression of the cellular superoxide dismutase activity. It is noteworthy that suppression of ROS accumulation by ROS scavengers butylated hydroxyanisole, and N-acetyl-l-cysteine prevented the luteolin-induced suppression of NF-κB and potentiation of JNK and significantly suppressed the synergistic cytotoxicity seen with cotreatment of luteolin and TNF. Taken together, these results suggest that the accumulation of ROS induced by luteolin plays a pivotal role in suppression of NF-κB and potentiation of JNK to sensitize lung cancer cells to undergo TNF-induced apoptosis.
Mineralization in a northeastern Greenland sediment: mathematical modelling, measured sediment pore water profiles and actual activities

A mathematical computer model describing mineralization processes and transport of solutes within sediments was developed based on the degradation of organic matter, stoichiometrically coupled to the consumption of O2 in the oxic layers, and to NO3and SO," in the anoxic layers. The reaction rates obey Michaelis-Menten type kinetics and all transport of solutes is assumed to take place by diffusion. The model was tested on a northeastern Greenland sediment and gave accurate simulations of the measured concentration profiles. In addition, measured processes of nitrification, coupled nitrification-denitrification. denitrification of water column NO3-, NH4t mineralization and the fluxes of NH4t and NO3across the sediment-water interface were predicted with great accuracy. Since the model is based on Michaelis-Menten type kinetics and diffusional transport mechanisms, it is of general use and provides an important tool to evaluate the regulation of biogeochemical cycling in sediments. This is shown in a series of simulations predicting the effect of various concentrations in the water column of 0, and NO3on the rates of nitrification and denitrification. The results are in good agreement with previously published measurements.
The Third Factor in Phonology

This article attempts to investigate how much of phonology can be explained by properties of general cognition and the Sensorimotor system — in other words, third-factor principles, in support of the evolutionary scenario posed by Hauser et al. (2002a). It argues against Pinker & Jackendoff’s (2005: 212) claim that “major characteristics of phonology are specific to language (or to language & music), [and] uniquely human,” and their conclusion that “phonology represents a major counterexample to the recursion-only hypothesis. ” Contrary to the statements by Anderson (2004) and Yip (2006a, 2006b) to the effect that phonology has not been tested in animals, it is shown that virtually all the abilities that underlie phonological competence have been shown in other species.
Comparative phylogenetic analysis of small GTP-binding genes of model legume plants and assessment of their roles in root nodules

Small GTP-binding genes play an essential regulatory role in a multitude of cellular processes such as vesicle-mediated intracellular trafficking, signal transduction, cytoskeletal organization, and cell division in plants and animals. Medicago truncatula and Lotus japonicus are important model plants for studying legume-specific biological processes such as nodulation. The publicly available online resources for these plants from websites such as http://www.ncbi. nih.gov, http://www.medicago. org, http://www.tigr. org, and related sites were searched to collect nucleotide sequences that encode GTP-binding protein homologues. A total of 460 small GTPase sequences from several legume species including Medicago and Lotus, Arabidopsis, human, and yeast were phyletically analysed to shed light on the evolution and functional characteristics of legume-specific homologues. One of the main emphases of this study was the elucidation of the possible involvement of some members of small GTPase homologues in the establishment and maintenance of symbiotic associations in root nodules of legumes. A high frequency of vesicle-mediated trafficking in nodules led to the idea of a probable subfunctionalization of some members of this family in legumes. As a result of the analyses, a group of 10 small GTPases that are likely to be mainly expressed in nodules was determined. The sequences determined as a result of this study could be used in more detailed molecular genetic analyses such as creation of RNA inteference silencing mutants for further clarification of the role of GTPases in nodulation. This study will also assist in furthering our understanding of the evolutionary history of small GTPases in legume species.
The NMR solution structure of human glutaredoxin in the fully reduced form.

The determination of the nuclear magnetic resonance (NMR) solution structure of fully reduced human glutaredoxin is described. A total of 1159 useful nuclear Overhauser effect (NOE) upper distance constraints and 187 dihedral angle constraints were obtained as the input for the structure calculations for which the torsion angle dynamics program DYANA has been utilized followed by energy minimization in water with the AMBER force field as implemented in the program OPAL. The resulting 20 conformers have an average root-mean-square deviation value relative to the mean coordinates of 0.54 A for all the backbone atoms N, Calpha and C', and of 1.01 A for all heavy atoms. Human glutaredoxin consists of a four-stranded mixed beta-sheet composed of residues 15 to 19, 43 to 47, 72 to 75 and 78 to 81, and five alpha-helices composed of residues 4 to 9, 24 to 34, 54 to 65, 83 to 91, and 94 to 100. Comparisons with the structures of Escherichia coli glutaredoxin-1, pig liver glutaredoxin and human thioredoxin were made. Electrostatic calculations on the human glutaredoxin structure and that of related proteins provide an understanding of the variation of pKa values for the nucleophilic cysteine in the active site observed among these proteins. In addition, the high-resolution NMR solution structure of human glutaredoxin has been used to model the binding site for glutathione and for ribonucleotide reductase B1 by molecular dynamics simulations.
Participation of intraluteal progesterone and prostaglandin F2 alpha in LH-induced luteolysis in pregnant rat.

We examined the participation of the intraluteal levels of progesterone (P4) and prostaglandin F2 alpha (PGF2 alpha) in the induction of luteolysis by LH and its relationship with the induction of the 20 alpha-hydroxysteroid dehydrogenase activity (20 alpha-HSD). Subcutaneous administration of four doses of 10 microgram ovine LH (oLH) at 0800, 0900, 1000 and 1100 h on day 19 of pregnancy induced a decrease in the activity of the enzyme 3 beta-HSD 24 and 48 h after treatment and an increase in luteal 20 alpha-HSD activity 48 h after oLH treatment when compared with control rats. Intraluteal and serum P4 levels were lower than control values 24 and 48 h after oLH treatment, with a significant increase in luteal PGF2 alpha content and a decrease in corpus luteum (CL) weight 48 h after oLH treatment. Intrabursal ovarian (i.b.) treatment with an inhibitor of PG's biosynthesis (diclofenac) (70 microgram/ovary) or P4 (3 microgram/ovary) on day 20 of pregnancy, prevented the increase in 20 alpha-HSD activity observed 48 h after oLH treatment, without any effect on 3 beta-HSD activity. The i.b. administration of P4 prevented the increase in intraluteal PGF2 alpha content induced by oLH treatment and the increases in 20 alpha-HSD activity and intraluteal PGF2 alpha content observed in control animals on day 21 of pregnancy. The inhibition of PG biosynthesis also prevents the decrease in intraluteal and serum P4 level induced by oLH. These results provide good evidence of the important participation of intraluteal P4 and PGF2 alpha on the oLH-induced luteolysis in pregnant rats. We also found the P4 produced by the CL is involved, in part, in the regulation of luteal PG synthesis. Thus, the early decline in 3 beta-HSD activity and the consequent fall in intraluteal P4 content, may trigger the synthesis of PGs and thereafter the increase in luteal 20 alpha-HSD activity to establish luteolysis.
LlMNOLOGICAL CONDITIONS AND GROWTH OF TROUT , ' , IN THREE LAKES NEAR ROTORUA

A small group of lakes near Rotorua has been the sub ject of research by the Marine Department for a number of years to determine the rate of growth of the resident rainbow trout (Salmo gairdnerii) (Smith 1959) and the effect of increasing these trout populations by artificial stocking with hatchery-reared fingerlings. As a result, fish size in some lakes has been noticeably reduced in recent years. It has been shown elsewhere that the quality of the water in a lake has an important effect upon the fish present (Hasler 1947). Some factors affecting water quality were therefore examined during the summer of 1962 in lakes Okataina, Ngapouri and Okaro. These data are correlated with others relating to those trout present which were over 20 em. long (smaller fish are caught nei ther by anglers nor by the gill nets used in research).