Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative evaluation of the efficacy of a herbal mouthwash and chlorhexidine mouthwash on select periodontal pathogens: An in vitro and ex vivo study

Background: Several herbal mouthwash and herbal extracts have been tested in vitro and in vivo in search of a suitable adjunct to mechanical therapy for long-term use. In this study, we aimed to look at the antimicrobial effect of the herbal mouthwash and chlorhexidine (CHX) mouthwash on select organisms in in vitro test and an ex vivo model. Materials and Methods: The antimicrobial effects were determined against standard strains of bacteria that are involved in different stages of periodontal diseases. The in vitro tests included determination of minimum inhibitory concentration (MIC) using broth dilution and agar diffusion. In the ex vivo part of the study supragingival dental plaque were obtained from 20 periodontally healthy adult volunteers. Descriptive analysis was done for the entire quantitative and qualitative variable recorded. Results: The MIC by broth dilution method found no statistically significant difference between the mouthwashes. The agar dilution method showed CHX was more effective as compared to the herbal mouthwash against standard strains of Streptococcus mutans, Streptococcus sanguinis, and Aggregatibacter actinomycetemcomitans. However, no difference was observed between the mouthwashes for Porphyromonas, Pseudomonas aeruginosa, and Fusobacterium nucleatum. The ex vivo results conclude that none of the selected mouthwashes were statistically significantly different from each other. Conclusion: In the present study, CHX showed higher levels of antimicrobial action than the herbal mouthwash against bacterial species. The results reinforce the earlier findings that the in vitro testing is sensitive to methods and due diligence is needed when extrapolating the data for further use. However, long-term use and in vivo effectiveness against the periopathogens need to be tested in well-planned clinical trials.
Bioreactor virome metagenomics sequencing using DNA spike-ins

With the emergence of Next Generation Sequencing, major advances were made with regard to identifying viruses in natural environments. However, bioinformatical research on viruses is still limited because of the low amounts of viral DNA that can be obtained for analysis. To overcome this limitation, DNA is often amplified with multiple displacement amplification (MDA), which may cause an unavoidable bias. Here, we describe a case study in which the virome of a bioreactor is sequenced using Ion Torrent technology. DNA-spiking of samples is compared with MDA-amplified samples. DNA for spiking was obtained by amplifying a bacterial 16S rRNA gene. After sequencing, the 16S rRNA gene reads were removed by mapping to the Silva database. Three samples were tested, a whole genome from Enterobacteria P1 Phage and two viral metagenomes from an infected bioreactor. For one sample, the new DNA-spiking protocol was compared with the MDA technique. When MDA was applied, the overall GC content of the reads showed a bias towards lower GC%, indicating a change in composition of the DNA sample. Assemblies using all available reads from both MDA and the DNA-spiked samples resulted in six viral genomes. All six genomes could be almost completely retrieved (97.9%–100%) when mapping the reads from the DNA-spiked sample to those six genomes. In contrast, 6.3%–77.7% of three viral genomes was covered by reads obtained using the MDA amplification method and only three were nearly fully covered (97.4%–100%). This case study shows that DNA-spiking could be a simple and inexpensive alternative with very low bias for sequencing of metagenomes for which low amounts of DNA are available.
Assembly of the Cutin Polyester: From Cells to Extracellular Cell Walls

Cuticular matrices covering aerial plant organs or delimiting compartments in these organs are composed of an insoluble hydrophobic polymer of high molecular mass, i.e., cutin, that encompass some cell wall polysaccharides and is filled by waxes. Cutin is a polyester of hydroxy and-or epoxy fatty acids including a low amount of glycerol. Screening of Arabidopsis and more recently of tomato (Solanum lycopersicum) mutants allowed the delineation of the metabolic pathway involved in the formation of cutin monomers, as well as their translocation in the apoplast. Furthermore, these studies identified an extracellular enzyme involved in the polymerization of these monomers, i.e., cutin synthase 1 (CUS1), an acyl transferase of the GDSL lipase protein family. By comparing the structure of tomato fruit cutins from wild type and down-regulated CUS1 mutants, as well as with the CUS1-catalyzed formation of oligomers in vitro, hypothetical models can be elaborated on the polymerization of cutins. The polymorphism of the GDSL-lipase family raises a number of questions concerning the function of the different isoforms in relation with the formation of a composite material, the cuticle, containing entangled hydrophilic and hydrophobic polymers, i.e., polysaccharides and cutin, and plasticizers, i.e., waxes.
Super-polynomial approximation branching algorithms

We give sufficient conditions for deriving moderately exponential and/or parameterized time approximation schemata (i.e., algorithms achieving ratios 1 ± , for arbitrarily small) for broad classes of combinatorial optimization problems via a well-known technique widely used for deriving exact algorithms, namely the branching tree pruning. Mathematics Subject Classification. 68W25, 05C85, 68Q25.
Influenza immunology evaluation and correlates of protection: a focus on vaccines

ABSTRACT Vaccination is the most effective method of controlling seasonal influenza infections and preventing possible pandemic events. Although influenza vaccines have been licensed and used for decades, the potential correlates of protection induced by these vaccines are still a matter of discussion. Currently, inactivated vaccines are the most common and the haemagglutination inhibition antibody titer is regarded as an immunological correlate of protection and the best available parameter for predicting protection from influenza infection. However, the assay shows some limitations, such as its low sensitivity to B and avian strains and inter-laboratory variability. Additional assays and next-generation vaccines have been evaluated to overcome the limitations of the traditional serological techniques and to elicit broad immune responses, underlining the need to revise the current correlates of protection. The aim of this review is to provide an overview of the current scenario regarding the immunological evaluation and correlates of protection of influenza vaccines.
High-speed turning of AISI 4140 steel by multi-layered TiN top-coated insert with minimum quantity lubrication technology and assessment of near tool-tip temperature using infrared thermography

Minimum quantity lubrication technology is emerging as a potential alternative to flood cooling to effectively control cutting temperature during machining. In this study, an in-house developed minimum quantity lubrication delivery system has been used for minimum quantity lubrication delivery of cutting fluid at the machining zone. An advanced nanofluid coolant was also used for the purpose of minimum quantity lubrication. Different methods have been attempted to measure the near tool-tip temperature during turning of AISI 4140 steel with multi-layered coated insert under dry, flood cooled and minimum quantity lubrication cooled condition. It was further attempted to identify the best technique for assessing near tool-tip temperature. Infrared thermography has shown the closest result to that obtained through a finite element analysis (DEFORM 3DTM) simulation. Potential of multi-walled carbon nanotube–based nanofluid in minimum quantity lubrication application has been thoroughly investigated in this case study, where high-speed turning of AISI 4140 steel was carried out by a multi-layered coated carbide insert. Design of experiments, based on Taguchi method, was used to find out the significance of cutting parameters on machinability under nanofluid environment. Multi-walled carbon nanotube–based nanofluid was found to outperform the rest in all conditions.
Evaluation of the Scaffolding Effect of Pt Nanowires Supported on Reduced Graphene Oxide in PEMFC Electrodes

The stacking and overlapping effect of two-dimensional (2D) graphene nanosheets in the catalyst coating layer is a big challenge for their practical application in proton exchange membrane fuel cells (PEMFCs). These effects hinder the effective transfer of reactant gases to reach the active catalytic sites on catalysts supported on the graphene surface and the removal of the produced water, finally leading to large mass transfer resistances in practical electrodes and poor power performance. In this work, we evaluate the catalytic power performance of aligned Pt nanowires grown on reduced graphene oxide (rGO) (PtNW/rGO) as cathodes in 16-cm2 single PEMFCs. The results are compared to Pt nanoparticles deposited on rGO (Pt/rGO) and commercial Pt/C nanoparticle catalysts. It is found that the scaffolding effect from the aligned Pt nanowire structure reduces the mass transfer resistance in rGO-based catalyst electrodes, and a nearly double power performance is achieved as compared with the Pt/rGO electrodes. However, although a higher mass activity was observed for PtNW/rGO in membrane electrode assembly (MEA) measurement, the power performance obtained at a large current density region is still lower than the Pt/C in PEMFCs because of the stacking effect of rGO.
Rapid purification of giant lipid vesicles by microfiltration

Giant lipid vesicles (GVs) are emerging models for investigating the properties and reactivity of cell-like microcompartments, providing useful information about plausible protocellular structures in primitive times, as well as for the modern synthetic biology goal of constructing the first artificial cell from its reconstituted and partly modified components. Here we explore a novel methodology of GV purification by microfiltration under reduced pressure, operated by a simple apparatus. The method has been characterized in terms of flow rate, amount of lipid loss, quality of recovered GVs, and size distribution. A case study is reported to show the practicability of GV microfiltration. A clickable fluorescent probe was encapsulated inside GVs; more than 99.9% of the non-entrapped probe was easily and rapidly removed by multiple microfiltrations. This novel methodology is briefly discussed as a future tool for selection experiments on GV populations.
Parenting and child adjustment: a comparison of Turkish and English families

ABSTRACT The links between parenting and child behaviour in cultural context have received increasing research attention. We investigated the effect of parenting on child adjustment using a multi-method design, comparing English and Turkish families. The socioeconomically diverse samples included 118 English and 100 Turkish families, each with two children aged 4–8 years. Mothers completed questionnaires as well as parent–child interaction being assessed using a structured Etch-a-Sketch task with each child separately. Children were interviewed about their relationships with their mothers using the Berkeley Puppet Interview. Multiple-group Confirmatory Analysis was used to test Measurement Invariance across groups, and a multi-informant approach was used to assess parenting. We found partial cross-cultural measurement invariance for parenting and child adjustment. Strikingly, the association between parenting and child adjustment was stronger among English families than Turkish families. Culturally distinct meanings of both parenting and child behaviour must be considered when interpreting their association.
Cytologic Diagnosis of Signet-Ring Cell Carcinoma of the Breast

OBJECTIVE To examine the cytologic features of signet-ring cell carcinoma (SRCC), defined as carcinoma dominated by signet-ring cells, of the breast and to discuss problems that occur in cytodiagnosis. STUDY DESIGN Five cases of SRCC of the breast were examined cytopathologically. Signet-ring cells were subclassified into intracytoplasmic lumina (ICL) type and non-ICL type. ICL type had large ICL containing mucin. Non-ICL-type cells had wide, amorphous cytoplasm diffusely dispersed with mucin. RESULTS In cases 1 and 2, fine needle aspiration biopsy (FNAB) revealed many signet-ring cells (non-ICL type), suggesting SRCC. Histologic diagnoses were ductal SRCC containing many signet-ring cells (non-ICL type). In cases 3 and 4, signet-ring cells (ICL type) were found sporadically among carcinoma cells without signet-ring features. Signet-ring cells were not regarded as the major component of the cells; thus, the cytologic diagnoses were lobular carcinoma, not otherwise specified. Pathologic diagnoses were lobular SRCC. Signet-ring cells were mostly ICL type. In case 5, most carcinoma cells on the smears showed signet-ring features (non-ICL type), suggesting SRCC. The histologic diagnosis was lobular SRCC, and signet-ring cells were mostly non-ICL type. CONCLUSION Ductal SRCC yielded more cellular smears as compared with lobular SRCC; therefore, cytologic diagnosis was easier in the former.
Microfluidic Device for Synthesis of Chitosan Nanoparticles

ABSTRACT Chitosan nanoparticles have a biodegradable, biocompati-ble, non-toxic structure, and commonly used for drug deliverysystems. In this paper, simulation of a microﬂuidic device for thesynthesis of chitosan nanoparticle is presented. The ﬂow ﬁled to-gether with the concentration ﬁeld within the microchannel net-work is simulated using COMSOL Multiphysics R simulation en-vironment. Different microchannel geometries are analyzed, andthe mixing performance of these conﬁgurations are compared.As a result, a 3D design for a microﬂuidics platform which in-cludes four channel each of which performs the synthesis in par-allel is proposed. Future research directions regarding the fabri-cation of the microﬂuidic device and experimentation phase areaddressed and discussed. NOMENCLATURE A o coefﬁcient used in Eq. (3)A 1 coefﬁcient used in Eq. (3)A 2 coefﬁcient used in Eq. (3)A 3 coefﬁcient used in Eq. (3) Address all correspondence to this author. B o coefﬁcient used in Eq. (4)B 1 coefﬁcient used in Eq. (4)B
The Influence of Random Filament Packing on the Elastic Properties of Composite Materials.

Abstract : A new method of micromechanical analysis of composite materials (such as boron- or glass-fiber-reinforced aluminum or epoxy) that takes account of the randomness of arrangement of the reinforcing filaments. Previous analyses assumed a regular geometric array, in which case a physically unrealistic square array showed surprising agreement with experimental data. Since available computers cannot handle a completely random arrangement, a basic pattern was generated by random-number techniques and was then reflected to obtain symmetry; this unit was assumed to repeat itself throughout the material. Solutions for the modulus of elasticity were obtained for a 10-by-10 random array, for each of 20 random geometries using constituent stiffness ratios corresponding to boron/aluminum, glass/epoxy, and boron/epoxy composites, for filament volume contents of 39, 55, and 70 percent. The assumed symmetry permitted the use of standard boundary/value solution methods. When the assumed filament packing array is randomized, the more physically realistic 'hexagonal random array' is in better agreement with the data than the 'square random array. ' Since the latter results in much higher local stress concentrations, use of the square array model could lead to unduly conservative analyses. (Author)
Taxonomic and functional organization of macroinvertebrate communities in subarctic streams

Ecological research based on both species and their traits help us to understand the main mechanisms and environmental factors structuring biological communities. In general, variation in community composition is thought to be a consequence of both stochastic and deterministic factors. In stream ecology, the traditional view has been that the local habitat conditions pose a strong environmental filter that selects only species with the right functional traits into the local communities. However, recent studies on streams have also suggested that the responses of species to environmental gradients may be independent of those of other species due to stochastic factors, such as species dispersal, which then result in more continuous communities along environmental gradients. The aim of this thesis was to explore the relative importance of the deterministic and stochastic factors in the structuring of taxonomic and functional trait-based macroinvertebrate communities in streams in a high-latitude catchment by comparing the variation in these community facets along environmental and spatial gradients. Also, the relationship between environment and the functionally-defined communities was explored closely. The results indicated how the taxonomic composition of the communities may be more closely related to the stochastic and dispersal-related factors, whereas the functional composition of the communities may be more closely related to the deterministic environmental filtering processes. However, the overall structure of the communities seems to be strongly controlled by the variation in environment, although the heterogeneous and harsh conditions of the streams may preclude the formation of predictable community types. Nonetheless, some noticeable responses of different traits to different environmental factors were found, suggesting that definable functional trait-environment relationships may be discovered if key traits of the species can be identified. Overall, these findings underline the benefits of describing both taxonomic and functional-based communities when exploring the mechanisms behind the structuring of macroinvertebrate communities. The results also have applications for conservation practices. Conservation efforts should focus on varying environmental conditions in order to cover all aspects of macroinvertebrate community variation.
Suppressor of Fused restraint of Hedgehog activity level is critical for osteogenic proliferation and differentiation during calvarial bone development

Hedgehog signaling plays crucial roles in the development of calvarial bone, relying on the activation of Gli transcription factors. However, the molecular mechanism of the role of regulated Gli protein level in osteogenic specification of mesenchyme still remains elusive. Here, we show by conditionally inactivating Suppressor of Fused (Sufu), a critical repressor of Hedgehog signaling, in Wnt1-Cre–mediated cranial neural crest (CNC) or Dermo1-Cre–mediated mesodermal lineages that Sufu restraint of Hedgehog activity level is critical for differentiation of preosteogenic mesenchyme. Ablation of Sufu results in failure of calvarial bone formation, including CNC-derived bones and mesoderm-derived bones, depending on the Cre line being used. Although mesenchymal cells populate to frontonasal destinations, where they are then condensed, Sufu deletion significantly inhibits the proliferation of osteoprogenitor cells, and these cells no longer differentiate into osteoblasts. We show that there is suppression of Runx2 and Osterix, the osteogenic regulators, in calvarial mesenchyme in the Sufu mutant. We show that down-regulation of several genes upstream to Runx2 and Osterix is manifested within the calvarial primordia, including Bmp2 and its downstream genes Msx1/2 and Dlx5. By contrast, we find that Gli1, the Hedgehog activity readout gene, is excessively activated in mesenchyme. Deletion of Sufu in CNC leads to a discernible decrease in the repressive Gli3 form and an increase in the full-length Gli2. Finally, we demonstrate that simultaneous deletion of Gli2 and Sufu in CNC completely restores calvarial bone formation, suggesting that a sustained level of Hedgehog activity is critical in specification of the osteogenic mesenchymal cells.
Activation of Astrocytes and Microglial Cells and CCL2/CCR2 Upregulation in the Dorsolateral and Ventrolateral Nuclei of Periaqueductal Gray and Rostral Ventromedial Medulla Following Different Types of Sciatic Nerve Injury

Peripheral nerve injuries (PNIs) may result in cellular and molecular changes in supraspinal structures possibly involved in neuropathic pain (NPP) maintenance. Activated glial cells in specific supraspinal subregions may affect the facilitatory role of descending pathways. Sterile chronic compression injury (sCCI) and complete sciatic nerve transection (CSNT) in rats were used as NPP models to study the activation of glial cells in the subregions of periaqueductal gray (PAG) and rostral ventromedial medulla (RVM). Molecular markers for activated astrocytes (glial fibrillary acidic protein, GFAP) and microglial cells (OX42) were assessed by quantitative immunohistochemistry and western blotting. The cellular distribution of CCL2/CCR2 was monitored using immunofluorescence. sCCI induced both mechanical and thermal hypersensitivity from day 1 up to 3 weeks post-injury. Unilateral sCCI or CSNT for 3 weeks induced significant activation of astrocytes bilaterally in both dorsolateral (dlPAG) and ventrolateral PAG (vlPAG) compared to naïve or sham-operated rats. More extensive astrocyte activation by CSNT compared to sCCI was induced bilaterally in dlPAG and ipsilaterally in vlPAG. Significantly more extensive activation of astrocytes was also found in RVM after CSNT than sCCI. The CD11b immunopositive region, indicating activated microglial cells, was remarkably larger in dlPAG and vlPAG of both sides from sCCI- and CSNT-operated rats compared to naïve or sham-operated controls. No significant differences in microglial activation were detected in dlPAG or vlPAG after CSNT compared to sCCI. Both nerve injury models induced no significant differences in microglial activation in the RVM. Neurons and activated GFAP+ astrocytes displayed CCL2-immunoreaction, while activated OX42+ microglial cells were CCR2-immunopositive in both PAG and RVM after sCCI and CSNT. Overall, while CSNT induced robust astrogliosis in both PAG and RVM, microglial cell activation was similar in the supraspinal structures in both injury nerve models. Activated astrocytes in PAG and RVM may sustain facilitation of the descending system maintaining NPP, while microglial activation may be associated with a reaction to long-lasting peripheral injury. Microglial activation via CCR2 may be due to neuronal and astrocytal release of CCL2 in PAG and RVM following injury.
Immersive Low-Cost Virtual Reality Treatment for Phantom Limb Pain: Evidence from Two Cases

Up to 90% of amputees experience sensations in their phantom limb, often including strong, persistent phantom limb pain (PLP). Standard treatments do not provide relief for the majority of people who experience PLP, but virtual reality (VR) has shown promise. This study provides additional evidence that game-like training with low-cost immersive VR activities can reduce PLP in lower-limb amputees. The user of our system views a real-time rendering of two intact legs in a head-mounted display while playing a set of custom games. The movements of both virtual extremities are controlled by measurements from inertial sensors mounted on the intact and residual limbs. Two individuals with unilateral transtibial amputation underwent multiple sessions of the VR treatment over several weeks. Both participants experienced a significant reduction of pain immediately after each VR session, and their pre-session pain levels also decreased greatly over the course of the study. Although preliminary, these data support the idea that VR interventions like ours may be an effective low-cost treatment of PLP in lower-limb amputees.