Miracle-dz/UniFAR-FTUs huggingface dataset:
Glucosylglycerate Phosphorylase, an Enzyme with Novel Specificity Involved in Compatible Solute Metabolism

ABSTRACT Family GH13_18 of the carbohydrate-active enzyme database consists of retaining glycoside phosphorylases that have attracted interest with their potential for synthesizing valuable α-sugars and glucosides. Sucrose phosphorylase was believed to be the only enzyme with specificity in this subfamily for many years, but recent work revealed an enzyme with a different function and hinted at an even broader diversity that is left to discover. In this study, a putative sucrose phosphorylase from Meiothermus silvanus that resides in a previously unexplored branch of the family's phylogenetic tree was expressed and characterized. Unexpectedly, no activity on sucrose was observed. Guided by a thorough inspection of the genomic landscape surrounding other genes in the branch, the enzyme was found to be a glucosylglycerate phosphorylase, with a specificity never before reported. Homology modeling, docking, and mutagenesis pinpointed particular acceptor site residues (Asn275 and Glu383) involved in the binding of glycerate. Various organisms known to synthesize and accumulate glucosylglycerate as a compatible solute possess a putative glucosylglycerate phosphorylase gene, indicating that the phosphorylase may be a regulator of its intracellular levels. Moreover, homologs of this novel enzyme appear to be distributed among diverse bacterial phyla, a finding which suggests that many more organisms may be capable of assimilating or synthesizing glucosylglycerate than previously assumed. IMPORTANCE Glycoside phosphorylases are an intriguing group of carbohydrate-active enzymes that have been used for the synthesis of various economically appealing glycosides and sugars, and they are frequently subjected to enzyme engineering to further expand their application potential. The novel specificity discovered in this work broadens the diversity of these phosphorylases and opens up new possibilities for the efficient production of glucosylglycerate, which is a remarkably potent and versatile stabilizer for protein formulations. Finally, it is a new piece of the puzzle of glucosylglycerate metabolism, being the only known enzyme capable of catalyzing the breakdown of glucosylglycerate in numerous bacterial phyla.
Cleaning Effectiveness of EndoActivator Irrigation after Single-File and Multi-File Instrumentation Systems

The complexity of the canal anatomy makes it very difficult to efficiently clean all ramifications of the root canal system. Different devices and techniques have been proposed to improve canal cleanliness. Instrumentation of the canal is an essential part of chemomechanical canal preparation. It facilitates removal of pulp tissue and debris and enhances bacterial elimination through apical delivery of irrigant [1]. Many rotary instrumentation systems are available to achieve these goals. Despite variations in file design, fabrication, and technique, significant portions of the canal are untouched, and some debris remains [2-4]. The recently introduced nickel-titanium (NiTi) files Reciproc (VDW, Munich, Germany) and WaveOne (Dentsply Maillefer, Ballaigues, Switzerland) are claimed to be able to completely prepare and clean root canals with only one instrument. These files are made of a special M-Wire NiTi-alloy that is created by an innovative thermal-treatment process. These files are used in a reciprocal motion that requires special automated devices. Reciproc files are available in different sizes 25, taper 08; 40, taper 06; 50, taper 05 and WaveOne are available in the sizes 21, taper 06; 25, taper 08; and 40, taper 08 [5].
The Morphologies and Photoluminescence of Ce3+-Doped 0.5La2O3-2SrO-0.5Al2O3 Phosphors with SrF2

Ce3+-doped 0.5La2O3-2SrO-0.5Al2O3 (LSA:Ce) phosphors had been successfully synthesized using a conventional solid-state reaction method under reducing atmosphere (H2/N2 =1/5). The phase, morphologies and luminescence properties of the LSA:Ce phosphors were investigated. The emission intensity of LSA:Ce phosphors was improved by the addition of SrF2 as flux, and red shift of PL spectra peak was observed in this phosphors. Research results shown that the LSA:Ce phosphors have the potential to meet the development of white light-emitting diodes.
Yelp Restaurant Photo Classification

This project is about attaching labels to restaurants based on the photos uploaded by users. In this paper we have explored different methods to extract image features, extract restaurant features and classify restaurants. For the training set, the F1 score considering all labels is 0.7306. The mean F1 score is 0.69719. The mean F1 score on hidden test set is 0.69059.
Blue Water Footprint Management in a UK Poultry Supply Chain under Environmental Regulatory Constraints

Chicken is the most consumed meat in the UK, accounting for 40% of meat consumption, while national production sufficiency reaches about 80%. As a farmed animal product, chicken meat is responsible for significant freshwater appropriation volumes during its production cycle. In this context, this research aims at exploring freshwater dynamics in the UK processed poultry industry. Specifically, we develop a System Dynamics model to capture the blue water footprint, as a key sustainability performance indicator of a poultry supply chain, in the case that relevant environmental and regulatory constraints are applied. The model contributes towards investigating the impact of two potential policy-making scenarios, namely, the “water penalty” and the “water tax”, on the nexus between profitability and water usage across the poultry supply chain. Responding to the regulatory constraints, the food processor either reconfigures the supply chain through rethinking desired inventory levels or implements a water management intervention. The results indicate that investing in water-friendly production technologies could offer a greater advantage to sustainable supply chains in terms of blue water efficiency and profitability, compared to employing inventory management strategies. Overall, our analysis highlights that effective policy-making and technology-driven interventions could provide potential towards ensuring economic growth and environmental sustainability of the UK poultry sector.
Future Protein Supply and Demand: Strategies and Factors Influencing a Sustainable Equilibrium

A growing global population, combined with factors such as changing socio-demographics, will place increased pressure on the world’s resources to provide not only more but also different types of food. Increased demand for animal-based protein in particular is expected to have a negative environmental impact, generating greenhouse gas emissions, requiring more water and more land. Addressing this “perfect storm” will necessitate more sustainable production of existing sources of protein as well as alternative sources for direct human consumption. This paper outlines some potential demand scenarios and provides an overview of selected existing and novel protein sources in terms of their potential to sustainably deliver protein for the future, considering drivers and challenges relating to nutritional, environmental, and technological and market/consumer domains. It concludes that different factors influence the potential of existing and novel sources. Existing protein sources are primarily hindered by their negative environmental impacts with some concerns around health. However, they offer social and economic benefits, and have a high level of consumer acceptance. Furthermore, recent research emphasizes the role of livestock as part of the solution to greenhouse gas emissions, and indicates that animal-based protein has an important role as part of a sustainable diet and as a contributor to food security. Novel proteins require the development of new value chains, and attention to issues such as production costs, food safety, scalability and consumer acceptance. Furthermore, positive environmental impacts cannot be assumed with novel protein sources and care must be taken to ensure that comparisons between novel and existing protein sources are valid. Greater alignment of political forces, and the involvement of wider stakeholders in a governance role, as well as development/commercialization role, is required to address both sources of protein and ensure food security.
Draft Genome Sequence of Actinobacterial Strain Kineosporia sp. R_H_3, a Neutrophilic Iron-Depositing Bacterium

ABSTRACT The draft genome sequence of a neutrophilic iron-depositing actinobacterial strain, Kineosporia sp. R_H_3, is reported here. Detailed analysis of the genome can elucidate the role of specific cytochromes for Fe oxidation and how this organism might receive energy from Fe oxidation. To date, this is the second publicly available genome sequence of a Kineosporia strain.
Natural variation in ENSO flavors

Using a multivariate, “patterns‐based”, red noise approach to 42 years of observed tropical SST, thermocline depth, and zonal wind stress seasonal anomalies, it is shown that natural random variations can account for the observed variability of Central Pacific (CP) and Eastern Pacific (EP) ENSO events. The recent multidecadal increase in the number of CP events relative to EP events, which has been hypothesized to be connected to anthropogenic change in the state of the ocean, is also found to be consistent with multivariate red noise and hence with stationary statistics. ENSO “flavors” are the consequence of differing combinations of two initially orthogonal spatial patterns that are precursors to CP or EP events of both signs. These precursors can be excited by random weather forcing and subsequently result in SST anomaly amplification primarily through surface or thermocline feedbacks, respectively.
Decentralization can help reduce deforestation when user groups engage with local government

Significance Decentralization is one of the most important innovations in environmental policy during the past 30 years. Despite the pervasiveness and large amounts of resources invested to implement these reforms, little is known about their environmental effects. Given worldwide interest in forest conservation, this lack of knowledge hampers efforts to improve the effectiveness of current policy initiatives. Using quasi-experimental methods, we find that the environmental effects of decentralization reforms depend on how the reforms affect the conditions for user groups to govern their forests. Our findings show that decentralization to general-purpose governments may be most effective in places where forest users take advantage of opportunities to engage with local politicians about forestry issues. Policy makers around the world tout decentralization as an effective tool in the governance of natural resources. Despite the popularity of these reforms, there is limited scientific evidence on the environmental effects of decentralization, especially in tropical biomes. This study presents evidence on the institutional conditions under which decentralization is likely to be successful in sustaining forests. We draw on common-pool resource theory to argue that the environmental impact of decentralization hinges on the ability of reforms to engage local forest users in the governance of forests. Using matching techniques, we analyze longitudinal field observations on both social and biophysical characteristics in a large number of local government territories in Bolivia (a country with a decentralized forestry policy) and Peru (a country with a much more centralized forestry policy). We find that territories with a decentralized forest governance structure have more stable forest cover, but only when local forest user groups actively engage with the local government officials. We provide evidence in support of a possible causal process behind these results: When user groups engage with the decentralized units, it creates a more enabling environment for effective local governance of forests, including more local government-led forest governance activities, fora for the resolution of forest-related conflicts, intermunicipal cooperation in the forestry sector, and stronger technical capabilities of the local government staff.
Bio-based Polymer from Ferulic Acid by Electropolymerization

Electropolymerization was carried out in order to obtain a bio-based polymer by a simple procedure. Ferulic acid, a component of gramineous plants, was selected for this purpose. A thin polymer film was produced in an organic solvent medium (i.e., CH2Cl2/methanol (4:1 v/v) in the presence of 0.2 M LiClO4), whereas it was not obtained in a totally aqueous medium (0.2 M NaOH). Scanning electron microscopic analysis showed that the polymer film had a porous lamellar structure of ~10 μm thickness. Most of the carboxyl groups remained, and IR spectroscopy and time-of-flight secondary ion mass spectrometry (TOF-SIMS) analyses revealed that o-quinones existed in the polymer film. After electropolymerization, caffeic acid, sinapic acid, 3,6-bis(4-hydroxy-3-methoxyphenyl)tetrahydrofuro[3,4-c]furan-1,4-dione (1), and 4,4’-dihydroxy-3,3’-dimethoxy-β,β’-bicinnamic acid (2) were detected in the organic reaction medium; this suggested that demethylation, methoxyl group addition, and radical coupling reactions occurred at the electrode surface.
Precise Long-Range Synchronization of Activity and Silence in Neocortical Neurons during Slow-Wave Sleep

Slow-wave sleep is characterized by alternating periods of activity and silence in corticothalamic networks. Both activity and silence are stable network states, but the mechanisms of their alternation remain unknown. We show, using simultaneous multisite intracellular recordings in cats, that slow rhythm involves all neocortical neurons and that both activity and silence started almost synchronously in cells located up to 12 mm apart. Activity appeared predominantly at the area 5/7 border and spread in both anterior and posterior directions. The activity started earlier in fast-spiking cells and intrinsically bursting cells than in regular-spiking neurons. These results provide direct evidence for two mechanisms of active state generation: spread of activity from a local focus and synchronization of weaker activity, originating at multiple locations. Surprisingly, onsets of silent states were synchronized even more precisely than the onsets of activity, showing no latency bias for location or cell type. This most intriguing finding exposes a major gap in understanding the nature of state alternation. We suggest that it is the synchronous termination of activity and occurrence of silent states of the neuronal network that makes the EEG picture during slow-wave sleep so characteristic. Synchronous onset of silence in distant neurons cannot rely exclusively on properties of individual cells and synapses, such as adaptation of neuronal firing or synaptic depression; instead, it implies the existence of a network mechanism. Revealing this yet unknown large-scale mechanism, which switches network activity to silence, will aid our understanding of the origin of brain rhythms in normal function and pathology.
THE ROLE OF SPECIES ABUNDANCE IN DETERMINING BREEDING ORIGINS OF MIGRATORY BIRDS WITH STABLE ISOTOPES

Understanding the breeding origins of migratory birds captured on their wintering grounds has important management and conservation implications for declining populations of songbirds. Stable isotopes have recently been used to infer origins for species where application of conventional markers fails. A natural method of linking wintering birds to breeding populations, and one that has not been previously applied to stable isotopes, is based on likelihood. Using a likelihood assignment rule, birds are associated with the breeding population under which their realized isotope signature is most likely to have been generated. We report the first illustration of using likelihood-based assignment with stable isotope data. Moreover, within a probability-based framework for assignment, we argue that a more natural formulation of the assignment problem should be based on the probability of origin given the observed data, or the posterior probability of origin. The relationship between posterior assignment and tha.
Effect of cooling rate and crack propagation direction on the mode 1 interlaminar fracture toughness of biaxial noncrimp warp‐knitted fabric composites made of glass/PP commingled yarn

The mode 1 interlaminar fracture toughness of biaxial (±45°) noncrimp warp-knitted fabric composites made of glass/PP commingled yarn was investigated. The crack propagation along the warp and weft directions, respectively, was considered for the composites cooled at two different rates during laminate molding. The interlaminar fracture toughness was characterized by determining the critical strain energy release rate (GIC) of initiation and propagation measured from the double cantilever beam tests. In the case of a slow cooling rate (1°C/min), most specimens possess pure interlaminar crack propagation and direction-independence characteristics. Nevertheless, the high-cooled (10°C/min) specimens fractured in both directions suffer extensive intraply damage (crack branching, debonding, and bridging of 45°-oriented interfacial yarns) and knit thread breakage, leading to GIC of propagation two times higher than that of the slow-cooled specimens, and the clear difference in the GIC values of initiation between the two directions may be due to the contribution of the knit thread breakage to the fracture energy. POLYM. COMPOS. , 2008 © 2007 Society of Plastics Engineers
Mode competition of rotating waves in reflection-symmetric Taylor–Couette flow

We report on the results of a combined experimental and numerical study on mode interactions of rotating waves in Taylor–Couette flow. Our work shows that rotating waves which originate at a Hopf bifurcation from the steady axisymmetric Taylor vortex flow interact with this axisymmetric flow in a codimension-two fold-Hopf bifurcation. This interaction gives rise to an (unstable) low-frequency modulated wave via a subcritical Neimark–Sacker bifurcation from the rotating wave. At higher Reynolds numbers, a complicated mode interation between stable modulated waves originating at a different Neimark–Sacker bifurcation and a pair of symmetrically related rotating waves that originate at a cyclic pitchfork bifurcation is found to organize complex $Z_2$-symmetry breaking of rotating waves via global bifurcations. In addition to symmetry breaking of rotating waves via a (local) cyclic pitchfork bifurcation, we found symmetry breaking of modulated waves via a saddle-node-infinite-period (SNIP) global bifurcation. Tracing these local and global bifurcation curves in Reynolds number/aspect ratio parameter space toward their apparant merging point, unexpected complexity arises in the bifurcation structure involving non-symmetric two-tori undergoing saddle-loop homoclinic bifurcations. The close agreement between the numerics and the experiment is indicative of the robustness of the observed complex dynamics.
The Influence of Overlap Length on Adhesive Joint Strength

The influence of overlap length on the strength and failure mode of bonded wood double lap joints was investigated in this study. The overlap lengths ranged from 12.7 mm (0.5 in.) to 44.45 mm (1.75 in.) in 6.35-mm (1/4-in.) increments. The side members were 50.8 mm (2 in.) long, and the center member was 88.9 mm (3.5 in.) long. All joint members were 25.4 mm x 25.4 mm (1 in. x 1 in.) in cross section. The type of wood was yellow-poplar ( Liriodendron tulipifera ), and the joints were loaded in double shear. The strength of the joint was found to increase slightly with increased overlap length. The failure mode of the joints shifted from cleavage of the side members for the shortest overlap lengths, to a combination of side splits and forward shear failures for the intermediate overlaps, to center splits for the longest overlap lengths studied. While the joint strength trends observed for the double lap wood joints were consistent with previous work on other materials and similar conditions, the failure modes with the wood adherends were different from any other studies to date.
Spatio-temporal diffusion of dynamic PET images

Positron emission tomography (PET) images are corrupted by noise. This is especially true in dynamic PET imaging where short frames are required to capture the peak of activity concentration after the radiotracer injection. High noise results in a possible bias in quantification, as the compartmental models used to estimate the kinetic parameters are sensitive to noise. This paper describes a new post-reconstruction filter to increase the signal-to-noise ratio in dynamic PET imaging. It consists in a spatio-temporal robust diffusion of the 4D image based on the time activity curve (TAC) in each voxel. It reduces the noise in homogeneous areas while preserving the distinct kinetics in regions of interest corresponding to different underlying physiological processes. Neither anatomical priors nor the kinetic model are required. We propose an automatic selection of the scale parameter involved in the diffusion process based on a robust statistical analysis of the distances between TACs. The method is evaluated using Monte Carlo simulations of brain activity distributions. We demonstrate the usefulness of the method and its superior performance over two other post-reconstruction spatial and temporal filters. Our simulations suggest that the proposed method can be used to significantly increase the signal-to-noise ratio in dynamic PET imaging.
Functional change in the pattern of swallowing through the performance of orofacial exercises.

Purpose The objective was to determine if there was functional improvement of swallowing pattern in subjects identified with risk of oropharyngeal dysphagia after four weeks of specific oropharyngeal exercises. These exercises have pre-determined intensity and duration. Methods It is a longitudinal study of functional effect, determined by initial and final comparative measures. Participants were adults and elderly, selected in a period of 24 months. A total of 68 participants were included. All subjects had a clinical evaluation of swallowing, and an initial measure in a functional scale. The individuals were split into two groups, according to the initial levelling of ASHA NOMS scale. In Group 1 (G1) - ASHA NOMS, initial of levels 1 and 2; Group 2 (G2) - ASHA NOMS, initial of levels 3, 4 and 5. All subjects executed an exercise protocol performed for four weeks. The protocol includes sessions with a speech therapist, and continuity of activities in home environment. Finally, new measurement of swallowing performance was held. Results For G2 group there was statistically significant improvement. For G1, the relation was insignificant, despite the intense change in ASHA NOMS scale, however, in this group there was a reduced number of individuals due to the profile severity. Conclusion The program was effective because after four exercise sessions, there was significant improvement in swallowing pattern, demonstrated by functional scale.