Miracle-dz/UniFAR-FTUs huggingface dataset:
The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype–phenotype maps

Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype–phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into ‘constrained' and ‘unconstrained' sequences, in the broadest possible sense. As ‘constrained' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. ‘Unconstrained' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with ‘coding' and ‘non-coding' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps.
Elucidating the Signal Responses of Multi-Parametric Surface Plasmon Resonance Living Cell Sensing: A Comparison between Optical Modeling and Drug–MDCKII Cell Interaction Measurements

In vitro cell-based assays are widely used during the drug discovery and development process to test the biological activity of new drugs. Most of the commonly used cell-based assays, however, lack the ability to measure in real-time or under dynamic conditions (e.g. constant flow). In this study a multi-parameter surface plasmon resonance approach in combination with living cell sensing has been utilized for monitoring drug-cell interactions in real-time, under constant flow and without labels. The multi-parameter surface plasmon resonance approach, i.e. surface plasmon resonance angle versus intensity plots, provided fully specific signal patterns for various cell behaviors when stimulating cells with drugs that use para- and transcellular absorption routes. Simulated full surface plasmon resonance angular spectra of cell monolayers were compared with actual surface plasmon resonance measurements performed with MDCKII cell monolayers in order to better understand the origin of the surface plasmon resonance signal responses during drug stimulation of cells. The comparison of the simulated and measured surface plasmon resonance responses allowed to better understand and provide plausible explanations for the type of cellular changes, e.g. morphological or mass redistribution in cells, that were induced in the MDCKII cell monolayers during drug stimulation, and consequently to differentiate between the type and modes of drug actions. The multi-parameter surface plasmon resonance approach presented in this study lays the foundation for developing new types of cell-based tools for life science research, which should contribute to an improved mechanistic understanding of the type and contribution of different drug transport routes on drug absorption.
THE RELATIONSHIP BETWEEN PRAYERS AND RELIGIOUS ORIENTATION WITH MENTAL HEALTH

Abstract Introduction: This study was conducted to determine the correlation of attending to prayers and religious orientation with mental health among university employees and non-employees. Methods: The study population consisted of 150 university employees and 150 non-employees, who were individually selected. All 300 participants filled out Alport’s religious orientation scale and Goldberg general health questionnaire. The data were analyzed using chi square and t test. Results: The results showed that university employees and non-employees were significantly different with regards to attending to prayers (P Conclusion: With respect to the role of prayers and religious orientation in mental health, it seems cultural authorities of the society especially the ones in the university should pay special attention to and plan special programs to reinforce prayers.
Standard metabolism and growth dynamics of laboratory-reared larvae of Sardina pilchardus.

This study provides the first measurements of the standard respiration rate (R(S)) and growth dynamics of European sardine Sardina pilchardus larvae reared in the laboratory. At 15° C, the relationship between RS (µl O(2) individual(-1) h(-1)) and larval dry mass (M(D), µg) was equal to: R(S) = 0·0057(±0·0007, ± s.e.)·M(D) (0·8835(±0·0268)), (8-11% M(D) day(-1)). Interindividual differences in RS were not related to interindividual differences in growth rate or somatic (Fulton's condition factor) or biochemical-based condition (RNA:DNA).
The Role of the Instrumental Contingency in the Motivational Control of Performance

In four experiments we investigated an irrelevant incentive effect based upon a transition from hunger to thirst. Hungry rats were trained to lever press either for sucrose solution or for food pellets before performance was tested in extinction while they were thirsty. Reinforcer-specific motivational control was found in the first experiment in that the animals pressed the lever more on tests following training with the sucrose solution rather than with food pellets. Moreover, this effect was seen only when testing was conducted following water, but not following food deprivation. The outcome of the remaining experiments suggests that this motivational control is not mediated by the instrumental contingency between lever pressing and the sucrose reinforcer during training. In these studies lever pressing and chain pulling were reinforced concurrently, one with sucrose and the other with food pellets, in order to equate the noninstrumental functions of the incentives. Following this training, lever pressing in extinction under thirst was unaffected by the type of incentive used as its reinforcer during training.
Viewing information needs through a Johari Window

Purpose – The purpose of this paper is to apply to the study of information needs the Johari Window framework that has long been accepted as a useful model for understanding interpersonal communication.Design/methodology/approach – The work presents a newly‐constructed version of the Window to delineate a typology of information needs and to identify implications that emerge for information professionals.Findings – The paper finds that information needs can be seen to fall into five broad categories: needs that are known to the individual but not to the information professional; needs that are known to both parties; needs that are known to the information professional but not the individual; needs that are misunderstood by the individual; and needs that are not known to either the individual or the information professional.Practical implications – Conceptualising information needs in terms of the revised Johari Window highlights how information professionals are of crucial importance in helping clients sa.
Photorefractoriness in broiler breeders: Sexual maturity and egg production evidence

1. Photorefractoriness was assessed in two lines of broiler breeders. In one trial, male-line and female-line pullets were reared on the floor and transferred to individual cages at 15 weeks. Birds were either maintained on 8-, 11- or 16-h photoperiods or transferred from 8- to 16-h photoperiods at 67 or 124 d. In the second trial, female-line pullets were concurrently housed in the same rearing facilities as trial 1 and transferred to adult floor-pens at 12 weeks. These birds were either maintained on 11- or 16-h photoperiods or transferred from 8- to 11-h or from 8- to 16-h photoperiods at 140 d. 2. In the cages, male-line and female-line birds responded similarly to the lighting treatments, but with the male-line maturing 1 to 2 weeks later than the female-line in each case. Birds on constant 11-h photoperiods matured 3 to 8 d earlier than constant 8-h birds, but 3 weeks earlier than constant 16-h birds. Birds photostimulated at 67 d matured at a similar time to constant 16-h birds, but almost 7 weeks later than those transferred from 8 to 16 h at 124 d. In the floor facilities, constant 11-h birds matured 3 weeks earlier than constant 16-h birds, but almost 2 weeks later than either of the photostimulated groups. Birds transferred from 8 to 16 h matured 4 d earlier than those transferred from 8 to 11 h. 3. Caged birds maintained on 16 h or transferred from 8 to 16 h at 67 d laid at least 24 fewer eggs, and had more hens not laying at 58 weeks, than birds maintained on 11-h days or those transferred from 8 to 16 h at 124 d. In the floor-pens, constant 11-h and both photostimulated groups produced about 20 more eggs to 56 weeks of age than the constant 16-h controls. 4. Collectively, these findings indicate that conventionally managed broiler breeders exhibit photorefractoriness. Additionally, a combination of photorefractoriness and controlled feeding appears to prevent broiler breeders from being photoresponsive until at least 10 weeks of age, and to cause some individuals still to be photoperiodically non-responsive at 18 weeks.
Data transmission over single-mode fiber by using 1.2-μm uncooled GaInAs-GaAs laser for Gb/s local area network

We demonstrate 2-Gb/s data transmission through a 5-km-long standard single-mode fiber by using a GaAs-based 1.2-/spl mu/m GaInAs-GaAs quantum well laser. The fabricated laser exhibits a high characteristic temperature of 140 K. The results indicate the possibility of Gigabit/s local area networks (LANs) using uncooled lasers (possibly surface-emitting lasers) operating at a 1.2-/spl mu/m wavelength band.
Nurse-Led Telephone Follow-up: Improving Options for Women With Endometrial Cancer

Background: Nurse-led follow-up (NLFU) has been identified as a suitable means of follow-up care in cancer patients, and its acceptability has already been demonstrated in other areas of cancer care. Objectives: The objectives of this study were to evaluate the effect of NLFU on quality of life and patient satisfaction compared with conventional follow-up (CFU) in women treated for endometrial cancer and to evaluate the feasibility of NLFU, in terms of patient acceptance and referral to consultant clinic. Methods: Participants included women diagnosed with endometrial cancer between 2008 and 2013. At time of study, 118 women were receiving NLFU, and 178 women were receiving CFU. Quality of life and patient satisfaction were evaluated through the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire and the In-patient Satisfaction With Care Measure questionnaires. Feasibility of NLFU was retrospectively assessed through patient’s records. Results: Seventy-eight women in NLFU and 112 women in CFU completed the questionnaires. Quality-of-life outcomes and satisfaction levels did not differ between both forms of follow-up. Almost all women in NLFU (98%) found NLFU an acceptable alternative to CFU. Conclusion: Women receiving NLFU reported similar quality of life and satisfaction with care as did women in CFU, making it a promising alternative for follow-up care of women with endometrial cancer. Implications for Practice: Options are improved for women with endometrial cancer by offering alternative follow-up strategies within the national healthcare.
Joint Effect of Alcohol Consumption and Educational Level on Alcohol-related Medical Events: A Danish Register-based Cohort Study

Background: Alcohol-related mortality is more pronounced in lower than in higher socioeconomic groups in Western countries. Part of the explanation is differences in drinking patterns. However, differences in vulnerability to health consequences of alcohol consumption across socioeconomic groups may also play a role. We investigated the joint effect of alcohol consumption and educational level on the rate of alcohol-related medical events. Methods: We pooled seven prospective cohorts from Denmark that enrolled 74,278 men and women age 30–70 years (study period, 1981 to 2009). We measured alcohol consumption at baseline using self-administrated questionnaires. Information on highest attained education 1 year before study entry and hospital and mortality data on alcohol-related medical events were obtained through linkage to nationwide registries. We performed analyses using the Aalen additive hazards model. Results: During follow-up (1,085,049 person-years), a total of 1718 alcohol-related events occurred. The joint effect of very high alcohol consumption (>21 [>28] drinks per week in women [men]) and low education on alcohol-related events exceeded the sum of their separate effects. Among men, we observed 289 (95% confidence interval = 123, 457) extra events per 100,000 person-years owing to education–alcohol interaction (P < 0.001). Similarly, among women, we observed 239 (95% confidence interval = 90, 388) extra events per 100,000 person-years owing to this interaction (P < 0.001). Conclusions: High alcohol consumption is associated with a higher risk of alcohol-related medical events among those with low compared with high education. This interaction may be explained by differences in vulnerability and drinking patterns across educational groups. See video abstract at, http://links.lww. com/EDE/B267.
Zero singularities of codimension two and three in delay differential equations

We give conditions under which a general class of delay differential equations has a point of Bogdanov–Takens or a triple zero bifurcation. We show how a centre manifold projection of the delay equations reduces the dynamics to two- or three-dimensional systems of ordinary differential equations. We put these equations in normal form and determine how the coefficients of the normal forms depend on the original parameters in the model. Finally we apply our results to two neural models and compare the predictions of the theory with numerical bifurcation analysis of the full equations. One model involves a transcritical bifurcation, hence we derive and analyse the appropriate unfoldings for this case.
Exploratory homeworks: an active learning tool for textbook reading

Constructivist learning theory suggests that learners must construct their own understandings, rather than have understanding passively dumped into their brains. These findings support the US National Research Council's recommendations for the adoption of active learning pedagogies in the classroom. However, the "classroom lecture" is only one of the resources students commonly have for learning in higher education. In this paper, we present exploratory homeworks -- a tool to support active learning for teaching programming languages. By leveraging the opportunity for the student to interact with the computer/compiler, we seek to provide a model for students of how to explore and understand programming language constructs and concepts. We report on the use of 15 exploratory homework assignments used in a CS0 course with 440 students in Winter 2011. We provide a model and advice for others wishing to develop exploratory homeworks for their programming courses and present quantitative and qualitative evidence regarding students' positive valuation of the homeworks.
Evaluation of the radiopacity of calcium silicate cements containing different radiopacifiers.

AIM To identify the suitable ratio of alternative radiopacifiers to impart the necessary radiopacity to calcium silicate cements (CSC) and assess the purity of the radiopacifying agents. METHODOLOGY Alternative radiopacifying materials for incorporation into CSC included barium sulphate, titanium oxide, zinc oxide, gold powder and silver/tin alloy. The chemical composition of the alternative radipacifying materials and bismuth oxide, which is used in mineral trioxide aggregate (MTA), was determined using energy dispersive X-ray analysis. In addition, using an aluminium step-wedge and densitometer, the radiopacity of each material was evaluated as recommended by international standards. The optical density was compared with the relevant thickness of aluminium (Al). A commercial MTA and CSC were used as controls. Statistical analysis comparing the radiodensity of the different cements to MTA was performed using anova with P = 0.05 and post hoc Tukey test. RESULTS All percentage replacements of bismuth oxide, gold and silver-tin alloy powder, and the 25% and 30% replacements with barium sulphate and zinc oxide had radiopacities greater than 3 mm thickness of aluminium (Al) recommended by ISO 6876 (2002). The 25% replacement of cement with gold powder and 20% replacement of cement with silver/tin alloy powder exhibited radiopacity values of 8.04 mm Al and 7.52 mm Al, respectively, similar to MTA (P > 0.05). The cement replaced with 20% bismuth oxide showed a radiopacity of 6.83 mm Al, lower than MTA (P = 0.003). CONCLUSIONS Silver/tin alloy and gold powder imparted the necessary radiopacity to a calcium silicate-based cement. Barium sulphate was also a suitable radiopacifier together with a lower concentration of silver/tin alloy and gold powder that achieved the radiodensity recommended by ISO 6876. Further research is required to investigate the broader properties of the calcium silicate-based cement with the different radiopacifiers.
Happiness increases verbal and spatial working memory capacity where sadness does not: Emotion, working memory and executive control

The effects of emotion on working memory and executive control are often studied in isolation. Positive mood enhances verbal and impairs spatial working memory, whereas negative mood enhances spatial and impairs verbal working memory. Moreover, positive mood enhances executive control, whereas negative mood has little influence. We examined how emotion influences verbal and spatial working memory capacity, which requires executive control to coordinate between holding information in working memory and completing a secondary task. We predicted that positive mood would improve both verbal and spatial working memory capacity because of its influence on executive control. Positive, negative and neutral moods were induced followed by completing a verbal (Experiment 1) or spatial (Experiment 2) working memory operation span task to assess working memory capacity. Positive mood enhanced working memory capacity irrespective of the working memory domain, whereas negative mood had no influence on performance. Thus, positive mood was more successful holding information in working memory while processing task-irrelevant information, suggesting that the influence mood has on executive control supersedes the independent effects mood has on domain-specific working memory.
Attendance at Religious Services and Mortality in a National Sample∗

Research and theory increasingly suggest that attendance at religious services is protective against premature mortality. However, prior studies are limited and do not extensively explore potential explanations for the relationship, especially in terms of religious beliefs and behaviors associated with service attendance. This study estimates the impact of service attendance on mortality in a national probability sample and provides the most extensive empirical examination of potential explanations. Individuals who report attending religious services once a month or more (just over 50 percent of the population) have a 30–35 percent reduced risk of death over a 7.5 year follow-up period after adjusting for potential confounding factors. Consistent with prior research, 20–30 percent of this effect may be explained by better health behaviors (especially physical activity) among regular service attendees. Surprisingly, other religious beliefs and behaviors do not explain, and often tend to suppress, the association between service attendance and mortality.
Epitope specificity and isoforms of the mycobacterial 19-kilodalton antigen

The topography and specificity of B- and T-cell stimulatory epitopes from the 19-kDa protein of Mycobacterium tuberculosis were investigated by using overlapping synthetic peptides. Murine antisera identified two cryptic epitopes (residues 11 to 30 and 61 to 80) and one species-specific immunodominant epitope (residues 140 to 159). Immunoglobulins G1 and G2a antibody isotypes varied for the respective peptide immunogens but without relationship to the T-cell cytokine profiles which were characterized by high gamma interferon and low interleukin 5 levels. Antisera to recombinant M. tuberculosis 19-kDa protein (rGST-19) cross-reacted with homologous proteins of similar size from organisms of the Mycobacterium avium-intracellulare complex. Two-dimensional gel electrophoresis revealed differences in the number, relative mobility, and charge of isoforms of the 19-kDa protein, possibly reflecting posttranslational modifications. The immunodominant T-cell epitope from the M. tuberculosis 19-kDa protein (residues 61 to 80) and the corresponding peptide sequence from Mycobacterium avium subsp. intracellulare (residues 64 to 83), differing at five residues, were both recognized in a genetically permissive manner. Peptides 61-80 and 64-83 stimulated cross-reactive responses in BALB/c (H-2d) mice, while in the C57BL/10 (H-2b) strain, responses to peptide 61-80 were species specific. In purified protein derivative-positive healthy individuals, the M. avium subsp. intracellulare peptide stimulated stronger responses than did the M. tuberculosis peptide, whereas patients with active tuberculosis had enhanced in vitro T-cell responses to both peptides.
Academically Productive Talk: One Size Does Not Fit All

We present a study in which we experimentally manipulate the form of support offered to groups of three students during collaborative learning. Specifically, we contrast two forms of Academically Productive Talk (APT) facilitation, known as Revoicing and Agree-Disagree. The first form has been demonstrated effective with the target age group (i.e., 9 th grade) on an earlier more difficult unit. The second form has been demonstrated effective with older kids. Results suggest that with this age group, facilitation with Revoicing may be more effective than Agree-Disagree. Implications for future work are discussed.