Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling a Hox Gene Network

The Hox genes show a striking segment specific pattern of expression in a variety of vertebrate embryos, and have been the topic of many experimental analyses. There are now sufficient data to construct a higher-level model for the interaction and regulation of the Hox genes. This thesis presents the results of an investigation into a regulatory network for the early Hox genes. Instead of using conventional differential equation approaches for analyzing the system, a stochastic simulation algorithm has been employed to model the network. The model can track the behavior of each component of a biochemical pathway and produce computerized movies of the time evolution of the system that is a result of the dynamic interplay of these various components. The simulation is able to reproduce key features of the wild-type pattern of gene expression, and in silico experiments yield results similar to their corresponding in vivo experiments. This work shows the utility of using stochastic methods to model biochemical networks and expands the stochastic simulation algorithm methodology to work in multi-cellular systems. In addition, the model has suggested several predictions that can be tested in vivo. A tight connection was also created between the modeling and laboratory experiments. To investigate a connection between two components of the network, retinoic acid (RA) and Hoxa1, a novel laboratory experiment was performed to perturb the system. An RA soaked bead was implanted into the neural tube of a developing chick embryo and the effect of the exogenous RA was assayed with an in situ hybridization for the gene Hoxa1. The resulting expression patterns suggested that one aspect of the model v design was not accurate, and based on these results the model was modified to encompass the new data, without losing the fit to the original data sets. The thesis work was therefore brought full circle, thus showing the utility of an interconnected effort: the act of constructing and using the model identified interesting biology questions, and the answer to one of those questions was used to enhance the model. vi Table of
Influence of shape and gradient refractive index in the accommodative changes of spherical aberration in nonhuman primate crystalline lenses.

PURPOSE To estimate changes in surface shape and gradient refractive index (GRIN) profile in primate lenses as a function of accommodation. To quantify the contribution of surface shape and GRIN to spherical aberration changes with accommodation. METHODS Crystalline lenses from 15 cynomolgus monkeys were studied in vitro under different levels of accommodation produced by a stretching system. Lens shape was obtained from optical coherence tomography (OCT) cross-sectional images. The GRIN was reconstructed with a search algorithm using the optical path measured from OCT images and the measured back focal length. The spherical aberration of the lens was estimated as a function of accommodation using the reconstructed GRIN and a homogeneous refractive index. RESULTS The lens anterior and posterior radii of curvature decreased with increasing lens power. Both surfaces exhibited negative asphericities in the unaccommodated state. The anterior surface conic constant shifted toward less negative values with accommodation, while the value of the posterior remained constant. GRIN parameters remained constant with accommodation. The lens spherical aberration with GRIN distribution was negative and higher in magnitude than that with a homogeneous equivalent refractive index (by 29% and 53% in the unaccommodated and fully accommodated states, respectively). Spherical aberration with the equivalent refractive index shifted with accommodation toward negative values (-0.070 μm/diopter [D]), but the reconstructed GRIN shifted it farther (-0.124 μm/D). CONCLUSIONS When compared with the lens with the homogeneous equivalent refractive index, the reconstructed GRIN lens has more negative spherical aberration and a larger shift toward more negative values with accommodation.
Comparison of Motor Inhibition in Variants of the Instructed-Delay Choice Reaction Time Task

Using instructed-delay choice reaction time (RT) paradigms, many previous studies have shown that the motor system is transiently inhibited during response preparation: motor-evoked potentials (MEPs) elicited by transcranial magnetic stimulation (TMS) over the primary motor cortex are typically suppressed during the delay period. This effect has been observed in both selected and non-selected effectors, although MEP changes in selected effectors have been more inconsistent across task versions. Here, we compared changes in MEP amplitudes in three different variants of an instructed-delay choice RT task. All variants required participants to choose between left and right index finger movements but the responses were either provided “in the air” (Variant 1), on a regular keyboard (Variant 2), or on a response device designed to control from premature responses (Variant 3). The task variants also differed according to the visual layout (more concrete in Variant 3) and depending on whether participants received a feedback of their performance (absent in Variant 1). Behavior was globally comparable between the three variants of the task although the propensity to respond prematurely was highest in Variant 2 and lowest in Variant 3. MEPs elicited in a non-selected hand were similarly suppressed in the three variants of the task. However, significant differences emerged when considering MEPs elicited in the selected hand: these MEPs were suppressed in Variants 1 and 3 whereas they were often facilitated in Variant 2, especially in the right dominant hand. In conclusion, MEPs elicited in selected muscles seem to be more sensitive to small variations to the task design than those recorded in non-selected effectors, probably because they reflect a complex combination of inhibitory and facilitatory influences on the motor output system. Finally, the use of a standard keyboard seems to be particularly inappropriate because it encourages participants to respond promptly with no means to control for premature responses, probably increasing the relative amount of facilitatory influences at the time motor inhibition is probed.
Female-demand/male-withdraw communication in Argentinian couples: A mediating factor between economic strain and relationship distress

Based on a dyadic version of R. D. Conger and colleagues' stress model, this study examined whether the demand/withdraw pattern in couples' communication mediates the association between partners' economic strain and their level of relationship distress. Data were from self-report questionnaires completed by 144 heterosexual couples seeking psychotherapy at a community clinic in Argentina 3 years after a major national economic crisis. As hypothesized, results from a path model analysis suggested that (a) regardless of provider role, females tended to experience more economic strain than males did; (b) the female-demand/male-withdraw pattern, but not the male-demand/female-withdraw pattern, mediated the positive association between economic strain and relationship distress; and (c) both partners' levels of relationship distress were affected by both patterns of demand/withdraw communication. Gender differences are discussed based on the gender role expectations in Argentina and the stress coping and demand/withdraw communication literatures. Study limitations and implications of the findings for research, programmatic approaches, and therapeutic interventions for couples under economic stress are considered. This study makes important contributions to our understanding of gender differences and the role of demand/withdraw communication in couples' responses to economic strain.
Techniques for Data Mapping and Buffering to Exploit Asymmetry in Multi-Level Cell (Phase Change) Memory

Phase Change Memory (PCM) is a promising alternative to DRAM to achieve high memory capacity at low cost per bit. Adding to its better projected scalability, PCM can also store multiple bits per cell (called multi-level cell, MLC), offering higher bit density. However, MLC requires precise sensing and control of PCM cell resistance, which incur higher memory access latency and energy. We propose a new approach to mapping and buffering data in MLC PCM to improve memory system performance and energy efficiency. The latency and energy to read or write to MLC PCM varies depending on the resistance state of the multi-level cell, such that one bit in a multi-bit cell can be accessed at lower latency and energy than another bit in the same cell. We propose to exploit this asymmetry between the different bits by decoupling the bits and mapping them to logically separate memory addresses. This exposes reduced read latency and energy in one half of the memory space, and reduced write latency and energy in the other half of memory, to system software. We effectively utilize the reduced latency and energy by mapping read-intensive pages to the read-efficient half of memory, and write-intensive pages to the write-efficient half. Decoupling the bits also provides flexibility in the way data is buffered in the memory device, which we exploit to manipulate the physical row buffer as two logical row buffers for increased data locality in the row buffer. Our evaluations for a multi-core system show that our proposal improves system performance by 19.2%, memory energy efficiency by 14.4%, and thread fairness by 19.3% over the state-of-the-art MLC PCM baseline system that does not employ bit decoupling. The improvements are robust across a wide variety of workloads and system configurations.
ECUE: A Spam Filter that Uses Machine Learning to Track Concept Drift

While text classification has been identified for some time as a promising application area for Artificial Intelligence, so far few deployed applications have been described. In this paper we present a spam filtering system that uses example-based machine learning techniques to train a classifier from examples of spam and legitimate email. This approach has the advantage that it can personalise to the specifics of the user's filtering preferences. This classifier can also automatically adjust over time to account for the changing nature of spam (and indeed changes in the profile of legitimate email). A significant software engineering challenge in developing this system was to ensure that it could interoperate with existing email systems to allow easy managment of the training data over time. This system has been deployed and evaluated over an extended period and the results of this evaluation are presented here.
Psychological and Physical Health in Military Amputees During Rehabilitation: Secondary Analysis of a Randomized Controlled Trial.

BACKGROUND Service members who have experienced combat trauma with resulting amputation are at risk for compromised quality of life postamputation. Monitoring mental and physical health in amputees returning from the war is of paramount importance. This study examined changes in physical and mental health-related quality of life in service members following traumatic unilateral, transtibial amputation (TTA) during a 12-week period of rehabilitation before and after receiving a prosthesis. METHOD This study is a secondary analysis from a randomized controlled trial (RCT) of military service members starting Military Amputee Rehabilitation Program (MARP) following a traumatic TTA. The study examined change in SF-36 Physical Component Summary (PCS) and Mental Component Summary (MCS) scores as two aspects of health-related quality of life. Forty-four injured service members, aged 19 to 46, were recruited into the RCT. Participants were randomized into 12 weeks of MARP plus home neuromuscular electrical stimulation therapy (n = 23) or MARP alone (N = 21) and compared at baseline, 6, and 12 weeks on: SF-36 PCS and MCS scores. Linear mixed models examined time and group differences and their interaction for the MCS and PCS scores. A multivariate mixed model tested whether MCS and PCS scores differed. RESULTS For the combined rehabilitation cohort, MCS did not differ over 12 weeks (p = 0.27) with scores at week 0 of M = 56.7 (SD = 11.9) and at week 12 of M = 52.7 (SD = 11.4), similar to healthy controls (age = 25-34, M = 51.0, SD = 7.6). Scores did not differ between treatment groups (p = 0.28) with no group by time interaction (p = 0.34). The MCS significantly declined over time (p = 0.05) after adjustment for covariates. PCS improved over 12 weeks (p < 0.0001) in the total rehabilitation group with scores at week 0 of M = 34.0 (SD = 8.1) to M = 41.8 (SD = 8.4) at week 12, significantly lower than healthy controls (age = 25-34, M = 54.1, SD = 6.6). Scores did not differ between treatment groups (p = 0.89), and there was no group by time interaction (p = 0.34). An interaction between the PCS and MCS was observed such that the PCS improved over time, whereas the MCS did not significantly change (p = 0.0005). DISCUSSION War-injured transtibial amputees are at risk for compromised quality of life during rehabilitation. Self-perceived physical health improved as might be expected from rehabilitation. Self-perceived mental health did not. During rehabilitation, physical healing, psychological adjustment, and lifestyle adaptation are occurring simultaneously. However, more attention may need to be directed toward mental health during rehabilitation.
Internationalisation, Ethnic Diversity and the Acquisition of Intercultural Competencies

This paper sheds light on the pedagogical processes involved in intercultural study environments and their effects on students. Studying "abroad" or in an ethnically diverse context "at home" is described metaphorically as an academic, cultural, intellectual and emotional journey that facilitates the acquisition of intercultural competencies as well as personal growth. It is stressed that universities have much to gain from approaching internationalisation and ethnic diversity in an integrated fashion. The situational character of the teacher's role in this process is also stressed. The discussion arrives at an interactive model of intercultural learning.
Inhibitory effect of zinc on glucose‐stimulated zinc/insulin secretion in an insulin‐secreting β‐cell line

• What is the central question of this study? The main aim of the present study was to determine glucose‐stimulated zinc secretion and the effect of zinc on glucose‐stimulated insulin secretion in pancreatic β‐cells. • What is the main finding and its importance? Using a newly developed approach, we demonstrated a robust glucose‐stimulated zinc secretion. Importantly, the application of zinc inhibited glucose‐stimulated insulin secretion. Our findings provide evidence that zinc, after being secreted, can regulate the insulin secretion of β‐cells by a negative feedback mechanism.
Microbial Community Degradation of Widely Used Quaternary Ammonium Disinfectants

ABSTRACT Benzalkonium chlorides (BACs) are disinfectants widely used in a variety of clinical and environmental settings to prevent microbial infections, and they are frequently detected in nontarget environments, such as aquatic and engineered biological systems, even at toxic levels. Therefore, microbial degradation of BACs has important ramifications for alleviating disinfectant toxicity in nontarget environments as well as compromising disinfectant efficacy in target environments. However, how natural microbial communities respond to BAC exposure and what genes underlie BAC biodegradation remain elusive. Our previous metagenomic analysis of a river sediment microbial community revealed that BAC exposure selected for a low-diversity community, dominated by several members of the Pseudomonas genus that quickly degraded BACs. To elucidate the genetic determinants of BAC degradation, we conducted time-series metatranscriptomic analysis of this microbial community during a complete feeding cycle with BACs as the sole carbon and energy source under aerobic conditions. Metatranscriptomic profiles revealed a candidate gene for BAC dealkylation, the first step in BAC biodegradation that results in a product 500 times less toxic. Subsequent biochemical assays and isolate characterization verified that the putative amine oxidase gene product was functionally capable of initiating BAC degradation. Our analysis also revealed cooperative interactions among community members to alleviate BAC toxicity, such as the further degradation of BAC dealkylation by-products by organisms not encoding amine oxidase. Collectively, our results advance the understanding of BAC aerobic biodegradation and provide genetic biomarkers to assess the critical first step of this process in nontarget environments.
Solving Fully Fuzzy Linear System with the Necessary and Sufficient Condition to have a Positive Solution

This paper proposes new matrix methods for solving positive solutions for a positive Fully Fuzzy Linear System (FFLS). All coefficients on the right hand side are collected in one block matrix, while the entries on the left hand side are collected in one vector. Therefore, the solution can be gained with a non-fuzzy common step. The necessary theorems are derived to obtain a necessary and sufficient condition in order to obtain the solution.The solution for FFLS is ob tained where the entries of coefficients are unknown. The methods and results are also capable of solving Left-Right Fuzzy Linear System (LR-FLS). To best illustrate the proposed methods, numerical examples are solved and compared to the existing methods to show the efficiency of the proposed method. New numerical examples are presented to demonstrate the contributions in this paper.
Aggression and Preference for First-Person Shooter and Action Games: Data From a Large-Scale Survey of German Gamers Aged 14 and Above

Cross-sectional studies on video game violence and aggression have yielded contradictory results. Parts of this inconclusiveness can be attributed to the limitation to particular age groups. The present study investigated the relationship between preference for action and first-person shooter (FPS) games and aggression for the groups of adolescents (14–18), younger (19–39), and older adults (40+) in a sample of German gamers (N = 4,500). The strength of the association differed between age groups. Even after controlling for gender, education, social support, self-efficacy, and overall video game use, we found a significant relationship between preference for action and FPS games and physical aggression that was strongest for the adolescents. We found no such association for anger and verbal aggression. The results indicate that potential selection or socialization effects are likely to differ with age and that research on video games and aggression can benefit from the inclusion of more heterogeneous samples.
Development, Freedom, and Rising Happiness: A Global Perspective (1981–2007)

Until recently, it was widely held that happiness fluctuates around set points, so that neither individuals nor societies can lastingly increase their happiness. Even though recent research showed that some individuals move enduringly above or below their set points, this does not refute the idea that the happiness levels of entire societies remain fixed. Our article, however, challenges this idea: Data from representative national surveys carried out from 1981 to 2007 show that happiness rose in 45 of the 52 countries for which substantial time-series data were available. Regression analyses suggest that that the extent to which a society allows free choice has a major impact on happiness. Since 1981, economic development, democratization, and increasing social tolerance have increased the extent to which people perceive that they have free choice, which in turn has led to higher levels of happiness around the world, as the human development model suggests.
Photosynthesis, Light Use Efficiency, and Yield of Reduced-Chlorophyll Soybean Mutants in Field Conditions

Reducing chlorophyll (chl) content may improve the conversion efficiency of absorbed photosynthetically active radiation into biomass and therefore yield in dense monoculture crops by improving light penetration and distribution within the canopy. The effects of reduced chl on leaf and canopy photosynthesis and photosynthetic efficiency were studied in two reportedly robust reduced-chl soybean mutants, Y11y11 and y9y9, in comparison to the wild-type (WT) “Clark” cultivar. Both mutants were characterized during the 2012 growing season whereas only the Y11y11 mutant was characterized during the 2013 growing season. Chl deficiency led to greater rates of leaf-level photosynthesis per absorbed photon early in the growing season when mutant chl content was ∼35% of the WT, but there was no effect on photosynthesis later in the season when mutant leaf chl approached 50% of the WT. Transient benefits of reduced chl at the leaf level did not translate to improvements in canopy-level processes. Reduced pigmentation in these mutants was linked to lower water use efficiency, which may have dampened any photosynthetic benefits of reduced chl, especially since both growing seasons experienced significant drought conditions. These results, while not confirming our hypothesis or an earlier published study in which the Y11y11 mutant significantly outyielded the WT, do demonstrate that soybean significantly overinvests in chl. Despite a >50% chl reduction, there was little negative impact on biomass accumulation or yield, and the small negative effects present were likely due to pleiotropic effects of the mutation. This outcome points to an opportunity to reinvest nitrogen and energy resources that would otherwise be used in pigment-proteins into increasing biochemical photosynthetic capacity, thereby improving canopy photosynthesis and biomass production.
Consensus and controversy

The word ’consensus’, of course, is spelled with an ’s’ because it is etymologically related to the words ’consent’ and ’sense’ as in agreeing or having a sense of direction rather than ’census’ or ’cents’ as in counting heads or tossing coins. However, in Alan Davies’s review of Issues in language testing research (ILTR; edited by yours truly, published by Newbury House in 1983), the word ‘consensus’ is about as distant from its correct spelling and etymology as the reviewer is from the facts addressed in ILTR. The contrast between the correct etymology and the erroneous one used three times in the review, is roughly parallel to the fundamental difference in Davies’s approach
A person-oriented approach in research on developmental psychopathology

There is a growing acceptance of a holistic, interactionistic view in which the individual is seen as an organized whole, functioning and developing as a totality. This view emphasizes the importance of patterns of operating factors. Within this framework, a standard variable-oriented approach, focusing on the variable as the main theoretical and analytical unit, has limitations. A person-oriented approach would often be preferable, where the main theoretical and analytical unit is the specific pattern of operating factors. Such an approach is presented here, focusing on individual development and psychopathology. A brief theoretical and methodological overview is given and a classification approach is emphasized. Empirical examples concerning the longitudinal study of adjustment problems illustrate a number of issues believed to be important to development and psychopathology: problem gravitation, the significance of single variables and of patterns, the developmental study of syndromes (=typical patterns), and the detection of “white spots” in development.