Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting gene function in Saccharomyces cerevisiae

MOTIVATION S.cerevisiae is one of the most important model organisms, and has has been the focus of over a century of study. In spite of these efforts, 40% of its open reading frames (ORFs) remain classified as having unknown function (MIPS: Munich Information Center for Protein Sequences). We wished to make predictions for the function of these ORFs using data mining, as we have previously successfully done for the genomes of M.tuberculosis and E.coli. Applying this approach to the larger and eukaryotic S.cerevisiae genome involves modifying the machine learning and data mining algorithms, as this is a larger organism with more data available, and a more challenging functional classification. RESULTS Novel extensions to the machine learning and data mining algorithms have been devised in order to deal with the challenges. Accurate rules have been learned and predictions have been made for many of the ORFs whose function is currently unknown. The rules are informative, agree with known biology and allow for scientific discovery. AVAILABILITY All predictions are freely available from http://www.genepredictions. org, all datasets used in this study are freely available from http://www.aber. ac.uk/compsci/Research/bio/dss/yeastdataand software for relational data mining is available from http://www.aber. ac.uk/compsci/Research/bio/dss/polyfarm.
Cell migration within confined sandwich-like nanoenvironments.

AIM We introduced sandwich-like culture as a tool to engineer the cellular nanoenvironment by tuning protein presentation and activation of dorsal and ventral receptors. We aim at studying cell migration under more similar conditions to the 3D physiological one. MATERIALS & METHODS We have investigated different nanoenvironments by changing the protein coating and using materials that adsorb proteins in different conformation, seeking to show their specific role in cell migration. RESULTS Cell migration within sandwich cultures greatly differs from 2D cultures, shares some similarities with migration within 3D environments and is highly dependent on the protein nanoenvironment. Beyond differences in cell morphology and migration, dorsal stimulation promotes cell remodeling of the extracellular matrix over simple ventral receptor activation in traditional 2D cultures. CONCLUSION Local(nano) stimulation of dorsal and ventral receptors within sandwich cultures alter cell migration in comparison to standard 2D environments.
Multilingual Children: Beyond Myths and Toward Best Practices

M ultilingualism is an international fact of life and increasing in the United States. Multilingual families are exceedingly diverse, and policies relevant to them should take this into account. The quantity and quality of a child’s exposure to responsive conversation spoken by fluent adults predicts both monolingual and multilingual language and literacy achievement. Contexts supporting optimal multilingualism involve early exposure to high quality conversation in each language, along with continued support for speaking both languages. Parents who are not fluent in English should not be told to speak English instead of their native language to their children; children require fluent input, and fluent input in another language will transfer to learning a second or third language. Messages regarding optimal multilingual practices should be made available to families using any and all available methods for delivering such information, including home visitation programs, healthcare settings, center-based early childhood programs, and mass media. *Subsequent to submitting the present report, a different report by Espinosa (2013) came to our attention. Her work on addressing myths regarding bilingualism is for practitioners and complements ours. The full report is available at http:// fcd-us.org/resources/ prek-3rd-challengingcommon-myths-aboutdual-language-learners-update-seminal2008-report#node-1367
Women with disabilities and their lived experiences of physical, psychological and sexual abuse in Croatia

ABSTRACT This research aims to generate a better understanding of the abuse of women with disabilities through a qualitative study with 28 women with disabilities in five towns in Croatia. The results show that more than half of the research participants had experienced physical, psychological and sexual abuse, and financial exploitation. Participants stressed the need for education and empowerment of women with disabilities as well as better training for professionals and ensuring that a formal support system is available in every local community. The role of social workers in emerging countries like Croatia needs to include developing individual, group and community support for women with disabilities and raising public awareness of the abuse and violence shown towards women with disabilities through political and community networks and events.
Cultures Of Relatedness New Approaches To The Study Of Kinship

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How succulent leaves of Aizoaceae avoid mesophyll conductance limitations of photosynthesis and survive drought

In several taxa, increasing leaf succulence has been associated with decreasing mesophyll conductance (g M) and an increasing dependence on Crassulacean acid metabolism (CAM). However, in succulent Aizoaceae, the photosynthetic tissues are adjacent to the leaf surfaces with an internal achlorophyllous hydrenchyma. It was hypothesized that this arrangement increases g M, obviating a strong dependence on CAM, while the hydrenchyma stores water and nutrients, both of which would only be sporadically available in highly episodic environments. These predictions were tested with species from the Aizoaceae with a 5-fold variation in leaf succulence. It was shown that g M values, derived from the response of photosynthesis to intercellular CO2 concentration (A:C i), were independent of succulence, and that foliar photosynthate δ13C values were typical of C3, but not CAM photosynthesis. Under water stress, the degree of leaf succulence was positively correlated with an increasing ability to buffer photosynthetic capacity over several hours and to maintain light reaction integrity over several days. This was associated with decreased rates of water loss, rather than tolerance of lower leaf water contents. Additionally, the hydrenchyma contained ~26% of the leaf nitrogen content, possibly providing a nutrient reservoir. Thus the intermittent use of C3 photosynthesis interspersed with periods of no positive carbon assimilation is an alternative strategy to CAM for succulent taxa (Crassulaceae and Aizoaceae) which occur sympatrically in the Cape Floristic Region of South Africa.
Adolescence as a Unique Period of Vulnerability to Environmental Stressors: Age-Dependent and Sex-Dependent effects of Nicotine Exposure on Anxiety Utilizing The Light-Enhanced Startle Paradigm

This study utilized a rodent model of anxiety in which the defensive behavior of rats provides a measure of operational anxiety known as “Light-Enhanced Startle” (LES; Walker & Davis, 1997). The focus of the study was to explore age-dependent and sex-dependent vulnerabilities to the anxiety-producing effects of nicotine in rats. An additional goal was to establish the LES paradigm for use in adolescent animals. The effect of acute first-time exposure to nicotine on the magnitude of light-enhanced startle in adolescent versus adult rats was measured. Adolescent and adult animals did not have similar dose-response patterns revealing age-dependent differences in nicotine’s effect on anxiety. Additionally, these different dose-response patterns depended on sex. In general, nicotine was anxiogenic in most conditions and females showed stronger anxiogenic responses to nicotine than males. Collectively, outcomes reveal age-dependent vulnerabilities to the anxiety-producing effects of nicotine that depend on drug dose and sex, and establish the light-enhanced startle paradigm for use as an animal model of anxiety expression in adolescence, which is viewed as a critical developmental period. Adolescence as a unique period of vulnerability to the effects of stress and advantages of the LES paradigm as an experimental model of anxiety are also discussed.
Are Skill Requirements in the Workplace Rising? Distinguishing Between Skill-Biased Technological Change and Over-Education

Both the skill-biased technological change hypothesis and the over-education hypothesis are consistent with the observed increased proportion of high-educated employees, but each has dierent predictions regarding occupational skill requirements. The analysis distinguishes between these two hypotheses by investigating the changing occupational skill requirements. It shows that changes in occupational skill requirements did keep pace with rising educational supplies. Skill requirements rose within occupations, even in those that were the least demanding in 1979. In addition, the analysis shows that workplace computerization is complementary to non-routine cognitive task, and substitutes for cognitive and manual routine tasks.
Improving decoding speed for parallel Distributed Video Coding architectures

The Distributed Video Coding (DVC) paradigm is suitable for devices which have limited encoding capabilities. However, it is characterized by excessive decoding delays which compromise their application for time constrained services. This limitation can be mitigated by adopting parallel DVC architectures. Yet, the traditional Gray-code or binary-code representations have a non-uniform distribution of mismatch across bit-planes, resulting in uneven decoding times which hinder parallel decoding. This work proposes an alternative indexing scheme, where mismatch is distributed more uniformly amongst bit-planes and thus comparable decoding delays are expected, facilitating parallel implementations. This method reduces decoding time by up to 32% compared to architectures using simple parallel techniques, with a slight loss of 0.06dB in RD performance.
Multi-Model Assessment of Regional Surface Temperature Trends: CMIP3 and CMIP5 20 th Century Simulations

Regional surface temperature trends from the CMIP3 and CMIP5 20 th century runs are compared with observations -at spatial scales ranging from global averages to individual grid points -using simulated intrinsic climate variability from pre-industrial control runs to assess whether observed trends are detectable and/or consistent with the models’ historical run trends. The CMIP5 models are also used to detect anthropogenic components of the observed trends, by assessing alternative hypotheses based on scenarios driven with either anthropogenic plus natural forcings combined, or with natural forcings only. Modeled variability is assessed via inspection of control run time series, standard deviation maps, spectral analyses, and low-frequency variance consistency tests. The models are found to provide plausible representations of internal climate variability, though there is room for improvement. The influence of observational uncertainty on the trends is assessed, and found to be generally small compared to intrinsic climate variability. Observed temperature trends over 1901-2010 are found to contain detectable anthropogenic warming components over a large fraction (about 80%) of the analyzed global area. In several regions, the observed warming is significantly underestimated by the models, including parts of the southern Ocean, south Atlantic, far eastern Atlantic, and far west Pacific. Regions without detectable warming signals include the high latitude North Atlantic, the eastern U.S., and parts of the eastern Pacific. For 1981-2010, the observed warming trends over about 45% of the globe are found to contain a detectable anthropogenic warming; this includes much of the globe within about 40-45 degrees of the equator, except for the eastern Pacific.
Diversity and Higher Education: Theory and Impact on Educational Outcomes

In the current context of legal challenges to affirmative action and race-based considerations in college admissions, educators have been challenged to articulate clearly the educational purposes and benefits of diversity. In this article, Patricia Gurin, Eric Dey, Sylvia Hurtado, and Gerald Gurin explore the relationship between students' experiences with diverse peers in the college or university setting and their educational outcomes. Rooted in theories of cognitive development and social psychology, the authors present a framework for understanding how diversity introduces the relational discontinuities critical to identity construction and its subsequent role in fostering cognitive growth. Using both single- and multi-institutional data from the University of Michigan and the Cooperative Institutional Research Program, the authors go on to examine the effects of classroom diversity and informal interaction among African American, Asian American, Latino/a, and White students on learning and democracy .
Intergenerational Risk Sharing Under Endogenous Labor Supply

This paper evaluates the welfare effects from labor-supply distortions in the context of a pre-funded social security scheme. The central feature of the pension fund model is that equity risk manifests itself in the form of implicit taxes and subsidies on the labor earnings of participants. The labor-supply choices of participants are assumed to be elastic with respect to wage-differentials, implying that risk-taking and risk-sharing induces distortions in labor markets. I show that labor-supply effects impede the pension fund from taking advantage of intergenerational risk-sharing. The analysis provides an economic justification for solvency rules that require financial losses to be recouped in a short time-period.
Dot1-Dependent Histone H3K79 Methylation Promotes Activation of the Mek1 Meiotic Checkpoint Effector Kinase by Regulating the Hop1 Adaptor

During meiosis, accurate chromosome segregation relies on the proper interaction between homologous chromosomes, including synapsis and recombination. The meiotic recombination checkpoint is a quality control mechanism that monitors those crucial events. In response to defects in synapsis and/or recombination, this checkpoint blocks or delays progression of meiosis, preventing the formation of aberrant gametes. Meiotic recombination occurs in the context of chromatin and histone modifications, which play crucial roles in the maintenance of genomic integrity. Here, we unveil the role of Dot1-dependent histone H3 methylation at lysine 79 (H3K79me) in this meiotic surveillance mechanism. We demonstrate that the meiotic checkpoint function of Dot1 relies on H3K79me because, like the dot1 deletion, H3-K79A or H3-K79R mutations suppress the checkpoint-imposed meiotic delay of a synapsis-defective zip1 mutant. Moreover, by genetically manipulating Dot1 catalytic activity, we find that the status of H3K79me modulates the meiotic checkpoint response. We also define the phosphorylation events involving activation of the meiotic checkpoint effector Mek1 kinase. Dot1 is required for Mek1 autophosphorylation, but not for its Mec1/Tel1-dependent phosphorylation. Dot1-dependent H3K79me also promotes Hop1 activation and its proper distribution along zip1 meiotic chromosomes, at least in part, by regulating Pch2 localization. Furthermore, HOP1 overexpression bypasses the Dot1 requirement for checkpoint activation. We propose that chromatin remodeling resulting from unrepaired meiotic DSBs and/or faulty interhomolog interactions allows Dot1-mediated H3K79-me to exclude Pch2 from the chromosomes, thus driving localization of Hop1 along chromosome axes and enabling Mek1 full activation to trigger downstream responses, such as meiotic arrest.
A Review of Cognitive Dissonance Theory in Management Research

Since its introduction to the social psychology literature 60 years ago, Festinger’s cognitive dissonance theory (CDT) has been frequently applied to the management literature to explain and predict the motivational nature of dissonance in producing attitude and behavior change in managerial decision making and the broader organizational context. Yet many of the popular constructs that stem from CDT have since lost touch with more recent developments in the field of origin. In this paper, we provide a review of the key constructs and predictions associated with CDT from Festinger’s early work to the latest developments. We then review key management research that has incorporated CDT. Drawing from the latest refinements to CDT, we describe how future management studies could benefit by integrating these refinements into their theoretical frameworks, rather than simply relying on Festinger’s seminal work on the 60th anniversary of its publication (1957).
Underestimation of the Calculated Area Under the Concentration-Time Curve Based on Serum Creatinine for Vancomycin Dosing

Background The ratio of the steady-state 24-hour area under the concentration-time curve (ssAUC24) to the MIC (AUC24/MIC) for vancomycin has been recommended as the preferred pharmacodynamic index. The aim of this study was to assess whether the calculated AUC24 (cAUC24) using the creatinine clearance (CLcr) differs from the ssAUC24 based on the individual pharmacokinetic data estimated by a commercial software. Materials and Methods The cAUC24 was compared with the ssAUC24 with respect to age, body mass index, and trough concentration of vancomycin and the results were expressed as median and interquartile ranges. A correlation between the cAUC24 and ssAUC24 and the trough concentration of vancomycin was evaluated. The probability of reaching an AUC24/MIC of 400 or higher was compared between the cAUC24 and ssAUC24 for different MICs of vancomycin and different daily doses by simulation in a subgroup with a trough concentration of 10 mg/L and higher. Results The cAUC24 was significantly lower than the ssAUC24 (392.38 vs. 418.32 mg·hr/L, P < 0.0001) and correlated weakly with the trough concentration (r = 0.649 vs. r = 0.964). Assuming a MIC of 1.0 mg/L, the probability of reaching the value of 400 or higher was 77.5% for the cAUC24/MIC and 100% for the ssAUC24/MIC in patients with a trough concentration of 10 mg/L and higher. If the MIC increased to 2.0 mg/L, the probability was 57.7% for the cAUC24/MIC and 71.8% for the ssAUC24/MIC at a daily vancomycin dose of 4,000 mg. Conclusions The cAUC24 using the calculated CLcr is usually underestimated compared with the ssAUC24 based on individual pharmacokinetic data. Therefore, to obtain a more accurate AUC24, therapeutic monitoring of vancomycin rather than a simple calculation based on the CLcr should be performed, and a more accurate biomarker for renal function is needed.
Chromatographic Behaviour Predicts the Ability of Potential Nootropics to Permeate the Blood-Brain Barrier

The log BB parameter is the logarithm of the ratio of a compound’s equilibrium concentrations in the brain tissue versus the blood plasma. This parameter is a useful descriptor in assessing the ability of a compound to permeate the blood-brain barrier. The aim of this study was to develop a Hansch-type linear regression QSAR model that correlates the parameter log BB and the retention time of drugs and other organic compounds on a reversed-phase HPLC containing an embedded amide moiety. The retention time was expressed by the capacity factor log k′. The second aim was to estimate the brain’s absorption of 2-(azacycloalkyl)acetamidophenoxyacetic acids, which are analogues of piracetam, nefiracetam, and meclofenoxate. Notably, these acids may be novel nootropics. Two simple regression models that relate log BB and log k′ were developed from an assay performed using a reversed-phase HPLC that contained an embedded amide moiety. Both the quadratic and linear models yielded statistical parameters comparable to previously published models of log BB dependence on various structural characteristics. The models predict that four members of the substituted phenoxyacetic acid series have a strong chance of permeating the barrier and being absorbed in the brain. The results of this study show that a reversed-phase HPLC system containing an embedded amide moiety is a functional in vitro surrogate of the blood-brain barrier. These results suggest that racetam-type nootropic drugs containing a carboxylic moiety could be more poorly absorbed than analogues devoid of the carboxyl group, especially if the compounds penetrate the barrier by a simple diffusion mechanism.
Addition of inspiratory resistance increases the amplitude of the slow component of O2 uptake kinetics.

The contribution of respiratory muscle work to the development of the O(2) consumption (Vo(2)) slow component is a point of controversy because it has been shown that the increased ventilation in hypoxia is not associated with a concomitant increase in Vo(2) slow component. The first purpose of this study was thus to test the hypothesis of a direct relationship between respiratory muscle work and Vo(2) slow component by manipulating inspiratory resistance. Because the conditions for a Vo(2) slow component specific to respiratory muscle can be reached during intense exercise, the second purpose was to determine whether respiratory muscles behave like limb muscles during heavy exercise. Ten trained subjects performed two 8-min constant-load heavy cycling exercises with and without a threshold valve in random order. Vo(2) was measured breath by breath by using a fast gas exchange analyzer, and the Vo(2) response was modeled after removal of the cardiodynamic phase by using two monoexponential functions. As anticipated, when total work was slightly increased with loaded inspiratory resistance, slight increases in base Vo(2), the primary phase amplitude, and peak Vo(2) were noted (14.2%, P < 0.01; 3.5%, P > 0.05; and 8.3%, P < 0.01, respectively). The bootstrap method revealed small coefficients of variation for the model parameter, including the slow-component amplitude and delay (15 and 19%, respectively), indicating an accurate determination for this critical parameter. The amplitude of the Vo(2) slow component displayed a 27% increase from 8.1 +/- 3.6 to 10.3 +/- 3.4 ml. min(-1). kg(-1) (P < 0.01) with the addition of inspiratory resistance. Taken together, this increase and the lack of any differences in minute volume and ventilatory parameters between the two experimental conditions suggest the occurrence of a Vo(2) slow component specific to the respiratory muscles in loaded condition.
Gender Bias in International Relations Graduate Education? New Evidence from Syllabi

ABSTRACT Gender diversity is good for the study of international relations (IR) and political science. Graduate training is an opportunity for scholars to affect the demographics of their field and the gendered practices within it. This article presents a first-cut investigation of the degree to which gender bias exists in graduate IR syllabi. The author found that the gender of the instructor for graduate courses matters significantly for what type of research is taught, in two ways. First, on average, female instructors assign significantly more research by female authors than male instructors. Second, women appear to be considerably more reluctant than men about assigning their own research as required readings. Some but not all of the difference between male- and female-taught courses might be explained by differences in course composition.