Miracle-dz/UniFAR-FTUs huggingface dataset:
Immobilization of D-allulose 3-Epimerase Into Magnetic Metal-Organic Framework Nanoparticles For E�cient Biocatalysis

D-allulose is a rare low-calorie sugar that has many fundamental biological functions. D-allulose 3-epimerase from Agrobacterium tumefaciens (AT-DAEase) catalyzes the conversion of D-fructose to D-allulose. The enzyme has attracted considerable attention because of its mild catalytic properties. However, the bioconversion e�ciency and reusability of AT-DAEase limit its industrial application. Magnetic metal-organic frameworks (MOFs) have uniform pore sizes and large surface areas and can facilitate mass transport and enhance the capacity for enzyme immobilization. Here, we successfully encapsulated cobalt-type AT-DAEase into the cobalt-based magnetic MOF ZIF-67@Fe 3 O 4 using a self-assembly strategy. The AT-DAEase@ZIF-67@Fe 3 O 4 nanoparticles had higher catalytic activity (65.1 U mg 1 ) and bioconversion ratio (38.1%) than the free AT-DAEase. The optimal conditions for maximum enzyme activity of the AT-DAEase@ZIF-67@Fe 3 O 4 nanoparticles were 55°C and pH 8.0, which were signi�cantly higher than those of the free AT-DAEase (50°C and pH 7.5). The AT-DAEase@ZIF-67@Fe 3 O 4 nanoparticles displayed signi�cantly improved thermal stability and excellent recycling performance, with 80% retention of enzyme activity at temperature range of 45-70°C and >45% of its initial activity after eight cycles of enzyme use. The AT-DAEase@ZIF-67@Fe 3 O 4 nanoparticles have great potential for large-scale industrial preparation of D-allulose by immobilizing cobalt-type AT-DAEase into magnetic MOF ZIF-67@Fe 3 O 4 .
Image‐based modeling of 3D objects with curved surfaces

This paper addresses an image‐based method for modeling 3D objects with curved surfaces based on the non‐uniform rational B‐splines (NURBS) representation. The user fits the feature curves on a few calibrated images with 2D NURBS curves using the interactive user interface. Then, 3D NURBS curves are constructed by stereo reconstruction of the corresponding feature curves. Using these as building blocks, NURBS surfaces are reconstructed by the known surface building methods including bilinear surfaces, ruled surfaces, generalized cylinders, and surfaces of revolution. In addition to them, we also employ various advanced techniques, including skinned surfaces, swept surfaces, and boundary patches. Based on these surface modeling techniques, it is possible to build various types of 3D shape models with textured curved surfaces without much effort. Copyright © 2007 John Wiley & Sons, Ltd.
Early treatment with lisinopril and spironolactone preserves cardiac and skeletal muscle in Duchenne muscular dystrophy mice.

BACKGROUND Nearly universal cardiomyopathy in Duchenne muscular dystrophy (DMD) contributes to heart failure and death. Because DMD patients show myocardial fibrosis well before functional impairment, we postulated that earlier treatment using drugs with antifibrotic effect may be beneficial. METHODS AND RESULTS Three groups of 10 utrn(+/-);mdx, or "het" mice, deficient for dystrophin and haploinsufficient for utrophin with skeletal myopathy and cardiomyopathy that closely mimics clinical DMD were studied. One het group received spironolactone and lisinopril starting at 8 weeks of life (het-treated-8); a second received the same starting at 4 weeks of life (het-treated-4), and the third het group was untreated. At 20 weeks, all mice had normal ejection fractions though circumferential strain rate was abnormal (-0.21±0.08) in untreated hets. This improved to -0.40±0.07 in het-treated-8 mice (P=0.003) and further improved to -0.56±0.10 in het-treated-4 mice (P=0.014 for het-treated-4 versus het-treated-8). Treated mice showed less cardiomyocyte damage, with a 44% reduction in intracardiomyocyte serum immunoglobulin G localization in het-treated-8 mice (P<0.0001) and a further 53% reduction in het-treated-4 mice (P=0.0003 versus het-treated-8); matrix metalloproteinases were similarly reduced. Cardiac, limb, and diaphragm function by ex vivo muscle testing remained at 80% of normal with early treatment compared to a decline to 40% of normal skeletal muscle function without treatment. CONCLUSIONS These findings offer clinically available medications with proven antifibrotic effect as a new therapeutic strategy in DMD. Early initiation greatly attenuated myocardial disease and, for the first time with these drugs, improved skeletal myopathy. Thus, early initiation of such agents warrants further clinical evaluation to maintain ambulatory, respiratory, and cardiac function for patients with DMD and related myopathies.
Punishment and Cooperation in Stochastic Social Dilemmas

Previous findings on punishment have focused on deterministic environments in which the outcomes are known with certainty. In this article, we conduct experiments to investigate how punishment affects cooperation in stochastic social dilemmas where each person can decide whether to cooperate, when the outcomes of alternative strategies are specified probabilistically. Two types of punishment mechanisms are studied: (1) an unrestricted punishment mechanism—both persons can punish—and (2) a restricted punishment mechanism—only cooperators can punish noncooperators. We compare behavior in a two-person deterministic prisoner’s dilemma game (DPD) with a two-person stochastic prisoner’s dilemma (SPD). In all treatments, participants are given information on the other person’s actions. We find that in both games, the restricted punishment mechanism promotes more cooperative behavior than unrestricted punishment. However, the difference in the degree of effectiveness between the two mechanisms is smaller in the SPD game than in the DPD game because noncooperative behavior is less likely to be punished when there is outcome uncertainty. Our findings provide useful information for designing efficient incentive mechanisms to induce cooperation in a stochastic social dilemma environment.
Assessing the neurocognitive correlates of resting brain entropy

The human brain exhibits large-scale spontaneous fluctuations that account for most of its total energy metabolism. Independent of any overt function, this immense ongoing activity likely creates or maintains a potential functional brain reserve to facilitate normal brain function. An important property of spontaneous brain activity is the long-range temporal coherence, which can be characterized by resting state fMRI-based brain entropy mapping (BEN), a relatively new method that has gained increasing research interest. The purpose of this study was to leverage the large resting state fMRI and behavioral data publicly available from the human connectome project to address three important but still unknown questions: temporal stability of rsfMRI-derived BEN; the relationship of resting BEN to latent functional reserve; associations of resting BEN to neurocognition. Our results showed that rsfMRI-derived BEN was highly stable across time; resting BEN in the default mode network (DMN) and executive control network (ECN) was related to brain reserve in a negative correlation to education years; and lower DMN/ECN BEN corresponds to higher fluid intelligence and better task performance. These results suggest that resting BEN is a temporally stable brain trait; BEN in DMN/ECN may provide a means to measure the latent functional reserve that bestows better brain functionality and may be enhanced by education.
Predictive haptic guidance: intelligent user assistance for the control of dynamic tasks

Intelligent systems are increasingly able to offer real-time information relevant to a user's manual control of an interactive system, such as dynamic system control space constraints for animation control and driving. However, it is difficult to present this information in a usable manner and other approaches which have employed haptic cues for manual control in "slow" systems often lead to instabilities in highly dynamic tasks. We present a predictive haptic guidance method based on a look-ahead algorithm, along with a user evaluation which compares it with other approaches (no guidance and a standard potential-field method) in a 1-DoF steered path-following scenario. Look-ahead guidance outperformed the other methods in both quantitative performance and subjective preference across a range of path complexity and visibility and a force analysis demonstrated that it applied smaller and fewer forces to users. These results (which appear to derive from the predictive guidance's supporting users in taking earlier and more subtle corrective action) suggest the potential of predictive methods in aiding manual control of dynamic interactive tasks where intelligent support is available.
The Coxiella burnetii QpH1 Plasmid Is a Virulence Factor for Colonizing Bone Marrow-Derived Murine Macrophages

All C. burnetii isolates carry one of four large, conserved, autonomously replicating plasmids or a plasmid-like chromosomally integrated sequence. The plasmid is a candidate virulence factor of unknown function. ABSTRACT Coxiella burnetii strains carry one of four large, conserved, autonomously replicating plasmids (QpH1, QpRS, QpDV, or QpDG) or a QpRS-like chromosomally integrated sequence of unknown function. Here, we report the characterization of the QpH1 plasmid of C. burnetii Nine Mile phase II by making QpH1-deficient strains. A shuttle vector pQGK containing the CBUA0036 to CBUA0039a region (predicted as being required for QpH1 maintenance) was constructed. The pQGK vector can be stably transformed into Nine Mile II and maintained at a similar low copy number like QpH1. Importantly, transformation with pQGK cured the endogenous QpH1 due to plasmid incompatibility. Compared to a Nine Mile II transformant of an RSF1010-ori-based vector, the pQGK transformant shows a similar growth curve in both axenic media and Buffalo green monkey kidney cells, a variable growth defect in macrophage-like THP-1 cells depending on the origin of inoculum, and dramatically reduced ability to colonize wild-type bone marrow-derived murine macrophages. Furthermore, we found that CBUA0037 to CBUA0039 open reading frames (ORFs) are essential for plasmid maintenance, and CBUA0037 and CBUA0038 ORFs account for plasmid compatibility. In addition, plasmid-deficient C. burnetii can be isolated by using CBUA0037 or CBUA0038 deletion vectors. Furthermore, QpH1-deficient C. burnetii strains caused a lesser extent of splenomegaly in SCID mice, but, intriguingly, they had significant growth in SCID mouse-sourced macrophages. Taken together, our data suggest that QpH1 encodes a factor(s) essential for colonizing murine, not human, macrophages. This study suggests a critical role of QpH1 for C. burnetii persistence in rodents and expands the toolkit for genetic studies in C. burnetii. IMPORTANCE All C. burnetii isolates carry one of four large, conserved, autonomously replicating plasmids or a plasmid-like chromosomally integrated sequence. The plasmid is a candidate virulence factor of unknown function. Here, we describe the construction of novel shuttle vectors that allow making plasmid-deficient C. burnetii mutants. With this plasmid-curing approach, we characterized the role of the QpH1 plasmid in in vitro and in vivo C. burnetii infection models. We found that the plasmid plays a critical role for C. burnetii growth in murine macrophages. Our work suggests an essential role of the QpH1 plasmid for the acquisition of colonizing capability in rodents by C. burnetii. This study represents a major step toward unravelling the mystery of the C. burnetii cryptic plasmids.
Specific Polarizability of Sand-Clay Mixtures with Varying Ethanol Concentration by

by Sundeep Sharma A Dissertation submitted to the Graduate School-Newark Rutgers, The State University of New Jersey In partial fulfillment of the requirements for the degree of Master of Science Graduate Program in Environmental Geology written under the direction of Lee D. Slater and approved by __________________________ __________________________ __________________________ __________________________ Newark, New Jersey
The Pitfalls of Capital Budgeting When Costs Correlate to Oil Price

This paper investigates the economic relationship that exists between oil price and operating costs in the E&P industry and its implications for the capital budgeting and decision-making processes. We present empirical evidence that there is a positive correlation between price and operating costs, and that overlooking this relationship has severe implications for the valuation of investment projects, both using a traditional Net Present Value (NPV) methodology or a Real Option approach. In the traditional NPV method, overlooking a price-cost correlation results in undervalued projects, and under Real Option Analysis, projects tend to be overvalued if such correlation is ignored.
stoichiometry of a neglected trophic level.

biomass, we applied a standardised model averaging approach investigating the effects of basal resource stoichiometry, litter mass, plant species richness, and soil pH on both consumer community characteristics. This standardised approach enabled us to identify differences and similarities in the magnitude and importance of such effects on consumer species richness and biomass. 4. Across consumer groups, we found litter mass to be the most important predictor of both species richness and biomass. Resource stoichiometry had a more pronounced impact on consumer species richness than on their biomass. As expected, taxonomic groups differed in which resource and habitat parameters (basal resource stoichiometry, litter mass, plant species richness, and pH) were most important for modulating their community characteristics. 5. The importance of litter mass for both species richness and biomass indicates that these tropical consumers strongly depend on habitat space and resource availability. Our study supports previous theoretical work indicating that consumer species richness is jointly influenced by resource availability and the balanced supply of multiple chemical elements in their resources.
Can olfactory training support improvement of memory functioning in patients with cognitive disorders?

Aim. According to some theoretical interpretations of the olfactory training effects, the training may indirectly exert positive influence on cognitive functioning in patients with Alzheimer’s dementia. The mechanism of action is stimulation of cerebral blood flow in areas of brain which are shared by olfactory and memory processes. The aim of this article is to verify a hypothesis that the olfactory training improves memory and attention functions in patients with amnestic mild cognitive impairment. Method. Participants with amnestic mild cognitive impairment (N = 35; 17 males and 18 females) constituted their own control group. During the first 12 weeks from the baseline evaluation no therapeutic actions were performed. The subjects underwent control neuropsychological assessment and entered in the second stage of the study. In that stage they were subjected to a daily olfactory training, which included two a few-minute-long sessions per day, which were performed for the following 3 months. Subject’s memory functioning was measured at three time points: at the baseline, after 3 months and after 6 months (from the baseline). Cross-over assignment was used as the intervention method – which means that the participants constituted their own control group. The scales employed in the study to measure memory and attention were: ACE–III, CVLT, and MMSE. Results. Statistically significant improvement in memory functions measured with the CVLT, MMSE, ACE–III Memory, and ACE–III Total Score was obtained. It is considered an artefact related to practice effects, not true training results. Moreover, trend suggesting improvement on the ACE–III Attention was noted as well. Conclusions. The authors review theoretical implications of the conducted study. Methodological challenges pertaining to the study design are discussed and future research directions are proposed.
Species Distribution Modeling And Assessment of Environmental Drivers Responsible To Distribution And Preferred Niche of Critically Endangered Endemic Ornamental Freshwater Fish Species of The Genus Sahyadria

India has different bio-climatic zones that support diverse aquatic habitats rich in biodiversity. For effective conservation of endangered species in its habitat, it is essential to know the distribution of the fish species in the environmental range and for this species distribution models are the efficient and innovative tools. The present study used MaxEnt model to develop the probability distribution model highlighting the distribution of the fish species by analyzing the known occurrence records of Denison barb under genus Sahyadria (Sahyadria denisonii Day 1865 and Sahyadria chalakkudiensis (Menon, Rema Devi & Thobias 1999)) in relation to environmental variables typically incorporating seasonal and temporal variability. AUC of the models for Sahyadria species depicted good fitness. Both the species were found sensitive to 'Solar radiation', 'Temperature seasonality' and 'Temperature annual range' and these variables were assessed as the significant predictors. The sensitivity of distribution of both species to these environmental variables was found correlated with their breading and spawning seasons. 'Precipitation' was determined as a significant climatic envelop influencing distribution of the species associated with the river flow. The models showed that distribution of S. denisonii in the higher precipitation areas compared to S. chalakkudiensi. The probability distribution model with respect to distribution of both the species indicates a lineage barrier at Palghat Gap supporting the studies of earlier workers. At the latitudinal scale, prediction of the suitable ecological habitat provides the detailed insight into the distribution of all the genetic lineages of the genus Sahyadria. Evidently, the findings of this study can assist in determining ecological niches for other threatened and endangered species of other areas and may aid in field surveys as well as developing conservation plans.
Cosmogenic 36Cl accumulation in unstable landforms: 2. Simulations and measurements on eroding moraines

Cosmogenic 36Cl surface exposure ages obtained for multiple boulders from single landforms are usually characterized by a variance larger than that of the analytical methods employed. This excessive boulder-to-boulder variability, progressively more profound with increasing age of landforms, is due to removal of soil and gradual exposure of boulders at the surface. In our gradual exposure model, boulders are initially buried in moraine matrix. With time, erosion lowers the moraine surface and the boulders are gradually exposed to cosmic rays. Because the cosmic ray intensity changes with depth, the boulders are subjected to variable production rates of the cosmogenic 36Cl. Initial depth of boulders and their chemical composition are variable, which results in different amounts of the accumulated cosmogenic 36Cl and thus different apparent ages of boulders. The shape of the resulting distribution of the apparent ages and the coefficient of variation depend on the erosion depth, while the first moment is a function of the true surface age and the erosion depth. These properties of the apparent age distributions permit calculation of the surface age, the erosion depth, and also the average erosion rate. We tested the model calculations using 26 boulders from a late Pleistocene moraine at Bishop Creek, Sierra Nevada, California. The set exhibited a bimodal distribution of the 36Cl surface exposure ages. We interpreted the older mode as the result of gradual exposure and the younger one as the result of surficial processes other than soil removal. The 10 samples that constitute the older mode produced a distribution which closely matches the modeled distribution calculated using an age of 85 kyr and erosion depth of 570 g cm−2. This age is the same as an independent estimate obtained from cation ratio studies, and the calculated erosion depth is very close to the erosion depth of 600 g cm−2 based on a simple analytical model of soil erosion. These results indicate that our statistical model adequately describes effects of soil erosion on accumulation of cosmogenic 36Cl. The approach can be used to simultaneously obtain the true landform age and the erosion rate from apparent 36Cl ages and thereifore may help in evaluation of surface exposure ages of eroding landforms.
Effect of compost application on the soil microflora

Compost is used in agriculture as a fertiliser or to improve the physical structure of the soil. In addition, compost amended soil has been found to be suppressive against plant diseases caused by nematodes, bacteria, or soil-borne fungi in various cropping systems (Hoitink and Fahy, 1986; Ringer, 1998). However, the opposite, an increase of disease incidence due to a compost application, has also been demonstrated (Tuitert et al., 1998). Several reasons for these inconsistent results can be given. There are many types of compost, i.e. they differ in composition of organic materials and in maturity. In addition, the method and time of the compost application is important for the final effect in the field. Application of organic material just before planting the crop can even stimulate pathogens. Up to now, it is still difficult to predict the beneficial effect of compost products in plant pathosystems. To understand the influence of compost applications on soil suppressiveness, the microflora in soil before and after compost application has to be studied in more detail.
Is migraine associated to brain anatomical alterations? New data and coordinate-based meta-analysis

A growing number of studies investigate brain anatomy in migraine using voxel-(VBM) and surface-based morphometry (SBM), as well as diffusion tensor imaging (DTI). The purpose of this article is to identify consistent patterns of anatomical alterations associated with migraine. First, 19 migraineurs without aura and 19 healthy participants were included in a brain imaging study. T1-weighted MRIs and DTI sequences were acquired and analyzed using VBM, SBM and tract-based spatial statistics. No significant alterations of gray matter (GM) volume, cortical thickness, cortical gyrification, sulcus depth and white-matter tract integrity could be observed. However, migraineurs displayed decreased white matter (WM) volume in the left superior longitudinal fasciculus. Second, a systematic review of the literature employing VBM, SBM and DTI was conducted to investigate brain anatomy in migraine. Meta-analysis was performed using Seed-based d Mapping via permutation of subject images (SDM-PSI) on GM volume, WM volume and cortical thickness data. Alterations of GM volume, WM volume, cortical thickness or white-matter tract integrity were reported in 72%, 50%, 56% and 33% of published studies respectively. Spatial distribution and direction of the disclosed effects were highly inconsistent across studies. The SDM-PSI analysis revealed neither significant decrease nor significant increase of GM volume, WM volume or cortical thickness in migraine. Overall there is to this day no strong evidence of specific brain anatomical alterations reliably associated to migraine. Possible explanations of this conflicting literature are discussed.NCT02791997, registrated February 6th, 2015.