Miracle-dz/UniFAR-FTUs huggingface dataset:
Similarity in Neuronal Firing Regimes across Mammalian Species

The architectonic subdivisions of the brain are believed to be functional modules, each processing parts of global functions. Previously, we showed that neurons in different regions operate in different firing regimes in monkeys. It is possible that firing regimes reflect differences in underlying information processing, and consequently the firing regimes in homologous regions across animal species might be similar. We analyzed neuronal spike trains recorded from behaving mice, rats, cats, and monkeys. The firing regularity differed systematically, with differences across regions in one species being greater than the differences in similar areas across species. Neuronal firing was consistently most regular in motor areas, nearly random in visual and prefrontal/medial prefrontal cortical areas, and bursting in the hippocampus in all animals examined. This suggests that firing regularity (or irregularity) plays a key role in neural computation in each functional subdivision, depending on the types of information being carried. SIGNIFICANCE STATEMENT By analyzing neuronal spike trains recorded from mice, rats, cats, and monkeys, we found that different brain regions have intrinsically different firing regimes that are more similar in homologous areas across species than across areas in one species. Because different regions in the brain are specialized for different functions, the present finding suggests that the different activity regimes of neurons are important for supporting different functions, so that appropriate neuronal codes can be used for different modalities.
Biomarkers of Nutrition for Development (BOND)—Vitamin A Review

The Biomarkers of Nutrition for Development (BOND) project is designed to provide evidence-informed advice to anyone with an interest in the role of nutrition in health. The BOND program provides information with regard to selection, use, and interpretation of biomarkers of nutrient exposure, status, function, and effect, which will be especially useful for readers who want to assess nutrient status. To accomplish this objective, expert panels are recruited to evaluate the literature and to draft comprehensive reports on the current state of the art with regard to specific nutrient biology and available biomarkers for assessing nutritional status at the individual and population levels. Phase I of the BOND project includes the evaluation of biomarkers for 6 nutrients: iodine, folate, zinc, iron, vitamin A, and vitamin B-12. This review of vitamin A is the current article in this series. Although the vitamin was discovered >100 y ago, vitamin A status assessment is not trivial. Serum retinol concentrations are under homeostatic control due in part to vitamin A’s use in the body for growth and cellular differentiation and because of its toxic properties at high concentrations. Furthermore, serum retinol concentrations are depressed during infection and inflammation because retinol-binding protein (RBP) is a negative acute-phase reactant, which makes status assessment challenging. Thus, this review describes the clinical and functional indicators related to eye health and biochemical biomarkers of vitamin A status (i.e., serum retinol, RBP, breast-milk retinol, dose-response tests, isotope dilution methodology, and serum retinyl esters). These biomarkers are then related to liver vitamin A concentrations, which are usually considered the gold standard for vitamin A status. With regard to biomarkers, future research questions and gaps in our current understanding as well as limitations of the methods are described.
Complex discharge‐affecting networks in juvenile myoclonic epilepsy: A simultaneous EEG‐fMRI study

Juvenile myoclonic epilepsy (JME) is a common subtype of idiopathic generalized epilepsies (IGEs) and is characterized by myoclonic jerks, tonic‐clonic seizures and infrequent absence seizures. The network notion has been proposed to better characterize epilepsy. However, many issues remain not fully understood in JME, such as the associations between discharge‐affecting networks and the relationships among resting‐state networks. In this project, eigenspace maximal information canonical correlation analysis (emiCCA) and functional network connectivity (FNC) analysis were applied to simultaneous EEG‐fMRI data from JME patients. The main findings of our study are as follows: discharge‐affecting networks comprising the default model (DMN), self‐reference (SRN), basal ganglia (BGN) and frontal networks have linear and nonlinear relationships with epileptic discharge information in JME patients; the DMN, SRN and BGN have dense/specific associations with discharge‐affecting networks as well as resting‐state networks; and compared with controls, significantly increased FNCs between the salience network (SN) and resting‐state networks are found in JME patients. These findings suggest that the BGN, DMN and SRN may play intermediary roles in the modulation and propagation of epileptic discharges. These roles further tend to disturb the switching function of the SN in JME patients. We also postulate that emiCCA and FNC analysis may provide a potential analysis platform to provide insights into our understanding of the pathophysiological mechanism of epilepsy subtypes such as JME. Hum Brain Mapp 37:3515–3529, 2016. © 2016 Wiley Periodicals, Inc.
Search-Based Uncertainty-Wise Requirements Prioritization

To ensure the quality of requirements, a common practice, especially in critical domains, is to review requirements within a limited time and monetary budgets. A requirement with higher importance, larger number of dependencies with other requirements, and higher implementation cost should be reviewed with the highest priority. However, requirements are inherently uncertain in terms of their impact on the requirements implementation cost. Such cost is typically estimated by stakeholders as an interval, though an exact value is often used in the literature for requirements optimization (e.g., prioritization). Such a practice, therefore, ignores uncertainty inherent in the estimation of requirements implementation cost. This paper explicitly takes into account such uncertainty for requirement prioritization and formulates four objectives for uncertainty-wise requirements prioritization with the aim of maximizing 1) the importance of requirements, 2) requirements dependencies, 3) the implementation cost of requirements, and 4) cost over-run probability. We evaluated the multi-objective search algorithm NSGA-II together with Random Search (RS) using the RALIC dataset and 19 artificial problems. Results show that NSGA-II can solve the requirements prioritization problem with a significantly better performance than RS. Moreover, NSGA-II can prioritize requirements with higher priority earlier in the prioritization sequence. For example, in the case of the RALIC dataset, the first 10% of prioritized requirements in the prioritization sequence are on average 50% better than RS in terms of prioritization effectiveness.
Assessment of ALOS PALSAR 25-m mosaic data for land cover mapping

In this study, performance of the Global 25m resolution ALOS-PALSAR mosaic and forest/non-forest map generated by Japan Space Exploration Agency's - JAXA was addressed. PALSAR imagery has dual polarimetric data (HH and HV) and these dataset are open and freely available. An additional band applying difference of two polarizations (HH-HV) was added as a third band. For the study area most populated city of Turkey Istanbul is selected due to its rapid and dense expanse. For the evaluation 2010 and 2015 mosaic PALSAR data was classified using k-Nearest Neighbors (k-NN) method as a practical image classification approach. Moreover, an accuracy analysis for the forest/non-forest maps was also investigated to expose its misleading interpretation. A change detection analyses was conducted to estimate the changes from 2010 to 2015. In addition to these, the classified data was compared with 30m GlobeLand30 global data product. Results indicated that high rate classification result as 86% and 89% overall was obtained by k-NN with the three bands of ALOS-PALSAR mosaic data of 2010 and 2015, respectively.
Metabolic variation in natural populations of wild yeast

Ecological diversification depends on the extent of genetic variation and on the pattern of covariation with respect to ecological opportunities. We investigated the pattern of utilization of carbon substrates in wild populations of budding yeast Saccharomyces paradoxus. All isolates grew well on a core diet of about 10 substrates, and most were also able to grow on a much larger ancillary diet comprising most of the 190 substrates we tested. There was substantial genetic variation within each population for some substrates. We found geographical variation of substrate use at continental, regional, and local scales. Isolates from Europe and North America could be distinguished on the basis of the pattern of yield across substrates. Two geographical races at the North American sites also differed in the pattern of substrate utilization. Substrate utilization patterns were also geographically correlated at local spatial scales. Pairwise genetic correlations between substrates were predominantly positive, reflecting overall variation in metabolic performance, but there was a consistent negative correlation between categories of substrates in two cases: between the core diet and the ancillary diet, and between pentose and hexose sugars. Such negative correlations in the utilization of substrate from different categories may indicate either intrinsic physiological trade-offs for the uptake and utilization of substrates from different categories, or the accumulation of conditionally neutral mutations. Divergence in substrate use accompanies genetic divergence at all spatial scales in S. paradoxus and may contribute to race formation and speciation.
HIV-1 envelope sequence-based diversity measures for identifying recent infections

Identifying recent HIV-1 infections is crucial for monitoring HIV-1 incidence and optimizing public health prevention efforts. To identify recent HIV-1 infections, we evaluated and compared the performance of 4 sequence-based diversity measures including percent diversity, percent complexity, Shannon entropy and number of haplotypes targeting 13 genetic segments within the env gene of HIV-1. A total of 597 diagnostic samples obtained in 2013 and 2015 from recently and chronically HIV-1 infected individuals were selected. From the selected samples, 249 (134 from recent versus 115 from chronic infections) env coding regions, including V1-C5 of gp120 and the gp41 ectodomain of HIV-1, were successfully amplified and sequenced by next generation sequencing (NGS) using the Illumina MiSeq platform. The ability of the four sequence-based diversity measures to correctly identify recent HIV infections was evaluated using the frequency distribution curves, median and interquartile range and area under the curve (AUC) of the receiver operating characteristic (ROC). Comparing the median and interquartile range and evaluating the frequency distribution curves associated with the 4 sequence-based diversity measures, we observed that the percent diversity, number of haplotypes and Shannon entropy demonstrated significant potential to discriminate recent from chronic infections (p<0.0001). Using the AUC of ROC analysis, only the Shannon entropy measure within three HIV-1 env segments could accurately identify recent infections at a satisfactory level. The env segments were gp120 C2_1 (AUC = 0.806), gp120 C2_3 (AUC = 0.805) and gp120 V3 (AUC = 0.812). Our results clearly indicate that the Shannon entropy measure represents a useful tool for predicting HIV-1 infection recency.
Attending an activity center: positive experiences of a group of home-dwelling persons with early-stage dementia

Background In Norway, there is a focus on home-dwelling people with dementia receiving the opportunity to participate in organized meaningful activities. The aim of this study was to elucidate the experiences of home-dwelling persons with early-stage dementia who attend an activity center and participate in adapted physical and social activities delivered by nurses and volunteers. Methods The study adopted a qualitative approach, with individual interviews conducted among eight people diagnosed with early-stage dementia. The interview texts were analyzed using manifest and latent content analysis. Results Four categories, ie, “appreciated activities”, “praised nurses and volunteers”, “being more active”, and “being included in a fellowship”, as well as the overall theme “participation in appreciated activities and a sense of feeling included in a fellowship may have a positive influence on health and well-being” emerged in the analysis. The informants appreciated the adapted physical and social activities and expressed their enjoyment and gratitude. They found the physical activities useful, and they felt themselves to be included in a fellowship through cheerful nurses and volunteers. The nurses were able to create a good atmosphere and spread joy in the center together with the volunteers. The informants felt themselves valued as the persons they were. These findings indicated that such activities may have had a positive influence on the informants’ health and well-being. Conclusion In order to succeed with this kind of activity center, it is decisive that the nurses are able to tailor meaningful activities and create an environment where the persons with dementia can feel that they are respected and valued. The municipality health care service should implement such activity centers with specialist nurses in dementia care together with volunteers.
Preparation and properties of polyethylene‐clay hybrids

Polyethylene-clay hybrids have been prepared successfully by melt compounding with maleic anhydride grafted polyethylene (MA-g-PE), organophilic clay and polyethylene. In these polyethylene-clay hybrids, the silicate layers of the clay were exfoliated and dispersed to the monolayers. The hybrids exhibit higher tensile yield strengths and tensile moduli than those of polyethylene matrices and those of polyethylene-inorganic clay composites. When the 5-wt% clays were loaded, the tensile yield strength and the tensile modulus of the hybrid were, respectively, 1.4 and 1.8 times higher than those of the polyethylene/MA-g-PE mixture. The gas permeability of that clay hybrid decreased 30% compared with polyethylene/MA-g-PE mixture.
The effects of enterotoxins and short-chain fatty acids on water and electrolyte fluxes in ileal and colonic loops in vivo in the rat.

The effect of cholera toxin (CT) and Escherichia coli heat-stable enterotoxin (ST) on the ileum and colon was examined in vivo in the rat in an attempt to clarify the effects of enterotoxins on colonic mucosa and to determine if these effects were influenced by short-chain fatty acids (SCFA). Both CT and ST induced similar changes in water and electrolyte fluxes, and the magnitude of these changes in loops of colon was similar to that observed in loops of ileum. The addition of luminal SCFA, acetate, propionate and butyrate did not influence the effect of either toxin in loops of ileum. However, in loops of colon exposed to CT, luminal butyrate (40 mM) largely reversed the effect of CT by converting net water secretion (mean +/- SE, -363 +/- 154 nl.cm-2.min-1) to net water absorption (470 +/- 194 nl.cm-2.min-1) and by significantly reducing the net secretion of sodium ions. In loops of colon exposed to ST, similar effects were observed although net water secretion (-784 +/- 114 nl.cm-2.min-1) was only partially reversed by butyrate (-318 +/- 102 nl.cm-2.min-1). In contrast to butyrate, acetate and propionate did not influence changes in colonic fluxes of water and sodium induced by enterotoxins. Oxidation of butyrate and glucose was observed to be depressed in colonocytes pre-exposed to CT but not to ST. In this model, colonic secretion induced by enterotoxins is similar to that observed in the ileum but differs from ileal secretion in its modulation by luminal butyrate.
Formation of silicone fluid at the surface of RTV silicone rubber coating due to heat

The formation of low-molecular-weight silicone fluid at the surface of room temperature vulcanizing (RTV) silicone rubber coatings is shown to occur as a direct result of applying heat. Two independent methods are employed to demonstrate this phenomenon. In the first, the specimen surface is subjected to bombardment by varying energy input from a laser beam to generate the heat. In the second experiment the RTV specimens are subjected to varying amounts of heat energy in a thermal oven at 240/spl deg/C by varying the length of time of exposure. In the latter experiment both the bulk and the surface of the coating are subjected to heat. Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy was used to investigate the formation of the silicone fluid after the specimen was subjected to heat. The formation of silicon fluid is shown to be more pronounced with higher energy input. The heat that penetrates into the bulk of the RTV coating changes the PDMS (polydimethylsiloxane) molecules and forms short PDMS chains. Therefore, the silicone fluid increases in the bulk of the RTV coating. <<ETX>>
A high-resolution simulation of groundwater and surface water over most of the continental US with the integrated hydrologic model ParFlow v3

Abstract. Interactions between surface and groundwater systems are well-established theoretically and observationally. While numerical models that solve both surface and subsurface flow equations in a single framework (matrix) are increasingly being applied, computational limitations have restricted their use to local and regional studies. Regional or watershed-scale simulations have been effective tools for understanding hydrologic processes; however, there are still many questions, such as the adaptation of water resources to anthropogenic stressors and climate variability, that can only be answered across large spatial extents at high resolution. In response to this grand challenge in hydrology, we present the results of a parallel, integrated hydrologic model simulating surface and subsurface flow at high spatial resolution (1 km) over much of continental North America (~ 6.3 M km2). These simulations provide integrated predictions of hydrologic states and fluxes, namely, water table depth and streamflow, at very large scale and high resolution. The physics-based modeling approach used here requires limited parameterizations and relies only on more fundamental inputs such as topography, hydrogeologic properties and climate forcing. Results are compared to observations and provide mechanistic insight into hydrologic process interaction. This study demonstrates both the feasibility of continental-scale integrated models and their utility for improving our understanding of large-scale hydrologic systems; the combination of high resolution and large spatial extent facilitates analysis of scaling relationships using model outputs.
Chemoembolization of liver cancer with drug-loading microsphere 50-100μm

Transcatheter arterial chemoembolization (TACE) is the mainstay of treatment for unresectable hepatocellular carcinoma (HCC). The efficacy of conventional TACE (cTACE) in liver metastases is not satisfactory, which might be due to the fact of embolic material used. Recently, as a new type of drug-loading microsphere, HepaSphere has been introduced in China. In this study, there were total 30 patients (18 males and 12 females) with liver cancer underwent embolization with Hepasphere microsphere. And a total of 44 TACE procedures were performed using 50-100μm HepaSphere. There were 16 patients diagnosed as HCC and 14 patients as liver metastases. The follow up period ranged from 3 to 15 months (median 10 months). Response rates were calculated on intention-to-treat basis. One month after TACE, total objective response was 63.3% and disease control rate was 86.7%. No severe complication (such as infection, liver abscess, abdominal bleeding, tumor rupture) was observed. In conclusion, chemoembolization with Hepasphere microsphere may be a safe and possibly effective palliative treatment for patients with liver cancer.
Effect of cholinergic agonists and antagonists on rat hypothalamic corticotropin-releasing hormone secretion in vitro.

Several lines of experimental evidence suggest that acetylcholine (ACh) is excitatory to the hypothalamic-pituitary-adrenal (HPA) axis. Since previous experiments have shown that ACh does not affect pituitary adrenocorticotropin secretion in vitro, we hypothesized that ACh stimulates the HPA axis by causing hypothalamic corticotropin-releasing hormone (CRH) secretion. We examined this hypothesis using an organ culture system that measures the ability of single rat hypothalami to secrete immunoreactive CRH (IR-rCRH) in vitro. ACh stimulated hypothalamic IR-rCRH secretion in a dose-dependent fashion, at concentrations ranging from 3.3 x 10(-10) to 10(-5) M. This effect was antagonized by the simultaneous presence of atropine and hexamethonium, a muscarinic and a nicotinic receptor antagonist, respectively (p less than 0.05). Further evidence for the cholinergic regulation of the CRH neuron was provided by the findings that both carbachol, a muscarinic receptor agonist, and nicotine, a nicotinic receptor agonist, stimulated IR-rCRH secretion in a dose-dependent fashion. These effects were antagonized by atropine and hexamethonium, respectively, suggesting that both muscarinic and nicotinic receptors are involved in the process. ACh stimulated hypothalamic IR-rCRH secretion in the presence of phentolamine, an alpha-adrenergic antagonist, and ritanserin, a serotonin2 receptor antagonist, suggesting that the cholinergic stimulation of CRH secretion is not mediated by alpha-adrenergic or serotonergic interneurons. We conclude that ACh stimulates hypothalamic CRH secretion via both muscarinic and nicotinic receptor mechanisms. (ABSTRACT TRUNCATED AT 250 WORDS)
A somatosensory‐to‐motor cascade of cortical areas engaged in perceptual decision making during tactile pattern discrimination

The processes underlying perceptual decision making are diverse and typically engage a distributed network of brain areas. It is a particular challenge to establish a sensory‐to‐motor functional hierarchy in such networks. This is because single‐cell recordings mainly study the nodes of decision networks in isolation but seldom simultaneously. Moreover, imaging methods, which allow simultaneously accessing information from overall networks, typically suffer from either the temporal or the spatial resolution necessary to establish a detailed functional hierarchy in terms of a sequential recruitment of areas during a decision process. Here we report a novel analytical approach to work around these latter limitations: using temporal differences in human fMRI activation profiles during a tactile discrimination task with immediate versus experimentally delayed behavioral responses, we could derive a linear functional gradient across task‐related brain areas in terms of their relative dependence on sensory input versus motor output. The gradient was established by comparing peak latencies of activation between the two response conditions. The resulting time differences described a continuum that ranged from zero time difference, indicative for areas that process information related to the sensory input and, thus, are invariant to the response delay instruction, to time differences corresponding to the delayed response onset, thus indicating motor‐related processing. Taken together with our previous findings (Li Hegner et al. [ ]: Hum Brain Mapp 36:3339–3350), our results suggest that the anterior insula reflects the ultimate perceptual stage within the uncovered sensory‐to‐motor gradient, likely translating sensory information into a categorical abstract (non‐motor) decision. Hum Brain Mapp 38:1172–1181, 2017. © 2016 Wiley Periodicals, Inc.