Miracle-dz/UniFAR-FTUs huggingface dataset:
The optimal design of stepped wedge trials with equal allocation to sequences and a comparison to other trial designs

Background/Aims We sought to optimise the design of stepped wedge trials with an equal allocation of clusters to sequences and explored sample size comparisons with alternative trial designs. Methods We developed a new expression for the design effect for a stepped wedge trial, assuming that observations are equally correlated within clusters and an equal number of observations in each period between sequences switching to the intervention. We minimised the design effect with respect to (1) the fraction of observations before the first and after the final sequence switches (the periods with all clusters in the control or intervention condition, respectively) and (2) the number of sequences. We compared the design effect of this optimised stepped wedge trial to the design effects of a parallel cluster-randomised trial, a cluster-randomised trial with baseline observations, and a hybrid trial design (a mixture of cluster-randomised trial and stepped wedge trial) with the same total cluster size for all designs. Results We found that a stepped wedge trial with an equal allocation to sequences is optimised by obtaining all observations after the first sequence switches and before the final sequence switches to the intervention; this means that the first sequence remains in the control condition and the last sequence remains in the intervention condition for the duration of the trial. With this design, the optimal number of sequences is 1 / ( 1 − R ) , where R = ρ m / ( 1 + ρ ( m − 1 ) ) is the cluster-mean correlation, ρ is the intracluster correlation coefficient, and m is the total cluster size. The optimal number of sequences is small when the intracluster correlation coefficient and cluster size are small and large when the intracluster correlation coefficient or cluster size is large. A cluster-randomised trial remains more efficient than the optimised stepped wedge trial when the intracluster correlation coefficient or cluster size is small. A cluster-randomised trial with baseline observations always requires a larger sample size than the optimised stepped wedge trial. The hybrid design can always give an equally or more efficient design, but will be at most 5% more efficient. We provide a strategy for selecting a design if the optimal number of sequences is unfeasible. For a non-optimal number of sequences, the sample size may be reduced by allowing a proportion of observations before the first or after the final sequence has switched. Conclusion The standard stepped wedge trial is inefficient. To reduce sample sizes when a hybrid design is unfeasible, stepped wedge trial designs should have no observations before the first sequence switches or after the final sequence switches.
Mammalian carnivore occupancy is inversely related to presence of domestic dogs in the high Andes of Ecuador

Although the Andes have long been occupied by people, habitat loss, fragmentation through deforestation, and other human activities such as introduction of invasive species have increased drastically during the past century. The Ecuadorian Andes are considered a biodiversity hotspot. However, the fauna and threats to the region are poorly studied, and understanding of factors that shape the distribution of species in habitats disturbed by human activities is needed to identify and mitigate region-wide threats to wildlife. We evaluated factors associated with patterns of occurrence of Andean carnivores in landscapes of the northern Ecuadorian Andes, particularly habitat loss, fragmentation, and occupancy of domestic dogs, and determined whether thresholds occurred for these factors beyond which carnivore occurrence declined markedly. Five study areas (each 20 x 20 km) were surveyed with a total effort of 2,800 camera trap nights. Occupancies of four of the eight carnivores known from the region were best predicted by occupancy of domestic dogs rather than measures of habitat loss and fragmentation [Andean fox (Pseudalopex culpaeus), puma (Puma concolor), striped hog-nosed skunk (Conepatus semistriatus), and Andean bear (Tremarctos ornatus)]. The two largest carnivores, puma and Andean bear, demonstrated significant threshold responses to the presence of domestic dogs at two sites. Four smaller carnivores were recorded too infrequently to model occupancy, and at least two of these species appear to be in decline. The magnitude of domestic dog impacts on native species in tropical areas like the Ecuadorian Andes currently are not recognized. Results of our study indicate that small and large carnivores are in urgent need of conservation and clearly point to dogs as a significant threat to a broad range of native species.
An integrated framework for human activity classification

This paper presents an integrated framework to enable using standard non-sequential machine learning tools for accurate multi-modal activity recognition. We develop a novel framework that contains simple pre- and post-classification strategies to improve the overall performance. We achieve this through class-imbalance correction on the learning data using structure preserving oversampling (SPO), leveraging the sequential nature of sensory data using smoothing of the predicted label sequence and classifier fusion, respectively. Through evaluation on recent publicly available activity datasets comprising of a large amount of multi-dimensional sensory data, we demonstrate that our proposed strategies are effective in improving classification performance over common techniques such as One Nearest Neighbor (1NN) and Support Vector Machines (SVM). Our framework also shows better performance over sequential probabilistic models, such as Conditional Random Field (CRF) and Hidden Markov Model (HMM) and when these models are used as meta-learners.
Utility of the chronic unpredictable mild stress model in research on new antidepressants

Abstract Unpredictable chronic mild stress model was developed as an animal model of depression more than 20 years ago. Essential for this model is that after prolonged exposure of tested animals to a series of unpredictable mild stressors, a condition similar to anhedonia develops, which is observed in the majority of depressive disorders. Unpredictable chronic mild stress model is used nowadays in numerous studies related to the neurobiological and biochemical changes associated with depressive illness. Their results confirm that chronic unpredictable mild stress induces in tested animals a number of changes, which reflect those seen in depressive disorders. Because the effects of unpredictable chronic mild stress can be used in a more accurate diagnosis of the pathophysiology of depressive illness and expand knowledge of its pharmacotherapy, therefore research in this area has been continued all the time.
Effects of initial (larval) size and host body temperature on growth in trematodes

For ectotherms, temperature is an important correlate of variation in body size within species. Variation in body size among related species could also be attributable in part to temperature if the different species grow under different thermal regimes. The roles of both initial (larval) size and host body temperature on final (adult) size of para - sitic trematodes were investigated in a comparative analysis. Trematodes are a good model group for such a study, with almost half of known species growing at high and constant temperatures in endothermic vertebrates and the rest at lower and fluctuating temperatures in ectothermic vertebrates. The relative growth of trematodes, i.e., their growth rela - tive to the size of their larvae, varied greatly among species. Increases in body size from the cercarial larval stage to the adult stage averaged almost 40-fold (maximum 1300-fold), whereas increases in size from the metacercarial stage to the adult stage averaged 6-fold (maximum 110-fold). There were no differences between trematodes in ectothermic hosts and trematodes in endothermic hosts with respect to these measures of relative growth, however, which suggests that host type and the thermal regime provided by the host have no effect on the growth of trematodes from larval to adult stages. In contrast, the final (adult) body size of trematodes appears to be determined to some extent by their ini - tial (larval) size, independently of the type of host in which they developed.
1&agr;‐Hydroxycholecalciferol improves the growth performance and up‐regulates the mRNA expression of vitamin D receptor in the small intestine and kidney of broiler chickens

ABSTRACT 1&agr;‐Hydroxycholecalciferol (1&agr;‐OH‐D3) is a vitamin D derivative. The objective of this study was to evaluate the effects of 1&agr;‐OH‐D3 on the growth and the mRNA expression of vitamin D receptor (VDR) in the small intestine and kidney of chickens. A total of 240 males of one‐day‐old Ross 308 broilers was randomly assigned to 4 treatments with 5 replicates of 12 birds per replicate. Three levels of 1&agr;‐OH‐D3 (1.25, 2.5, and 5 &mgr;g/kg) were added to a basal diet containing 0.50% calcium (Ca), 0.25% non‐phytate phosphorus (NPP), and without supplemental cholecalciferol (vitamin D3). The control diet contained 1.00% Ca, 0.45% NPP, and 25 &mgr;g/kg cholecalciferol. Dietary 1&agr;‐OH‐D3 levels linearly improved the average daily feed intake (ADFI), average daily gain (ADG), femur and tibia mineralization, and plasma Ca concentration, and retained Ca and total phosphorus (tP) amounts in broilers from 1 to 21 d of age (P < 0.05). In addition, 1&agr;‐OH‐D3 also linearly up‐regulated the mRNA expression levels of VDR in the duodenum as well as those of VDR and sodium‐phosphate cotransporter NaPi‐IIa and NaPi‐IIc in the kidney of broilers (P < 0.05). However, 1&agr;‐OH‐D3 did not affect the mRNA levels of 25‐hydroxylase in the liver or NaPi‐IIb in the duodenum (P > 0.05). No differences were observed in the ADFI, ADG, bone length, plasma mineral concentration, retained tP amount, or the mRNA levels of the above genes (except for VDR in the kidney) between the birds fed the diet with 5 &mgr;g/kg 1&agr;‐OH‐D3 and the birds fed the control diet (P > 0.05). By contrast, the weight, ash weight, ash percentage, and Ca percentage of the bone, retained Ca amount, and the mRNA level of VDR in the kidney were lower in the birds fed the diet with 5 &mgr;g/kg 1&agr;‐OH‐D3 than in the birds fed the control diet (P < 0.05). These data indicate that 1&agr;‐OH‐D3 up‐regulates the gene expression of VDR in the small intestine and kidney at the transcriptional level, thereby improving the growth performance and bone mineralization of broiler chickens from 1 to 21 d of age.
A Parameter Setting Method for Spiral Optimization from Stability Analysis of Dynamic Equilibrium Point

In recent years, the authors have proposed an effective metaheuristic method for continuous optimization problems based on an analogy of spiral phenomena in nature. This method is called Spiral Optimization (SPO). SPO has two setting parameters: the convergence rate and the rotation rate. Depending on computational and/or problem conditions, the values of these parameters affect search performance. However, effective setting methods for these parameters without trial and error, including analyses of search dynamics needed for such methods, have not yet been studied. This paper analyzes the stability of the dynamic equilibrium point of the SPO model and proposes a parameter-setting method for the convergence rate r based on results from stability analysis. The effectiveness of the proposed method is confirmed through simulation for some benchmark functions and comparison with other representative metaheuristic methods.
Dissimilar Friction Stir Welding Between 5083 and 6082 Al Alloys Reinforced With TiC Nanoparticles

Dissimilar friction stir welding between aluminum alloys thick plates reinforced with TiC nanoparticles was conducted. The defect-free welds are characterized by good mechanical mixing between the joined materials as well as by good nanoparticle distribution and further grain refinement in comparison with the unreinforced weld. The local mechanical behavior of the produced metal matrix composites was studied and compared with their bulk counterparts and parent materials. Specifically, the measured mechanical properties in microscale and nanoscale (namely hardness and elastic modulus) are correlated with microstructure and the presence of fillers. The hardness, elastic modulus, ultimate tensile strength, percentage of elongation, and yield values increase with the presence of TiC nanoparticles.
Deconstructing Innovation: An Exploratory Study of the US Furniture Industry

The Merriam-Webster's dictionary defines innovation as (1) the introduction of something new or (2) a new idea, method, or device. Many empirical studies suggest that innovation is an important driver for developing or maintaining firm competitiveness. Innovation has been linked to improving products, production processes, supply chain efficiencies, market research, customer retention, business systems, relationships with exchange partners, profitability, and competitiveness. But how does it work? How can innovation be measured? In this study, we examined innovation in the US furniture industry. First, we deconstructed innovation into three broad categories: product, production processes, and company culture. Second, we examined relationships between the innovation subcomponents and the internal/external demographic characteristics of company size, company location population, age of employees, and education level of employees. Results show that although we were able to develop the three innovation constructs, only 25 percent of their hypothesized relationships to demographic factors followed hypothesized patterns of significance or directionality.
Recognizing and Imitating Programmer Style: Adversaries in Program Authorship Attribution

Abstract Source code attribution classifiers have recently become powerful. We consider the possibility that an adversary could craft code with the intention of causing a misclassification, i.e., creating a forgery of another author’s programming style in order to hide the forger’s own identity or blame the other author. We find that it is possible for a non-expert adversary to defeat such a system. In order to inform the design of adversarially resistant source code attribution classifiers, we conduct two studies with C/C++ programmers to explore the potential tactics and capabilities both of such adversaries and, conversely, of human analysts doing source code authorship attribution. Through the quantitative and qualitative analysis of these studies, we (1) evaluate a state-of-the-art machine classifier against forgeries, (2) evaluate programmers as human analysts/forgery detectors, and (3) compile a set of modifications made to create forgeries. Based on our analyses, we then suggest features that future source code attribution systems might incorporate in order to be adversarially resistant.
A Wireless Powered Feedback Protocol for Opportunistic Beamforming Using Rectenna Arrays

This paper proposes an opportunistic beamforming (OBF) protocol with limited feedback in the context of wireless powered communication networks. The terminals are randomly deployed around an access point (AP) and are equipped with multiple antennas as well as a rectenna array to harvest energy. In the OBF scheme, the AP acquires channel related feedback from the network’s terminals and allocates the orthonormal beams to the users with the best link. We consider the case, where the feedback is solely powered by energy harvested from electromagnetic radiation. Specifically, each terminal adjusts the length of its feedback based on the amount of harvested energy; when the energy is not sufficient to feed back at least one bit, the terminal is considered to be in outage. We study two fundamental rectenna architectures, the direct-current combiner and the radio-frequency combiner (coherent and non-coherent), as well as a hybrid architecture of these two. Furthermore, to alleviate the doubly near-far problem, we consider a scheme where a terminal adapts the number of rectenna elements according to its distance from the origin. By using higher order statistics and stochastic geometry, the beam outage probability is derived in closed form for all considered architectures and scenarios.
RankClus: integrating clustering with ranking for heterogeneous information network analysis

As information networks become ubiquitous, extracting knowledge from information networks has become an important task. Both ranking and clustering can provide overall views on information network data, and each has been a hot topic by itself. However, ranking objects globally without considering which clusters they belong to often leads to dumb results, e.g., ranking database and computer architecture conferences together may not make much sense. Similarly, clustering a huge number of objects (e.g., thousands of authors) in one huge cluster without distinction is dull as well. In this paper, we address the problem of generating clusters for a specified type of objects, as well as ranking information for all types of objects based on these clusters in a multi-typed (i.e., heterogeneous) information network. A novel clustering framework called RankClus is proposed that directly generates clusters integrated with ranking. Based on initial K clusters, ranking is applied separately, which serves as a good measure for each cluster. Then, we use a mixture model to decompose each object into a K-dimensional vector, where each dimension is a component coefficient with respect to a cluster, which is measured by rank distribution. Objects then are reassigned to the nearest cluster under the new measure space to improve clustering. As a result, quality of clustering and ranking are mutually enhanced, which means that the clusters are getting more accurate and the ranking is getting more meaningful. Such a progressive refinement process iterates until little change can be made. Our experiment results show that RankClus can generate more accurate clusters and in a more efficient way than the state-of-the-art link-based clustering methods. Moreover, the clustering results with ranks can provide more informative views of data compared with traditional clustering.
Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding

Many experimental and theoretical studies have suggested a significant role for nonnative interactions in protein folding pathways, but the energetic contributions of these interactions are not well understood. We have addressed the energetics and the position specificity of nonnative hydrophobic interactions by developing a continuum coarse-grained chain model with a native-centric potential augmented by sequence-dependent hydrophobic interactions. By modeling the effect of different hydrophobicity values at various positions in the Fyn SH3 domain, we predicted energetically significant nonnative interactions that led to acceleration or deceleration of the folding rate depending on whether they were more populated in the transition state or unfolded state. These nonnative contacts were centered on position 53 in the Fyn SH3 domain, which lies in an exposed position in a 310-helix. The energetic importance of the predicted nonnative interactions was confirmed experimentally by folding kinetics studies combined with double mutant thermodynamic cycles. By attaining agreement of theoretical and experimental investigations, this study provides a compelling demonstration that specific nonnative interactions can significantly influence folding energetics. Moreover, we show that a coarse-grained model with a simple consideration of hydrophobicity is sufficient for the accurate prediction of kinetically important nonnative interactions.
Biomarkers of Endolithic Communities within Gypsum Crusts (Southern Tunisia)

Evaporite accumulations produced by artesian waters in the arid zones of southern Tunisia led to the formation of subrounded, gypsiferous mounds consisting of irregular alternations of mineral precipitates and aeolian sand. The joint occurrence of gypsum crusts and plant colonization determined the stabilization of their top surface. Careful examination of the pigmented (green-brown) crusts revealed endolithic microbial communities just below the surface. In previous optical and scanning electron microscope studies cyanobacteria were the dominant component of these communities. Molecular diversity studies based on small subunit ribosomal RNA (SSU rRNA) gene analysis revealed that Flavobacteria, Actinobacteria, Deinococcales, Alpha- and Gamma- Proteobacteria are also important components of the microbial assemblage. Their pigment analyses, determined by high performance liquid chromatography (HPLC), detected the presence of carotenoids and chlorophyll (chl) a and b. Microbial communities that produce pigmentation and display an endolithic lifestyle typify the extreme environments as those found in arid/semiarid and hot desert regions.
Mental health and well-being concerns of fly-in fly-out workers and their partners in Australia: a qualitative study

Objectives Fly-in fly-out (FIFO) work involves commuting long distances to the worksite and living in provided accommodation for 1–4 weeks while on shift. While the potentially detrimental impact of FIFO work on the health and well-being of workers has been documented, little attention has been paid to how workers, or their partners, cope with this impact. This study sought to investigate how workers and their partners negotiate the impact of FIFO on their mental health and well-being. Design The study design was qualitative. FIFO workers and partners responded to open-ended questions on concerns about the FIFO lifestyle and the support they use. Setting Australian FIFO workers and partners responded to the questions via email. Participants Participants were 34 FIFO workers (25 men, M age=41 years) and 26 partners of FIFO workers (26 women, M age=40 years). Results Participant-validated thematic analysis generated three main themes: managing multiple roles, impact on mental health and well-being, and social support needs. Results revealed difficulties in adjusting between the responsibilities of perceptually distinct on-shift and off-shift lives, and managing potential psychological distance that develops while workers are on site. Participants emphasised the importance of maintaining quality communication and support from family members. Workers and partners attempted to maintain mental health and well-being by regularly engaging with support networks, although many felt organisational support was tokenistic, stigmatised or lacking. Conclusions Recommendations for enhancing support provided by FIFO organisations are offered. In particular, organisations should emphasise the importance of good mental health and well-being, maintain transparency regarding potential challenges of FIFO lifestyles, and offer professional support for managing multiple social roles and effective communication.