Miracle-dz/UniFAR-FTUs huggingface dataset:
Foraging for Development: a Comparison of Food insecurity, Production, and risk among Farmers, Forest Foragers, and marine Foragers in Southwestern madagascar

International programs for combating food insecurity including the recent FAO “How to Feed the World in 2050: Highlevel Expert Forum” promote agricultural intensification among the main solutions to global hunger. We argue here that hunting and gathering on land and at sea will often result in less food insecurity than farming. In southwestern Madagascar, questionnaire data find farmers more food insecure than neighboring forest foragers and marine foragers. Production data show that farmers produce a greater quantity of food energy, but foragers sell their goods for higher prices resulting in comparable market-valued incomes among all three subsistence modes. A stochastic model finds farming portfolios an order of magnitude more risky (lower z-scores) than foraging portfolios, except when foraging portfolios have low means. This is because farmers experience only three to five harvests per year while foragers may experience 365 harvests. As farmers await future harvests of uncertain quantity, they are more likely than foragers to depend on formal and informal credit. The stochastic model shows that diversification, mixing foraging with farming, can only reduce the risks of farming under limited conditions. We conclude that pressuring foragers to become farmers will increase rather than diminish regional food insecurity.
Multivariate Analysis of Factors Affecting Presence and/or Agenesis of Third Molar Tooth

To investigate the presence and/or agenesis of third molar (M3) tooth germs in orthodontics patients in Malaysian Malay and Chinese population and evaluate the relationship between presence and/or agenesis of M3 with different skeletal malocclusion patterns and sagittal maxillomandibular jaw dimensions. Pretreatment records of 300 orthodontic patients (140 males and 160 females, 219 Malaysian Malay and 81 Chinese, average age was 16.27±4.59) were used. Third-molar agenesis was calculated with respect to race, genders, number of missing teeth, jaws, skeletal malocclusion patterns and sagittal maxillomandibular jaw dimensions. The Pearson chi-square test and ANOVA was performed to determine potential differences. Associations between various factors and M3 presence/agenesis groups were assessed using logistic regression analysis. The percentages of subjects with 1 or more M3 agenesis were 30%, 33% and 31% in the Malaysian Malay, Chinese and total population, respectively. Overall prevalence of M3 agenesis in male and female was equal (P>0.05). The frequency of the agenesis of M3s is greater in maxilla as well in the right side (P>0.05). The prevalence of M3 agenesis in those with a Class III and Class II malocclusion was relatively higher in Malaysian Malay and Malaysian Chinese population respectively. Using stepwise regression analyses, significant associations were found between Mx (P<0.05) and ANB (P<0.05) and M3 agenesis. This multivariate analysis suggested that Mx and ANB were significantly correlated with the M3 presence/agenesis.
Implementation and impact of the Gold Standards Framework in community palliative care: a qualitative study of three primary care trusts

The Gold Standards Framework (GSF) has been widely adopted within UK general practices, yet there is little understanding of its impact on the provision of community palliative care services. This study presents data on the anticipation and adoption of the GSF within three Primary Care Trusts in North West England. Forty-seven interviews were conducted with generalist and specialist palliative and primary care professionals. Important aspects of the GSF identified were the patient register, communication and out-of-hours protocols. Positive benefits to professionals included improved communication between professionals and appropriate anticipatory prescribing. Negative aspects included increased nursing workload and the possibility of fewer or later visits for patients. Many respondents believed that the GSF needed local champions to be sustainable. Slow or incomplete adoption was reported. The GSF was recognised as important because it facilitated changes to previously difficult aspects of work between professionals, but few respondents reported direct benefits to patient care.
TERRAIN SURFACE RECONSTRUCTION BY THE USE OF TETRAHEDRON MODEL WITH THE MDL CRITERION

A LIDAR filtering technique is used to differentiate on-terrain poi nts and off-terrain points from a cloud of 3-D point data collected by a LIDAR system. A major issue of concern in this low-level filter is to design a methodology to have a continual adaptation to terrain surface variations. To this end, several essential observations are discussed in this paper: i) the terrain surface can be fragmented into a set of piecewise “homogeneous” plane surfaces, in which terrain surface variations are smoothed out, ii) a criterion for differentiating onand off-terrain point from plane terrain surf ace can be equivalently applied to these terrain segments assumed as being plane, and iii) an interand intra-relationship of onand off-terrain points can be as verifying the a priori taken assumption of the plane terrain surface. The main strategy implemented in our LIDAR filtering technique is to iteratively generate a number of terrain surface models in order to hypothesize and test a plane terrain surface over a local area. Finally, the most reliable plane terrain surface model is selected as an optimised solution and thus the terrain surface model is refined. To this end, we devise a two-step divide-and-conquer triangulation in terms of downward and upward model refinement; in this framework, a tetrahedron is used in order to hypothesize a plane terrain surface and the Minimum Description Length (MDL) criterion is employed for the selection of an optimized plane terrain surface model. The useful characteristics of this method are discussed with results derived from real LIDAR data.
Software Tools for Technology Transfer Manuscript No. Expressing Checkable Properties of Dynamic Systems: the Bandera Speciication Language

Research on how to reason about correctness properties of software systems using model checking is advancing rapidly. Work on extracting nite-state models from program source code and on abstracting those models is focused on enabling the tractable checking of program properties such as freedom from deadlock and assertion violations. For the most part, the problem of specifying more general program properties has not been considered. In this paper, we report on the support for specifying properties of dynamic multi-threaded Java programs that we have built into the Bandera system. Bandera extracts nite-state models, in the input format of several existing model checkers, from Java code based on the property to be checked. The Bandera Speciication Language (BSL) provides a language for deening general assertions and pre/post conditions on methods. It also supports the deenition of observations that can be made of the state of program objects and the incorporation of those observations as predicates that can be instantiated in the scope of object quantiiers and used in describing common forms of state/event sequencing properties. We illustrate how BSL can be used to formulate a variety of system correctness properties for several multi-threaded Java applications.
Coupling membranes as energy-transmitting cables. I. Filamentous mitochondria in fibroblasts and mitochondrial clusters in cardiomyocytes

An hypothesis considering mitochondria as intracellular power- transmitting protonic cables was tested in human fibroblasts where mitochondria are thin and long and in rat cardiomyocytes where they show cluster organization. Mitochondria in the cell were specifically stained with fluorescent-penetrating cation ethylrhodamine, which electrophoretically accumulates in the mitochondrial matrix. A 40- micron-long mitochondrial filament of fibroblast was illuminated by a very narrow (less than or equal to 0.5 micron) laser beam to induce local damage of the mitochondrial membranes. Such a treatment was found to induce quenching of the ethylrhodamine fluorescence in the entire filament. According to the electron microscope examination, the laser- treated filament retained its continuity after the laser illumination. Other mitochondrial filaments (some of which were localized at a distance less than 10 micron from the laser-treated one) remained fluorescent. In a cell where mitochondrial filaments seemed to be united in a network, laser illumination of one filament resulted in fluorescence quenching in the whole network, whereas fluorescence of small mitochondria not connected with the network was unaffected. The illumination of cardiomyocyte was found to result in the fluorescence quenching not only in a laser-illuminated mitochondrion but also in a large cluster of organelles composed of many mitochondria. Electron microscopy showed that all the mitochondria in the cluster change from the orthodox to the condensed state. It was also found that mitochondria in the cluster are connected to one another with specific junctions. If a mitochondrion did not form junctions with a quenched cluster, its fluorescence was not decreased even when this mitochondrion was localized close to an illuminated one. The size of the mitochondrial cluster may be as long as 50 micron. The cluster is formed by branched chains of contacting mitochondria, which may be defined as Streptio mitochondriale. In the cardiomyocyte there are several mitochondrial clusters or, alternatively, the quenched cluster is a result of decomposition of a supercluster uniting all the mitochondria of the cell. Cluster organization of mitochondria could also be revealed when a single mitochondrion was punctured in situ with a microcapillary. The obtained data are in agreement with the idea that mitochondrial junctions are H+ permeable so that, within the cluster, delta psi may be transmitted from one mitochondrion to another. The above results are consistent with the assumption that mitochondrial filaments or networks represent a united electrical system. (ABSTRACT TRUNCATED AT 400 WORDS)
Software testing for mobile and ubiquitous computing

We describe a framework that is used to build and test software for ubiquitous and mobile computing. The approach involves software-level emulators for computing devices. Since each emulator is implemented as a mobile agent, it can dynamically carry its target software to each of the sub-networks that its device is connected to, on behalf of the device, and it permits the software to interact with other servers in its current sub-network. The framework can simulate the mobility and reconnection of mobile or ubiquitous computing devices by using the logical mobility of mobile agent-based emulators. That is, it can test software designed to run on a mobile or ubiquitous device in the same way as if the software were disconnected from the network, moved with the device, and reconnected to and executed on another network. This paper describes the lessons we earned from exploiting the framework in developing typical application software for mobile and ubiquitous computing devices.
Triglyceride Blisters in Lipid Bilayers: Implications for Lipid Droplet Biogenesis and the Mobile Lipid Signal in Cancer Cell Membranes

Triglycerides have a limited solubility, around 3%, in phosphatidylcholine lipid bilayers. Using millisecond-scale course grained molecular dynamics simulations, we show that the model lipid bilayer can accommodate a higher concentration of triolein (TO) than earlier anticipated, by sequestering triolein molecules to the bilayer center in the form of a disordered, isotropic, mobile neutral lipid aggregate, at least 17 nm in diameter, which forms spontaneously, and remains stable on at least the microsecond time scale. The results give credence to the hotly debated existence of mobile neutral lipid aggregates of unknown function present in malignant cells, and to the early biogenesis of lipid droplets accommodated between the two leaflets of the endoplasmic reticulum membrane. The TO aggregates give the bilayer a blister-like appearance, and will hinder the formation of multi-lamellar phases in model, and possibly living membranes. The blisters will result in anomalous membrane probe partitioning, which should be accounted for in the interpretation of probe-related measurements.
A novel approach to estimating and testing specific mediation effects in educational research: explication and application of Macho and Ledermann’s (2011) phantom model approach

This paper addresses the issue of estimating and testing specific indirect effects in recursive structural equation models by considering Macho and Ledermann’s (2011) novel approach to testing specific mediation hypotheses. Mediating processes are critical to understanding the underlying pathways through which predictor variables influence criterion variables. Notwithstanding the utility of assessing mediation for elucidating underlying psychological processes, only recently have educational researchers become increasingly concerned with performing empirical significance tests of specific mediation hypotheses. Following an overview of statistical mediation and consideration of the limitations of widely-used structural equation modelling (SEM) programs in handling tests of specific indirect effects, this paper argues for the use of Macho and Ledermann’s (2011) phantom model approach among applied educational researchers to test specific indirect effect hypotheses.
Advances in cancer epidemiology in Japan

Epidemiologists in Japan have been performing calculations to estimate nationwide cancer incidence rates as well as 5‐year survival rates using population‐based cancer registry data. There have been remarkable changes in cancer incidence and/or mortality in cancers of the lung, liver and stomach, which were thought to be attributed to the changing impact of exposure to cigarette smoking, chronic hepatitis C virus infection and Helicobacter pylori infection, respectively. In systematic reviews providing evidence in risk/protective factors for cancer sites using case–control and cohort studies of the Japanese population, there were associations between cancer sites (esophagus, stomach, colo‐rectum, liver, pancreas, lung and breast) and various lifestyle factors. In the past 10 years, a hospital‐based case–control study at Aichi Cancer Center provided valuable evidence of gene‐environment interaction on the development of cancer [i.e., the effects of aldehyde dehydrogenase‐2 (ALDH2) polymorphism and heavy alcohol drinking on esophageal cancer, ALDH2 polymorphism and smoking on lung cancer, methylenetetrahydrofolate reductase polymorphism and heavy alcohol drinking on pancreatic cancer]. The database with stored DNA was also used and identified seven loci containing significant but low‐penetrance polymorphisms associated with the development of breast cancer. These findings together with established risk factors are likely to be useful to predict personalized breast cancer risk in East Asian women. In 2005, the Japan Multi‐Institution Collaborative Cohort (J‐MICC) study was launched to elucidate gene‐environment interactions as well as to confirm preclinical diagnostic biomarkers of cancer. J‐MICC, which has recruited 92,000 healthy individuals by the end of 2012, will follow the individuals until 2025.
Antimicrobial effects of sodium metasilicate against Listeria monocytogenes.

Sodium metasilicate (SMS) is a U.S. Department of Agriculture-approved antimicrobial for use in meat and poultry processing and has been known to be effective against various foodborne pathogens. However, its antimicrobial mechanism has not yet been revealed. In this study, we attempted to elucidate the mechanism by which SMS inactivates Listeria monocytogenes, a Gram-positive bacterial pathogen encountered commonly in ready-to-eat meat and poultry products. L. monocytogenes (Scott A) cells were treated with different concentrations of SMS (1.0, 2.0, 3.0, 4.0, 5.0, and 6.0% [wt/vol]) and compared with high pH treatment (0.1, 0.2, and 0.3N NaOH solutions) for 1, 10, and 30 min. SMS exhibited concentration and time effects on inactivation of L. monocytogenes. The effect of SMS on the membrane integrity and viability of L. monocytogenes was determined by use of propidium iodide (PI) and SYTO9 nucleic acid stains with subsequent flow cytometry. The breakage in membrane integrity was observed by uptake of PI by cells treated with SMS with subsequent flow cytometry. Ultrastructural changes from corresponding transmission electron micrographs further revealed the disruption in the cytoplasmic membrane and changes in the morphology of the cells treated with SMS and high pH. The results from flow cytometry experiment and transmission electron microscopy study indicated that following SMS treatment, the membrane integrity of L. monocytogenes was compromised leading to leakage of intracellular contents and subsequent cell death.
A Graduated Assignment Algorithm for Graph Matching

A graduated assignment algorithm for graph matching is presented which is fast and accurate even in the presence of high noise. By combining graduated nonconvexity, two-way (assignment) constraints, and sparsity, large improvements in accuracy and speed are achieved. Its low order computational complexity [O(lm), where l and m are the number of links in the two graphs] and robustness in the presence of noise offer advantages over traditional combinatorial approaches. The algorithm, not restricted to any special class of graph, is applied to subgraph isomorphism, weighted graph matching, and attributed relational graph matching. To illustrate the performance of the algorithm, attributed relational graphs derived from objects are matched. Then, results from twenty-five thousand experiments conducted on 100 mode random graphs of varying types (graphs with only zero-one links, weighted graphs, and graphs with node attributes and multiple link types) are reported. No comparable results have been reported by any other graph matching algorithm before in the research literature. Twenty-five hundred control experiments are conducted using a relaxation labeling algorithm and large improvements in accuracy are demonstrated.
Evaluation of the Solitaire System in a Canine Arterial Thromboembolic Occlusion Model: Is it Safe for the Endothelium?

The Solitaire system has recently been increasingly used for acute stroke treatment in which the endothelial safety immediately after its use has not been evaluated. This study was performed to evaluate the endothelial status when using a Solitaire system in a canine arterial occlusion model. Thromboembolic occlusion of both internal maxillary arteries was achieved in five mongrel dogs. In each animal, the Solitaire system (ev3, Irvine, CA, USA) was used for primary thrombectomy on the right side and for temporary stenting on the left side. Efficacy was assessed by comparing the recanalization rates, and safety was assessed using angiographic and microscopic assessments. Endothelial injuries were evaluated with light microscopy (LM) and scanning electron microscopy (SEM). Successful revascularizations were observed following primary thrombectomy in all five animals (100%) and after temporary stenting in two (40%). There was no incidence of vasospasm or vessel perforation in either group. Distal migration of the clot occurred in two animals that underwent primary thrombectomy. Endothelial injury was seen after primary thrombectomy in two animals (40%) and after temporary stenting in one (20%). The lesions presented as defects of the internal elastic lamina on LM and denudation of the wavy endothelial surface on SEM. During mechanical thrombectomy, the Solitaire system can cause endothelial injury both in primary thrombectomy and temporary stenting. Primary thrombectomy is likely to have a higher recanalization rate with increased endothelial injury.
Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding

Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206‐L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina‐sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance.
Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data

Recently, several experimental techniques have emerged for probing RNA structures based on high-throughput sequencing. However, most secondary structure prediction tools that incorporate probing data are designed and optimized for particular types of experiments. For example, RNAstructure-Fold is optimized for SHAPE data, while SeqFold is optimized for PARS data. Here, we report a new RNA secondary structure prediction method, restrained MaxExpect (RME), which can incorporate multiple types of experimental probing data and is based on a free energy model and an MEA (maximizing expected accuracy) algorithm. We first demonstrated that RME substantially improved secondary structure prediction with perfect restraints (base pair information of known structures). Next, we collected structure-probing data from diverse experiments (e.g. SHAPE, PARS and DMS-seq) and transformed them into a unified set of pairing probabilities with a posterior probabilistic model. By using the probability scores as restraints in RME, we compared its secondary structure prediction performance with two other well-known tools, RNAstructure-Fold (based on a free energy minimization algorithm) and SeqFold (based on a sampling algorithm). For SHAPE data, RME and RNAstructure-Fold performed better than SeqFold, because they markedly altered the energy model with the experimental restraints. For high-throughput data (e.g. PARS and DMS-seq) with lower probing efficiency, the secondary structure prediction performances of the tested tools were comparable, with performance improvements for only a portion of the tested RNAs. However, when the effects of tertiary structure and protein interactions were removed, RME showed the highest prediction accuracy in the DMS-accessible regions by incorporating in vivo DMS-seq data.
The influence of Chinese-Western Bilingualism on Rationality in Decision Making Behavior

This study aimed to investigate the influence of bilingualism on the decision making behavior of Chinese-Western bilinguals. Three tasks, including gain-loss asymmetry, loss aversion and myopic loss aversion, were conducted with 30 Chinese-Western bilingual participants. The results indicated that Chinese-Western bilinguals behaved more rationally in a Chinese language context than in an English language context.