Miracle-dz/UniFAR-FTUs huggingface dataset:
Stochastic Hillclimbing as a Baseline Mathod for Evaluating Genetic Algorithms

We investigate the effectiveness of stochastic hillclimbing as a baseline for evaluating the performance of genetic algorithms (GAs) as combinatorial function optimizers. In particular, we address two problems to which GAs have been applied in the literature: Koza's 11-multiplexer problem and the jobshop problem. We demonstrate that simple stochastic hillclimbing methods are able to achieve results comparable or superior to those obtained by the GAs designed to address these two problems. We further illustrate, in the case of the jobshop problem, how insights obtained in the formulation of a stochastic hillclimbing algorithm can lead to improvements in the encoding used by a GA.
A Dynamical Systems Analysis of Spontaneous Movements in Newborn Infants

The authors evaluated the characteristics of infants' spontaneous movements by using dynamical systems analysis. Participants were 6 healthy 1-month-old full-term newborn infants (3 males, 3 females). They used a triaxial accelerometer to measure limb acceleration in 3-dimensional space. Acceleration signals were recorded during 200 s from the right wrist when the infant was in an active alert state and lying supine (sampling rate 200 Hz). and was stored in the system's memory. Digitized data were transferred to a PC for subsequent processing with analysis software. The acceleration time series data were analyzed linearly and nonlinearly. Nonlinear time series analysis suggested that the infants' spontaneous movements are characterized by a nonlinear chaotic dynamics with 5 or 6 embedding dimensions. The production of infants'spontaneous movements involves chaotic dynamic systems that are capable of generating voluntary skill movements.
Two Approaches to Dialectical Argumentation: Admissible Sets and Argumentation Stages

Currently there is a revival of the study of dialectical argumentation in the artificial intelligence community. There are good reasons why: First, the notions of argument and counterargument shed new light on nonmonotonic reasoning. Second, the process character of dialectical argumentation inspires new computational techniques. In a recent important paper, Dung [1] has studied the relations of (unstructured) arguments and their counterarguments in terms of admissible sets. He has investigated the relations between several types of extensions of argumentation theories. In this paper, we propose a model of the stages of argumentation, related to that of Verheij [2, 3]. Each stage is characterized by the arguments that have been taken into account and by the status of these arguments, either undefeated or defeated. This stage approach provides better understanding of the process of argumentation, because sequences of stages can be interpreted as lines of argumentation. The stage approach also gives naturally rise to two new types of extensions. Their definitions formalize the idea that as many arguments are taken into account as possible. We show the connections with Dung’s work and give a number of examples. It turns out that the argumentation stage approach generalizes the admissible set approach. The main conclusion of the paper is that the argumentation stage approach can give more insight in the procedural nature of dialectical argumentation than the admissible set approach.
Using Dynamic Time Warping to Find Patterns in Time Series

Knowledge discovery in databases presents many interesting challenges within the context of providing computer tools for exploring large data archives. Electronic data repositories are growing quickly and contain data from commercial, scientific, and other domains. Much of this data is inherently temporal, such as stock prices or NASA telemetry data. Detecting patterns in such data streams or time series is an important knowledge discovery task. This paper describes some preliminary experiments with a dynamic programming approach to the problem. The pattern detection algorithm is based on the dynamic time warping technique used in the speech recognition field.
Gender Differences in Real-Home Sleep of Young and Older Couples.

STUDY OBJECTIVES To understand gender differences in sleep quality, architecture and duration of young healthy couples in comparison to older couples in their natural sleep environment. DESIGN Sleep was monitored in a naturalistic setting using a headband sleep monitoring device over a period of two weeks for young couples and home polysomnography for the older couples. PARTICIPANTS Ten heterosexual young couples (male mean age: 28.2±1.0[SD] years/female mean age: 26.8±0.9 years) and 14 older couples (male mean age: 59.3±9.6 years/female mean age: 58.8±9.1 years). MEASUREMENTS AND RESULTS In the young couples, total sleep time (395±66 vs. 367±54 min., p<0.05), sleep efficiency (97.0±3.0 vs. 91.1±7.9, p<0.001), and % REM (31.1±4.8 vs. 23.6±5.5, p<0.001) in males was higher than in females. In contrast, % light sleep (51.7±7.1 vs. 59.7±6.7, p<0.001) and number of arousals (2.9±1.9 vs. 5.3±1.9, p<0.001) were lower. These differences persisted after controlling for evening mood and various evening pre-sleep activities. In the older couples, there were no differences between genders. In addition, children in the household adversely impacted sleep. CONCLUSIONS In couples recorded in the home, young males slept longer and had better sleep quality than young females. This difference appears to dissipate with age. In-home assessment of couples can aid in understanding of gender differences in sleep and how they are affected by age and social environment.
Factor-Group-Generated Polar Spaces and (Multi-)Qudits

Recently, a number of interesting relations have been discovered between genera- lised Pauli/Dirac groups and certain finite geometries. Here, we succeeded in finding a general unifying framework for all these relations. We introduce gradually necessary and sufficient conditions to be met in order to carry out the following programme: Given a group G, we first construct vector spaces over GF(p), p a prime, by factorising G over appropriate normal subgroups. Then, by expressing GF(p) in terms of the commutator subgroup of G, we construct alternating bilinear forms, which reflect whether or not two elements of G commute. Restricting to p = 2, we search for "refinements" in terms of quadratic forms, which capture the fact whether or not the order of an element of G is 2. Such factor-group-generated vector spaces admit a natural reinterpretation in the language of symplectic and orthogonal polar spaces, where each point becomes a "condensation" of several distinct elements of G. Finally, several well-known physical examples (single- and two-qubit Pauli groups, both the real and complex case) are worked out in detail to illustrate the fine traits of the formalism.
Assessing the utility of satellite transmitters for identifying nest locations and foraging behavior of the threatened Marbled Murrelet Brachyramphus marmoratus

NORTHRUP, J.M. , RIVERS, J.W. , NELSON, S.K. , ROBY, D.D. & BETTS, M.G. 2018. Assessing the utility of satellite transmitters for identifying nest locations and foraging behavior of the threatened Marbled Murrelet Brachyramphus marmoratus. Marine Ornithology 46: 47–55. Understanding movements of small seabirds has been particularly challenging due to limitations in tracking technology. As tracking devices become smaller and more powerful, and are deployed on smaller bird species, they need to be evaluated. We assessed whether small, platform terminal transmitters (PTTs; 5 g) could be used to study the nesting, movement, and foraging behaviors of the Threatened Marbled Murrelet Brachyramphus marmoratus in Oregon, US. We attached PTTs that transmitted locations and temperature measurements through the Argos satellite system to seven adult murrelets. We fit continuous-time correlated random-walk models to location data to examine coarse movement patterns and determine whether murrelets were moving inland to potential nesting habitat. We used temperature measurements from the PTTs to examine murrelet diving patterns, indicative of foraging. Sixteen independent movements appeared to be consistent with inland movements. However, the PTT-tagged murrelets appeared to be on the ocean during nearly all of these movements, based on concurrent temperature readings. To further assess the utility of PTTs in locating murrelet nests, we deployed 3 PTTs in trees within suitable nesting habitat. Naive observers required 2–9 d to attain sufficient high-quality locations to attempt to locate these PTTs, and 4–13 h of searching to locate the exact trees. The PTTs we tested can be useful for describing coarse patterns of movement and foraging, but are not an improvement over VHF transmitters for locating nests. All of the tagged murrelets ceased movement during the course of the study. Three were found dead, and the rest were unrecoverable. We suspect that tagging negatively affected welfare of these birds. We recommend waiting for future versions of these tags that weigh less and include GPS technology before deploying them on small diving seabirds such as the Marbled Murrelet.
Nonobligate Role of Early or Sustained Expression of Immediate-Early Gene Proteins c-Fos, c-Jun, and Zif/268 in Hippocampal Mossy Fiber Sprouting

Axon sprouting in dentate granule cells is an important model of structural plasticity in the hippocampus. Although the process can be triggered by deafferentation, intense activation of glutamate receptors, and other convulsant stimuli, the specific molecular steps required to initiate and sustain mossy fiber (MF) reorganization are unknown. The cellular immediate early genes (IEGs)c-fos, c-jun, and zif/268are major candidates for the initial steps of this plasticity, because they encode transcription factors that may trigger cascades of activity-dependent neuronal gene expression and are strongly induced in all experimental models of MF sprouting. The mutant mouse stargazer offers an important opportunity to test the specific role of IEGs, because it displays generalized nonconvulsive epilepsy and intense MF sprouting in the absence of regional cell injury. Here we report that stargazer mice show no detectable elevations in c-Fos, c-Jun, or Zif/268 immediate early gene proteins (IEGPs) before or during MF growth. Experimental results in stargazer, including (1) a strong IEGP response to kainate-induced convulsive seizures, (2) no IEGP response after prolongation of spike-wave synchronization, (3) no IEGP increase at the developmental onset of seizures or after prolonged seizure suppression, and (4) unaltered levels of the intracellular Ca2+-buffering proteins calbindin-D28kor parvalbumin, exclude the possibility that absence of an IEGP response in stargazer is either gene-linked or suppressed by known refractory mechanisms. These data demonstrate that increased levels of these IEGPs are not an obligatory step in MF-reactive sprouting and differentiate the early downstream molecular cascades of two major seizure types.
The Drivers of Atmospheric Methane Fluctuations over the Last Three Decades

Understanding the processes behind the observed methane fluctuations over the last three decades is crucial for reliable projections of future levels of atmospheric methane, the second most important greenhouse gas. After a period of continuous increase, the methane growth rate decreased from about 12 ppbv/yr in the 1980s to about 6 ppbv/yr in the 1990s. From 1999 to 2006 atmospheric methane concentrations reached a plateau, but since 2007, methane is on the rise again. Measurements of the carbon isotopes of methane suggest that an isotopic light source of methane related to biogenic processes is responsible for the increase. Although general nature of sources and sinks of methane are well known, their relative contributions to methane fluctuations are still subject to scientific debate. The goal of this thesis is to disentangle the roles of changes in methane sources and in the main tropospheric methane sink, the reaction with the hydroxyl radical (OH), in determining the observed methane variations over the last three decades. In addition to covering the last three decades, this work pays special attention to the time period after the volcanic eruption of Mount Pinatubo in 1991 and the observed rise after 2007. Global chemistry-climate models (CCMs) are an ideal tool to investigate the atmospheric methane cycle and its interactions with atmospheric chemistry and climate in a self-consistent way. In the framework of this thesis, model simulations with the CCM SOCOL have been performed, using a unique model set up. In contrast to the common approach of using prescribed mixing ratios as lower boundary conditions for methane, CH4 emission fluxes were applied in SOCOL, which has only been done by a limited number of CCMs so far. In order to track the methane emissions from various source categories such as anthropogenic activities or wetlands and from different geographical regions, 48 diagnostic tracers were implemented into the model. To ensure best comparability with observational data the model was forced with prescribed meteorological fields from reanalysis data. In order to further constrain the simulated methane budget, a methyl chloroform tracer, commonly used as a proxy for OH variations, as well as two stable carbon isotopes of methane, namely CH4 and CH4, were employed in SOCOL. In order to investigate the methane variations over the last three decades, four transient model simulations combining two different data sets for anthropogenic emissions (EDGAR4.2 and SCHWIETZKE) with two data sets for wetland emissions (LPJWSL and SDGVM), respectively, were performed. EDGAR4.2 and SCHWIETZKE differ in the reported total amount and temporal evolution of methane emissions from fossil fuel production, with SCHWIETZKE data set showing a more pronounced decrease over Eurasia after 1991 and a less steep increase in Chinese emissions after 2001. With respect to CH4 emissions from wetlands, SDGVM shows larger total emissions
Active buildings: modelling physical activity and movement in office buildings. An observational study protocol

Introduction Health benefits of regular participation in physical activity are well documented but population levels are low. Office layout, and in particular the number and location of office building destinations (eg, print and meeting rooms), may influence both walking time and characteristics of sitting time. No research to date has focused on the role that the layout of the indoor office environment plays in facilitating or inhibiting step counts and characteristics of sitting time. The primary aim of this study was to investigate associations between office layout and physical activity, as well as sitting time using objective measures. Methods and analysis Active buildings is a unique collaboration between public health, built environment and computer science researchers. The study involves objective monitoring complemented by a larger questionnaire arm. UK office buildings will be selected based on a variety of features, including office floor area and number of occupants. Questionnaires will include items on standard demographics, well-being, physical activity behaviour and putative socioecological correlates of workplace physical activity. Based on survey responses, approximately 30 participants will be recruited from each building into the objective monitoring arm. Participants will wear accelerometers (to monitor physical activity and sitting inside and outside the office) and a novel tracking device will be placed in the office (to record participant location) for five consecutive days. Data will be analysed using regression analyses, as well as novel agent-based modelling techniques. Ethics and dissemination The results of this study will be disseminated through peer-reviewed publications and scientific presentations. Ethical approval was obtained through the University College London Research Ethics Committee (Reference number 4400/001).
Qualitative study of the quality of sleep in marginalized individuals living with HIV

Sleep disturbances have been reported to be higher in human immunodeficiency virus (HIV)-infected individuals compared to the general population. Despite the consequences of poor quality of sleep (QOS), research regarding sleep disturbances in HIV infection is lacking and many questions regarding correlates of poor QOS, especially in marginalized populations, remain unanswered. We conducted one-on-one qualitative interviews with 14 marginalized HIV-infected individuals who reported poor QOS to examine self-reported correlates of sleep quality and explore the relationship between QOS and antiretroviral adherence. Findings suggest a complex and multidimensional impact of mental health issues, structural factors, and physical conditions on QOS of these individuals. Those reporting poor QOS as a barrier to antiretroviral adherence reported lower adherence due to falling asleep or feeling too tired to take medications in comparison to those who did not express this adherence barrier. These interviews underscore the importance of inquiries into a patient’s QOS as an opportunity to discuss topics such as adherence, depression, suicidal ideation, and substance use.
Sequence analysis of the VP7 gene of human rotaviruses G2 and G4 isolated in Japan, China, Thailand, and Vietnam during 2001–2003

Sequence and phylogenetic analyses of the rotavirus VP7 gene were performed on 52 human G2 and G4 strains isolated in Japan, China, Thailand, and Vietnam during 2001–2003. All genotype G2 strains included in the study clustered into lineage II of the phylogenetic tree, together with the majority of global G2 strains detected since 1995. The amino acid substitution at position 96 from aspartic acid to asparagine was noted among the emerging or re‐emerging G2 rotavirus strains in Japan, Thailand, and Vietnam during 2002–2003. Genotype G4 strains detected in Vietnam grouped into lineage Ia of the phylogenetic tree, whereas Japanese G4 strains clustered in lineage Ic which included emerging G4 strains from Argentina, Italy, Paraguay, and Uruguay. It is noteworthy that an insertion of asparagine was found at position 76 in all the Japanese strains and that its presence might be involved in the emergence of G4 rotavirus in Japan during 2002–2003. J. Med. Virol. 82: 878–885, 2010. © 2010 Wiley‐Liss, Inc.
Diabetes mellitus and the risk of gastric cancer: a meta-analysis of cohort studies

Studies examining the relationship between diabetes mellitus (DM) and the risk of gastric cancer incidence or gastric cancer mortality have produced inconsistent results. The purpose of this study was to evaluate the evidence regarding the relationship between DM and subsequent gastric cancer incidence or gastric cancer mortality risk on the basis of cohort studies. A systematic search of articles in PubMed, EmBase, the Cochrane Library, and reference lists was conducted to identify relevant literature. Twenty-two cohort studies reporting data on 8,559,861 participants were included in the study. Overall, participants with DM had little or no change in the risk of gastric cancer, or gastric cancer mortality. There was no evidence of difference in the RR for gastric cancer between men and women. Participants with DM had a non-significant trend towards an increased risk of gastric cancer mortality in men. There was no significant difference between men and women for this relationship. Finally, although subgroup analysis suggested DM was associated with a significant impact on gastric cancer incidence and gastric cancer mortality risk in several specific populations, a significance based on gender difference was not observed. In conclusion, DM might increase the risk of gastric cancer in men when the study used standard incidence/mortality ratio as effect estimate. Further, DM were associated with higher risk of gastric cancer mortality in men if the mean age at baseline less than 55.0 years, used RR or HR as effect estimate, the study adjusted smoking or not, and the study not adjusted alcohol drinking.
Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure

Proteins have been shown to exhibit strange/anomalous dynamics displaying non-Debye density of vibrational states, anomalous spread of vibrational energy, large conformational changes, nonexponential decay of correlations, and nonexponential unfolding times. The anomalous behavior may, in principle, stem from various factors affecting the energy landscape under which a protein vibrates. Investigating the origins of such unconventional dynamics, we focus on the structure-dynamics interplay and introduce a stochastic approach to the vibrational dynamics of proteins. We use diffusion, a method sensitive to the structural features of the protein fold and them alone, in order to probe protein structure. Conducting a large-scale study of diffusion on over 500 Protein Data Bank structures we find it to be anomalous, an indication of a fractal-like structure. Taking advantage of known and newly derived relations between vibrational dynamics and diffusion, we demonstrate the equivalence of our findings to the existence of structurally originated anomalies in the vibrational dynamics of proteins. We conclude that these anomalies are a direct result of the fractal-like structure of proteins. The duality between diffusion and vibrational dynamics allows us to make, on a single-molecule level, experimentally testable predictions. The time dependent vibrational mean square displacement of an amino acid is predicted to be subdiffusive. The thermal variance in the instantaneous distance between amino acids is shown to grow as a power law of the equilibrium distance. Mean first passage time analysis is offered as a practical tool that may aid in the identification of amino acid pairs involved in large conformational changes.