Miracle-dz/UniFAR-FTUs huggingface dataset:
Injectable hydrogel-based scaffolds for tissue engineering applications

Abstract Hydrogels are highly hydrated materials that may absorb from 10% to 20% up to hundreds of times their dry weight in water and are composed of three-dimensional hydrophilic polymeric networks that are similar to those in natural tissue. The structural integrity of hydrogels depends on cross-links formed between the polymer chains. Hydrogels have been extensively explored as injectable cell delivery systems, owing to their high tissue-like water content, ability to mimic extracellular matrix, homogeneously encapsulated cells, efficient mass transfer, amenability to chemical and physical modifications, and minimally invasive delivery. A variety of naturally and synthetically derived materials have been used to form injectable hydrogels for tissue engineering applications. The current review article focuses on these biomaterials, on the design parameters of injectable scaffolds, and on the in situ gelling of their hydrogel systems. The last section of this article describes specific examples of catheter-based delivery systems.
Relationships between PTEN and clinicopathological features of hepatocellular carcinoma : a meta-analysis

We performed a meta-analysis to demonstrate the relationship between PTEN expression in immunochemical staining and clinicopathological features of hepatocellular cancer (HCC). There were 11 eligible researches encompassing 872 HCC patients from the databases we used, including PubMed, Embase, and Web of Science. We are using the odds ratios (ORs) with 95% confidence intervals (95% CIs) to evaluate for absence of heterogeneity in a fixed effects model. Significant associations between positive PTEN expression and high tumor grades (OR = 2.56, 95% CI: 1.89-3.47, P < 0.00001), early tumor stage (OR = 3.26, 95% CI: 1.48-7.22, P < 0.00001), less cirrhosis (OR = 0.61, 95% CI: 0.42-0.89, P = 0.01) were found. However, according to the results, we found no significant associations between PTEN expression and gender, tumor size and capsule invasion of HCC patients.
Altered spring phenology of North American freshwater turtles and the importance of representative populations

Abstract Globally, populations of diverse taxa have altered phenology in response to climate change. However, most research has focused on a single population of a given taxon, which may be unrepresentative for comparative analyses, and few long‐term studies of phenology in ectothermic amniotes have been published. We test for climate‐altered phenology using long‐term studies (10–36 years) of nesting behavior in 14 populations representing six genera of freshwater turtles (Chelydra, Chrysemys, Kinosternon, Malaclemys, Sternotherus, and Trachemys). Nesting season initiation occurs earlier in more recent years, with 11 of the populations advancing phenology. The onset of nesting for nearly all populations correlated well with temperatures during the month preceding nesting. Still, certain populations of some species have not advanced phenology as might be expected from global patterns of climate change. This collection of findings suggests a proximate link between local climate and reproduction that is potentially caused by variation in spring emergence from hibernation, ability to process food, and thermoregulatory opportunities prior to nesting. However, even though all species had populations with at least some evidence of phenological advancement, geographic variation in phenology within and among turtle species underscores the critical importance of representative data for accurate comprehensive assessments of the biotic impacts of climate change.
Effective Long-term Monitoring Strategies by Integrating Reactive Transport Models with In situ Geochemical Measurements – 16212

Long-term monitoring of contaminant transport in groundwater is expected to account for a large fraction of future life-cycle cleanup costs at the DOE sites. The Attenuation-Based Remedies in the Subsurface Applied Field Research Initiative (ABRS AFRI) is developing an innovative approach for cost-effective in situ long-term monitoring. The approach is based on strategically adding the measurements of controlling variables (such as pH, redox potential, electrical conductivity, and groundwater level), which control the plume mobility and its spatial and temporal distribution. In situ measurements of these variables – supplemented with a reduced number of standard periodic groundwater samples – are expected to lead to more cost-effective monitoring, and can also serve as an early warning system for detecting unexpected plume migration. The objective of this study is to support the development of such a long-term monitoring approach through the application of advanced computational methods, including (1) statistical data mining and analysis, and (2) three-dimensional flow and reactive chemical transport modeling. We have performed the statistical data analysis of historical and current monitoring data at the Savannah River Site (SRS) F-Area to quantify the correlations between the controlling variables and radioactive contaminant concentrations. In parallel, we have used 3D modeling of flow and contaminant transport to provide the prediction of the contaminant plume evolution. The results of both data analysis and modeling confirmed that the correlations between controlling variables and contaminant concentrations are significant. Modeling results also suggest that the correlation parameters will change in the future, which is important to assess the long-term efficacy of the proposed monitoring
Safe exposure distances for transcranial magnetic stimulation based on computer simulations

The results of a computer simulation examining the compliance of a given transcranial magnetic stimulation device to the 2010 International Commission on Non-Ionizing Radiation Protection (ICNIRP) guidelines are presented. The objective was to update the safe distance estimates with the most current safety guidelines, as well as comparing these to values reported in previous publications. The 3D data generated was compared against results available in the literature, regarding the MCB-70 coil by Medtronic. Regarding occupational exposure, safe distances of 1.46 m and 0.96 m are derived from the simulation according to the 2003 and 2010 ICNIRP guidelines, respectively. These values are then compared to safe distances previously reported in other studies.
Interfacial properties of model colloid–polymer mixtures

We summarize the main results of our recent investigations of the interfacial properties of the simplest model of a colloid–polymer mixture, namely that introduced by Asakura & Oosawa and by Vrij, in which colloid–colloid and colloid–polymer interactions are treated as hard sphere–like, while the polymer–polymer interaction is ideal (perfectly interpenetrating coils). In spite of its simplicity, we find that the model exhibits rich interfacial behaviour which depends on the size ratio q ≡ σp/σc, where σp and σc denote the diameters of polymer and colloid, respectively. For highly asymmetric mixtures, q < 0.1547, an explicit and exact mapping of the binary mixture to an effective one–component Hamiltonian for the colloids allows one to perform computer simulations for inhomogeneous mixtures. We investigate a mixture with q = 0.1 and find that small amounts of polymer give rise to strong depletion effects at a hard wall. The colloid density at contact with the wall is several times greater than that for pure hard spheres at a hard wall. However, for states removed from the bulk fluid–solid coexistence curve we find no evidence of wall–induced crystallization. In order to treat less asymmetric cases, where stable fluid–fluid demixing occurs in bulk, we have designed a density functional theory specifically for this model mixture. For q = 0.6 we find a first order wetting transition from partial to complete wetting by the colloid–rich phase at the hard–wall–colloid–poor interface as the packing fraction ηrp of polymer in the reservoir is decreased. At a slightly higher value of ηrp, there is a novel single layering transition, characterized by a jump in the densities in the first two adsorbed layers, as the bulk colloid packing fraction ηc is increased. The same density functional has been used to investigate the surface tension and colloid and polymer density profiles at the free interface between the demixed fluid phases.
Representation of Categories Metaphorical Use of the Container Schema

In the present study we investigated whether the mental representation of the concept categories is represented by the container image schema (Lakoff & Johnson, 1980). In two experiments participants decided whether two pictures were from the same category (animal or vehicle). Pictures were presented inside or outside a frame that should activate the container schema. We found that performance to pictures was influenced by the frame in congruence with the metaphorical mapping (same category – inside bounded region; different category – not in same bounded region). These results show that the concept categories is metaphorically represented by containers.
Molecular Identification of Candida Species in Clinical Isolates

Candida exists as a normal flora on skin and mucosa. The prevalence of Candida-induced infections specially mucosal and vaginal infections have been raised in the world in last decade due to increase in predisposing factors. C.albicans is the major etiological agent of candidiasis, but infections due to other species have been increasing. The aim of this study was to determine Candida species by using polymerase chain reaction (PCR) in patient with oral and vulvovaginal candidiasis that referred to clinics of Babol University of Medical Sciences, Babol, Iran. Sixty clinical samples were collected from mouth (no= 29) and vagina (no= 31). Identification of Candida species was done by using a combination of conventional and PCR methods. Germ tube and vesicle (chlamidoconidia) were seen in 43(71.67%) and 42(75%) of Candida isolates, respectively. Assimilation of sugars and Gel electrophoresis of PCR products showed that 78.34% and 75% of isolates were C.albicans, respectively, followed by C.parapsilosis, C.guilliermondii, C.tropicalis and C.glabrata. According to our results, C.albicans was the major causative agent in mouth, and also in vulvovaginal candidiasis. We concluded that Candida spp. is prevalent in mouth and vagina, indicating the necessity for preventing candidiasis by using some antifungal drugs.
New Results on Directed Edge Dominating Set

We study a family of generalizations of Edge Dominating Set on directed graphs called Directed $(p,q)$-Edge Dominating Set. In this problem an arc $(u,v)$ is said to dominate itself, as well as all arcs which are at distance at most $q$ from $v$, or at distance at most $p$ to $u$. First, we give significantly improved FPT algorithms for the two most important cases of the problem, $(0,1)$-dEDS and $(1,1)$-dEDS (that correspond to versions of Dominating Set on line graphs), as well as polynomial kernels. We also improve the best-known approximation for these cases from logarithmic to constant. In addition, we show that $(p,q)$-dEDS is FPT parameterized by $p+q+tw$, but W-hard parameterized by $tw$ (even if the size of the optimal is added as a second parameter), where $tw$ is the treewidth of the underlying graph of the input. We then go on to focus on the complexity of the problem on tournaments. Here, we provide a complete classification for every possible fixed value of $p,q$, which shows that the problem exhibits a surprising behavior, including cases which are in P; cases which are solvable in quasi-polynomial time but not in P; and a single case $(p=q=1)$ which is NP-hard (under randomized reductions) and cannot be solved in sub-exponential time, under standard assumptions.
Functional comparison of anoctamin 1 antagonists on human uterine smooth muscle contractility and excitability

Background: Pre-term birth is a major health care challenge throughout the world, and preterm labor represents a potentially reversible component of this problem. Current tocolytics do not improve preterm labor beyond 48 h. We have previously shown that anoctamin 1 (ANO1) channel blockade results in relaxation of pre-contracted human uterine smooth muscle (USM). Three drug classes with reported medicinal effects in humans also have members with ANO1 antagonism. In this study, we compared the ability of representatives from these 3 classes to reduce human USM contractility and excitability. Objective: This study sought to examine the comparative potency of 3 ANO1 antagonists on pregnant human USM relaxation, contraction frequency reduction, inhibition of intracellular calcium release and membrane hyperpolarization. Methods: Experiments were performed using: 1) Ex vivo organ bath (human pregnant tissue), 2) Oxytocin-induced calcium flux (in vitro human USM cells) and 3) Membrane potential assay (in vitro human USM cells). Results: Benzbromarone (BB) demonstrated the greatest potency among the compounds tested with respect to force, frequency inhibition, reducing calcium elevation and depolarizing membrane potential. Conclusion: While all 3 ANO1 antagonists attenuate pregnant human uterine tissue contractility and excitability, BB is the most potent tocolytic drug. Our findings may serve as a foundation for future structure-function analyses for novel tocolytic drug development.
Biogeosciences Detecting anthropogenic carbon dioxide uptake and ocean acidification in the North Atlantic Ocean

Fossil fuel use, cement manufacture and land-use changes are the primary sources of anthropogenic carbon dioxide (CO2) to the atmosphere, with the ocean absorbing approximately 30 % (Sabine et al., 2004). Ocean uptake and chemical equilibration of anthropogenic CO 2 with seawater results in a gradual reduction in seawater pH and saturation states ( ) for calcium carbonate (CaCO 3) minerals in a process termed ocean acidification. Assessing the present and future impact of ocean acidification on marine ecosystems requires detection of the multi-decadal rate of change across ocean basins and at ocean time-series sites. Here, we show the longest continuous record of ocean CO 2 changes and ocean acidification in the North Atlantic subtropical gyre near Bermuda from 1983–2011. Dissolved inorganic carbon (DIC) and partial pressure of CO 2 (pCO2) increased in surface seawater by ∼40 μmol kg−1 and∼50 μatm ( ∼20 %), respectively. Increasing Revelle factor ( β) values imply that the capacity of North Atlantic surface waters to absorb CO 2 has also diminished. As indicators of ocean acidification, seawater pH decreased by ∼0.05 (0.0017 yr −1) and values by ∼7–8 %. Such data provide critically needed multi-decadal information for assessing the North Atlantic Ocean CO 2 sink and the pH changes that determine marine ecosystem responses to ocean acidification.
Training a neural network to count: A genetic approach

Recurrent neural networks (RNNs) are capable of learning languages. However, the learning performance is not satisfactory. Recent studies have revealed that the main reason lies in the complex relationship between the weightspace and the dynamics of the RNN. As a result, traditional gradient-based algorithms such as backpropagation through time (BPTT) tend to encounter difficulty. This project tries to solve this problem by considering the application of Genetic Algorithms (GAs) in RNNs training. We first show that a GA can also be used as the training algorithm of a RNN on a simple task. Furthermore, we propose a handcrafted GA that is more suitable for learning the context-free a n b n language. The performance of this GA on learning the context-sensitive a n b n c n language is also investigated. We conclude that the GA is a promising training algorithm for RNNs on language learning tasks and more work needs to be done to further improve its performance.
An Emergence Model for Wild Oat (Avena fatua)

Abstract Wild oat is an economically important annual weed throughout small grain producing regions of the United States and Canada. Timely and more accurate control of wild oat may be developed if there is a better understanding of its emergence patterns. The objectives of this research were to evaluate the emergence pattern of wild oat and determine if emergence could be predicted using soil growing degree days (GDD) and/or hydrothermal time (HTT). Research plots were established at Crookston, MN, and Fargo, ND, in 2002 and 2003. On a weekly basis, naturally emerging seedlings were counted and removed from six 0.37-m2 permanent quadrats randomly distributed in a wild oat–infested area. This process was repeated until no additional emergence was observed. Wild oat emergence began between May 1 and May 15 at both locations and in both years and continued for 4 to 6 wk. Base soil temperature and soil water potential associated with wild oat emergence were determined to be 1 C and −0.6 MPa, respectively. Seedling emergence was correlated with GDD and HTT but not calendar days (P = 0.15). A Weibull function was fitted to cumulative wild oat emergence and GDD and HTT. The models for GDD (n = 22, r2 = 0.93, root mean square error [RMSE] = 10.7) and HTT (n = 22, r2 = 0.92, RMSE = 11.2) closely fit observed emergence patterns. The latter model is the first to use HTT to predict wild oat emergence under field conditions. Both models can aid in the future study of wild oat emergence and assist growers and agricultural professionals with planning timely and more accurate wild oat control. Nomenclature: Wild oat, Avena fatua L. AVEFA
The Global Islands Invasive Vertebrate Eradication Database: A tool to improve and facilitate restoration of island ecosystems

Islands are important for the conservation of biodiversity because they house 20% of terrestrial plant and vertebrate species, have suffered 64% of IUCN-listed extinctions and have 45% of IUCN-listed critically endangered species. Yet islands make up only about fi ve percent of the earth’s surface. The main cause of extinction and endangerment to biodiversity on islands is the presence of invasive vertebrates. Fortunately, many future extinctions can be prevented by eradicating invasive vertebrates from islands. To assess the current state of this conservation tool, we are compiling a global database of terrestrial vertebrate eradications from islands, including successes and failures. To date, in the Global Islands Invasives Vertebrate Eradication Database we have documented approximately 950 island eradication attempts involving 28 species of invasive vertebrates in 12 families. These are preliminary data and will be updated and checked for accuracy as part of the Island Invasives: Eradication and Management conference, Auckland 2010. Most eradication attempts have been of rodents (>350) and bovid ungulates (>160). Moderate numbers of eradication attempts have been of cats (>90), suid ungulates (>55), and rabbits (>45). Most projects have been on islands smaller than 500 ha (68%) and in temperate climates (72%). Targeting eradications on larger and more tropical islands would lead to the protection of more biodiversity. To this end, our vision is to maintain an accurate, web-accessible, regularly updated database that can be used to promote and improve the protection of island ecosystems by eradicating invasive vertebrates.
Selective molecular assembly patterning - A new approach to micro- and nanochemical patterning of surfaces for biological applications

A novel patterning technique based on selective self-assembly of alkane phosphates on metal oxide surfaces is presented. Standard photolithography was used to create patterns of titanium dioxide within a matrix of silicon dioxide. Alkane phosphates were found to self-assemble on TiO2, but not on SiO2, surfaces. Subsequent adsorption of poly(l-lysine)-g-poly(ethylene glycol) (PLL-g-PEG) rendered the exposed SiO2 surface resistant to protein adsorption. X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry were employed to monitor the assembly processes. Protein-adsorption studies by means of fluorescence microscopy conclusively established that the resulting surfaces displayed protein-adhesive, alkyl phosphate modified TiO2 features, arranged within a protein-resistant PLL-g-PEG-modified SiO2 matrix. Human foreskin fibroblasts, incubated in a serum-containing medium, were found to selectively attach to the protein-adhesive areas, where they developed focal contacts. No interac.
Arctigenin suppresses inflammation and plays a neuroprotective effect in mice with spinal cord injury

Inflammation plays a key role in secondary injury after spinal cord injury (SCI) leading to spinal cord demyelination and neuronal death. Previous studies have shown that arctigenin markedly inhibits the phosphorylation of MAPKs and the activation of NF-κB, and reduced the expression of IL-1, IL-6, and TNF-α, resulting in anti-inflammatory effects. However, it remains unclear whether arctigenin can be used to treat SCI. In the present study, SCI mice were treated with different concentrations of arctigenin, and their motor functional recovery, neuronal density, microglial activation, and inflammatory cytokine levels were investigated. We found that arctigenin improved the basso mouse scale score, regularity index, and MaxContact area, and enhanced the amplitude of motor evoked potentials, promoted functional recovery in a dose and time-dependent manner in the SCI mice. In addition, arctigenin protected the neurons in a dose-dependent manner. Furthermore, arctigenin inhibited microglial activation, down-regulated the expression of TNF-α, IFN-γ, IL-17, MCP-1, IL-6, and G-CSF, and the effect became more obvious as the concentration of arctigenin increased. In conclusion, arctigenin plays a neuroprotective role by inhibiting the activation of microglia, and reducing the expression of inflammation in the early stage of SCI in mice.
Anomalously low dielectric constant of confined water

Water's surface dielectric Theoretical studies predict that the inhibition of rotational motion of water near a solid surface will decrease its local dielectric constant. Fumagalli et al. fabricated thin channels in insulating hexagonal boron nitride on top of conducting graphene layers (see the Perspective by Kalinin). The channels, which varied in height from 1 to 300 nanometers, were filled with water and capped with a boron nitride layer. Modeling of the capacitance measurements made with an atomic force microscope tip revealed a surface-layer dielectric constant of 2, compared with the bulk value of 80 for water. Science, this issue p. 1339; see also p. 1302 Capacitance measurements reveal a low dielectric constant for atomically thin layers of water next to solid surfaces. The dielectric constant ε of interfacial water has been predicted to be smaller than that of bulk water (ε ≈ 80) because the rotational freedom of water dipoles is expected to decrease near surfaces, yet experimental evidence is lacking. We report local capacitance measurements for water confined between two atomically flat walls separated by various distances down to 1 nanometer. Our experiments reveal the presence of an interfacial layer with vanishingly small polarization such that its out-of-plane ε is only ~2. The electrically dead layer is found to be two to three molecules thick. These results provide much-needed feedback for theories describing water-mediated surface interactions and the behavior of interfacial water, and show a way to investigate the dielectric properties of other fluids and solids under extreme confinement.