Miracle-dz/UniFAR-FTUs huggingface dataset:
A discrete particle swarm optimization algorithm for phylogenetic tree reconstruction

The similarity of molecular mechanisms of the organisms that have been studied strongly suggests that all organisms of Earth had a common ancestor. Thus any set of species is related, and the relationship is called a phylogeny. Usually a phylogenetic tree can represent the relationship. The task of phylogenetics is to infer this tree from observations upon the existing organisms. At present, the accuracy of the tree is not still ideal enough to reconstruction through the computer simulation. This paper introduce particle swarm optimization algorithm, and the discrete particle swarm optimization algorithm is used to inference and optimize the phylogenetic tree for the first time, and show the actual effect of this algorithm through the experiment.
FOUNDATIONS OF PROGRAMMED INSTRUCTION

One can gain appreciable insights to the present day status of the field of instructional technology (IT) from examining its early beginnings and the origins of current practice. Programmed Instruction (PI) was an integral factor in the evolution of the instructional design process, and serves as the foundation for the procedures in which IT professionals now engage for the development of effective learning environments. In fact, the use of the term programming was applied to the production of learning materials long before it was used to describe the design and creation of computerized outputs. Romizowski (1986) states that while PI may not have fulfilled its early promise, “the influence of the Programmed Instruction movement has gone much further and deeper than many in education care to admit” (p. 131). At the very least, PI was the first empirically determined form of instruction and played a prominent role in the convergence of science and education. Equally important is its impact on the evolution of the instructional design and development process. This chapter addresses the historical origins of PI, its underlying psychological principals and characteristics, and the design process for the generation of programmed materials. Programmed Instruction is renowned as the most investigated form of instruction, leaving behind decades of studies that examine its effectiveness. That history of PI-related inquiry is addressed herein. Finally, the chapter closes with current applications of PI and predictions for its future use. 20.1 HISTORICAL ORIGINS OF PROGRAMMED INSTRUCTION
Development and psychometric evaluation of the Interactive Test of Interpersonal Behavior (ITIB): a pilot study examining interpersonal deficits in chronic depression.

Chronic depression is assumed to be caused and maintained by interpersonal deficits. We describe the development and psychometric evaluation of the Interactive Test of Interpersonal Behavior (ITIB) that we developed for self-assessment of these deficits. Participants with chronic depression (CD, N = 15), episodic depression (ED, N = 15) and healthy controls (HC, N = 15) participated in this pilot study. They completed the ITIB and a number of pen and paper questionnaires including the Lübeck Questionnaire of Preoperational Thinking (LQPT) and the inventory of interpersonal problems (IIP). The ITIB was highly acceptable for use in these participants. Internal consistency for the ITIB was adequate for group comparisons (Cronbach's alpha = 0.649). Item-total correlations indicated adequate discriminatory power of five of the six items. The ITIB correlated moderately with the LQPT (r = 0.524) and the IIP (r = -0.568). The ITIB score differed significantly between the diagnostic groups (ANOVA F(2,42) = 6.22, p = 0.004). It was the only measure that - albeit at a trend level - was associated with diagnostic group (CD vs. ED) on multinomial logistic regression analysis (B = 0.049 ± 0.029; OR 1.051; p = 0.088). We found preliminary evidence that the ITIB is an acceptable and psychometrically adequate measure of interpersonal behavior that distinguishes between patients with CD and patients with ED. If replicated with an improved version of the test, our results could support the hypothesis that having interpersonal problems is a core deficit in patients with CD.
Nutrient and growth responses of cattail (Typha domingensis) to redox intensity and phosphate availability.

BACKGROUND AND AIMS In the Florida Everglades, the expansion of cattail (Typha domingensis) into areas once dominated by sawgrass (Cladium jamaicense) has been attributed to altered hydrology and phosphorus (P) enrichment. The objective of this study was to quantify the interactive effects of P availability and soil redox potential (Eh) on the growth and nutrient responses of Typha, which may help to explain its expansion. METHODS The study examined the growth and nutrient responses of Typha to the interactive effects of P availability (10, 80 and 500 microg P L(-1)) and Eh level (-150, +150 and +600 mV). Plants were grown hydroponically in a factorial experiment using titanium (Ti(3+)) citrate as a redox buffer. KEY RESULTS Relative growth rate, elongation, root-supported tissue/root ratio, leaf length, lateral root length and biomass, as well as tissue nutrient concentrations, were all adversely affected by low Eh conditions. P availability compensated for the negative effect of low Eh for all these variables except that low P stimulated root length and nutrient use efficiency. The most growth-promoting treatment combination was 500 microg P L(-1)/ + 600 mV. CONCLUSIONS These results, plus previous data on Cladium responses to P/Eh combinations, document that high P availability and low Eh should benefit Typha more than Cladium as the growth and tissue nutrients of the former species responded more to excess P, even under highly reduced conditions. Therefore, the interactive effects of P enrichment and Eh appear to be linked to the expansion of Typha in the Everglades Water Conservation Area 2A, where both low Eh and enhanced phosphate availability have co-occurred during recent decades.
New Iterative Algorithm for Improving Depth Resolution in Ionic Analysis: Effect of Iterations Number

— In this paper, the improvement by deconvolution of the depth resolution in Secondary Ion Mass Spectrometry (SIMS) analysis is considered. Indeed, we have developed a new Tikhonov-Miller deconvolution algorithm where a priori model of the solution is included. This is a denoisy and pre-deconvoluted signal obtained from: firstly, by the application of wavelet shrinkage algorithm, secondly by the introduction of the obtained denoisy signal in an iterative deconvolution algorithm. In particular, we have focused the light on the effect of the iterations number on the evolution of the deconvoluted signals. The SIMS profiles are multilayers of Boron in Silicon matrix.
Low serum creatine kinase activity.

Subnormal activity of creatine kinase (CK, ATP: creatine N -phosphotransferase, EC 2.7.3.2) in serum has been observed in a variety of clinical conditions. Subnormal activity may be found as a consequence of diminished efflux of the muscle enzyme into serum from reduced physical activity caused by illness or advanced age or may result from reduced muscle mass accompanying muscle wasting or cachectic states. Low serum CK values reported in acute viral hepatitis have been explained on the basis of reduced physical activity because these patients have been confined to bed for therapeutic reasons or because of the severity of the illness (1). Low CK activities in patients with alcoholic liver disease (2) have been considered to reflect the reduced muscle mass commonly observed in alcoholics. Reduced serum CK activity has also been observed in patients with connective tissue …
NEOBRAIN – An EU-Funded Project Committed to Protect the Newborn Brain

funded in the Sixth Framework Programme of the European Commission for 3 years with a grant to the budget of 3.3 million Euros, and was kicked off in Brussels on October 25–26, 2006. The initiative was launched by 5 companies and 8 academic partners, who have joined forces to study biomarkers of brain damage in animal models as well as in extremely low gestational age newborns (ELGANs, defined by a gestational age ! 28 weeks). Magnetic resonance and ultrasound imaging, electrophysiologic brain function monitoring and biomarker epidemiology are the hallmarks of the clinical component of NEOBRAIN, which aims at the recruitment of at least a few hundred ELGANs, in whom proteomic, metabolomic and genomic biomarker profiles will be correlated with adverse outcome. The partners from higher education are from the Perinatal Epidemiology Unit at the Hannover Medical School and the Department of Neonatology at the Charité University Hospital Berlin (Germany), the Department of Neonatology at Lund University and the Sahlgrenska Perinatal Center and Department of Physiology at Gothenburg University (Sweden), the Department of Pediatrics at Geneva University (Switzerland), INSERM at the Robert Debré Hospital in Paris (France), the Departments of Psychoneuroimmunology and Neonatology at the University Medical Center Utrecht (The NetherBrain damage and its adverse neurodevelopmental sequelae are among the most devastating correlates of preterm birth. Clinical and scientific efforts have not led to an appreciable reduction of either preterm delivery or brain damage among preterm infants. With improved neonatal care over the past decades and the concomitant increasing survival of the most immature, the prevalence of long-term neurodevelopmental disability among preterm children will probably even increase [1] . In light of these troublesome data, the glaring absence of neuroprotective strategies from the neonatologists’ armamentarium seems even more striking. While recent studies suggest a protective effect of hypothermia in neonatal encephalopathy of term infants [2, 3] , the most feasible interventions in preterm children are the administration of 1 course of antenatal steroids to the mother and the careful limitation of postnatal intervention to the lowest possible level of invasiveness [4] . Moreover, the natural history of brain damage in preterm newborns is still a matter of debate, incorporating multiple possible pathways, such as inflammation [5] , ischaemia [6] , free radicals [6] or multiple insults [7] . In essence, there is a desperate need for further research in this area. To fill this knowledge gap, a specific targeted research project, Neonatal Estimation of Brain Damage Risk and Identification of Neuroprotectants in Preterm Infants (NEOBRAIN; www.neobrain.eu), was Published online: May 21, 2007 formerly Biology of the Neonate
Evidence based educational policy and practice: the case of applying the educational effectiveness knowledge base

Evidence based educational policy and practice means, first of all, that new programs use relevant scientific knowledge for design purposes, or for critical review of initial program ideas (ex ante evaluation). Secondly, before programs are implemented on a large scale it is considered desirable to conduct smaller scale try-out and pilots, preferably designed as randomized experiments. Third and finally, rigorous ex post or summative evaluation of the implemented program is to be conducted. In this article the first condition is further analysed. It depends on the availability of broadly confirmed relatively stable research outcomes that make sense in a theoretical and practical way. The illustration that is used in this article is the educational effectiveness knowledge base and its application for decision making on school improvement and educational reform. The state of the art on educational effectiveness research provides some guidelines for successful general reform strategies, but also underlines the limits of malleability in education, in the sense that effect sizes of even the most successful strategies tend to be small.
Strategic tactical and operational production-distribution models: a review

The concept of supply chain management is gaining so much importance that the firms can compete in today's global economy. This paper provides a detailed literature survey of previous research on supply chain management literature at strategic, tactical, operational levels and reverse logistics, but we limited our research only to the models developed for production and distribution problems. We scrutinise the previous reviews in order to distinguish our research from the others. In the light of these previous reviews, we have developed our classification scheme. The models reviewed in this research have been classified in terms of the solution methodology used. These are: optimisation-based models, metaheuristic-based models, information technology (IT)-driven models and hybrid models. The objective is to develop a framework for the existing literature to reveal major trends in the literature and to explore research opportunities in this area.
HIV Seroconversion Among Public Sexually Transmitted Disease Clinic Patients: Analysis of Risks to Facilitate Early Identification

Objectives: We identified risks for HIV seroconversion among public sexually transmitted disease (STD) clinic patients. Design: This was a retrospective cohort study conducted January 1993 through October 2002 of STD clinic attendees aged ≥12 years in Baltimore, Maryland. Methods: A negative HIV enzyme immunoassay (EIA) test was required for staggered cohort entry. Observation time was 30 days to 3 years. The outcome for multivariate Poisson regression was HIV seroconversion (positive EIA and/or Western blot test) compared among patients with or without sexual risk behaviors, drug use, an STD diagnosis, and signs and symptoms at an initial HIV test. Results: One hundred twenty-five HIV seroconversions occurred among 10,535 individuals and 13,693 person-years of observation, for an incidence of 0.91 HIV seroconversions per 100 person-years (95% confidence interval [CI]: 0.76 to 1.09). Median time to HIV seroconversion was 1.54 years (95% CI: 1.11 to 1.73). In multivariate analysis, increased HIV seroconversion risk was associated with older age, drug use, a sexual partner with syphilis or HIV, genital ulcers, and gonorrhea. HIV incidence per 100 person-years was 4.86 for subjects with an HIV-positive sexual partner, 3.06 for those with injection drug use, and 2.40 for those with genital ulcers. Conclusions: We found a high rate of HIV seroconversion among STD clinic patients with specific risks. Algorithms with HIV RNA testing targeted to patients at the highest risk for seroconversion may optimize prevention and resource utilization.
Leader-Follower Strategies for Energy Management of Multi-Microgrids

This paper presents the application of bilevel programming for analyzing competitive situations of hierarchical decision making between an Energy Services Provider representing several microgrids (MGs)-each one comprising controllable loads and dispatchable distributed generation units-and a large central production unit. The rules of the interaction between the two entities are determined in a bilateral contract. This operation is compared to the vertically integrated operation of this system, i.e., only one entity manages both the central production unit and the distributed resources of the MG. This comparison highlights the benefits of applying a two level structure in the simulated interaction.
Prototype of the evaluation framework for functional requirements of RE-tools

For a complex activity like requirement engineering (RE), a powerful tool support is clearly useful. However, the mainstream of RE practice relies on office tools rather than targeted RE-tools (e.g. DOORS, CaliberRM, and RequisitePro). One of the reasons for not using RE-tools remains the difficulty to assess them before acquiring to organisation. Only few approaches are followed with some limited software tool support. Nor the approaches neither the tools are targeted towards the RE-tool domain; therefore, their applications are time consuming and domain knowledge demanding. Furthermore, the existing RE-tool frameworks list only RE-tool requirements which in most cases are development-oriented, and not supported by the application for the RE-tool evaluation. This paper presents a prototype tool of the evaluation framework for functional requirements of the RE-tools. The framework application is performed according to the systematic guidelines of the RE-tool evaluation approach (R-TEA).
Changing sites of colorectal cancer in the Israeli Jewish ethnic populations and its clinical implications

Countries at risk for colorectal cancer noted an increase in right-sided colorectal cancer. We examined this in the Israeli Jewish populations. Israel Cancer Registry data, 1982–2001, were computed by sex, age, ethnic group and colorectal cancer site: ‘rectal cancer’ included the recto-sigmoid junction, ‘right-sided’ colorectal cancer included proximal colon up to and including the splenic flexure. In both sexes, colorectal cancer trends increased significantly owing to colonic cancer (P<0.01) whereas rectal cancer decreased (P<0.01). Left and right colorectal cancer trends decreased in Israel born people (P<0.01), but in Asia-Africa born people increases were seen at both sites in the male (P=0.02 and 0.06, respectively) and female (P=0.03 and 0.01, respectively) population. In those ≥65 years old, right colorectal cancer trends increased in all men (P=0.05) and women (P=0.01). On comparing data from 1982–1986 with that from 1997–2001 right colorectal cancer showed an increase in both sexes (P<0.01): to 32.7% of male colorectal cancer and 57.6% of female colorectal cancer. In the period 1997–2001, the total male population ≥65 years had increased relatively by 7.5% (P<0.01), and women by 22.6% (P<0.01) and the proportion of right colorectal cancer in ≥65 years olds increased relatively by 10.9% in the male population, and 18.2% in the female population, with one-third of this increase occurring in Russian immigrants arriving after 1990. In conclusion, there is a trend for right colorectal cancer in Jews aged ≥65 years. The proportion and amount of colorectal cancer increased most significantly in older women, which was partially explained by their increasing numbers and by colorectal cancer occurring in recent immigrants from Russia, who were at high-risk for colorectal cancer. These results should influence colorectal cancer screening and diagnostic methodologies used.
The effect of mammary gland expression of human lysozyme on the properties of milk from transgenic mice.

Transgenic mice were used as model systems to evaluate the impact of human lysozyme expression in the mammary gland. We previously generated two lines of transgenic mice that express human lysozyme mRNA in the mammary gland under the tissue-specific and developmentally correct control of the bovine gene promoter for alpha s1-casein. Concentrations of human lysozyme protein in milk of transgenic mice varied from . 25 to . 71 micrograms/microliters of milk. Human lysozyme secreted into mouse milk retained its antimicrobial activity, as determined by a denaturing polyacrylamide gel activity assay. The physical and functional properties of the milk were also altered, because mouse milk containing human lysozyme had a 35% decrease in rennet clotting time, a smaller median micelle size (157 nm vs. 172 nm), and a 2.5- to 3-fold greater gel strength than control milk. From these results, we conclude that the use of transgenic animals producing lysozyme in the milk is feasible and potentially useful to the dairy industry.
A New Saliency Based Video Coding Method with HEVC

In saliency based video coding, the salient parts of the each frame are encoded with higher quality than non salient areas to improve the signal to noise ratio and get higher compression ratio. In this paper, the background of the saliency based video perceptual coding technology is introduced first. Then the characteristics of motion, color and texture are extracted to form the saliency map. The quantization control in high efficiency video coding (HEVC) is incorporated with the visual saliency map to reduce the bit rate by adaptively changing the quantization parameter. Experimental results show that the proposed method can save the bit rate with improving the perceptual quality of regions-of-interest.
GRIMM: genome rearrangements web server

SUMMARY Genome Rearrangements In Man and Mouse (GRIMM) is a tool for analyzing rearrangements of gene orders in pairs of unichromosomal and multichromosomal genomes, with either signed or unsigned gene data. Although there are several programs for analyzing rearrangements in unichromosomal genomes, this is the first to analyze rearrangements in multichromosomal genomes. GRIMM also provides a new algorithm for analyzing comparative maps for which gene directions are unknown. AVAILABILITY A web server, with instructions and sample data, is available at http://www-cse.ucsd. edu/groups/bioinformatics/GRIMM.
Radical of filters in BL‐algebras

In this paper, the notion of the radical of a filter in BL‐algebras is defined and several characterizations of the radical of a filter are given. Also we prove that A/F is an MV‐algebra if and only if Ds(A) ⊆ F. After that we define the notion of semi maximal filter in BL‐algebras and we state and prove some theorems which determine the relationship between this notion and the other types of filters of a BL‐algebra. Moreover, we prove that A/F is a semi simple BL‐algebra if and only if F is a semi maximal filter of A. © 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim
A non-enumerative path delay fault simulator for sequential circuits

We extend the path status graph (PSG) method of delay fault simulation to sequential circuits. By devising a layered PSG and restricting the number of time-frames over which a fault must be detected, we preserve the non-enumerative nature of the simulation algorithm. The program is capable of simulating a wide variety of circuits (synchronous, asynchronous, multiple-clock and tri-state logic.) Both rated and variable clock modes, as well as robust, non-robust or functional sensitization detection options, are available. The simulation can be stopped and restarted through a check pointing facility. The program can target any given list of paths. This path list can also be generated by the program based on user-selectable criteria (all paths, longest paths, paths between certain I/O pairs, etc.) User reports include a histogram of path coverage versus path length. Detected and undetected path data remain implicit in the PSG and can be retrieved through post-processing commands. Due to its non-enumerative stature, the program can process most production level digital logic circuits.