Miracle-dz/UniFAR-FTUs huggingface dataset:
Flavonoids from edible fruits as therapeutic agents in neuroinflammation – a comprehensive review and update

Abstract Neuroinflammation is a key process in the pathogenesis of many neurological disorders, i.e. Alzheimer’s disease and Parkinson’s disease. However, there are no anti-inflammatory medical interventions recommended so far in the treatment of neuroinflammation-related brain disorders. Therefore, the burden of searching for effective and safe antineuroinflammatory agents is well founded, especially in the aging society. Compounds of plant origin, mainly (poly)phenols, have attracted considerable attention in recent years. Notably, the role of flavonoids in ameliorating neuroinflammation is in the limelight. Thus, we used comprehensive literature retrieval to summarize the effects and active components of edible fruits and their phenolic compounds. As a result, this review presents a valuable summary of results of in vitro, ex vivo, and in vivo studies on the antineuroinflammatory effects of edible fruits and their (poly)phenolic extracts as well as dietary flavonoids and other selected (poly)phenols based on the detailed description of foregoing studies. Additionally, problems resulting from the limited bioavailability of (poly)phenols were discussed.
Applications of the Chick Chorioallantoic Membrane as an Alternative Model for Cancer Studies

A variety of in vivo experimental models have been established for the studies of human cancer using both cancer cell lines and patient-derived xenografts (PDXs). In order to meet the aspiration of precision medicine, the in vivomurine models have been widely adopted. However, common constraints such as high cost, long duration of experiments, and low engraftment efficiency remained to be resolved. The chick embryo chorioallantoic membrane (CAM) is an alternative model to overcome some of these limitations. Here, we provide an overview of the applications of the chick CAM model in the study of oncology. The CAM model has shown significant retention of tumor heterogeneity alongside increased xenograft take rates in several PDX studies. Various imaging techniques and data analysis have been applied to study tumor metastasis, angiogenesis, and therapeutic response to novel agents. Lastly, to practically illustrate the feasibility of utilizing the CAM model, we summarize the general protocol used in a case study utilizing an ovarian cancer PDX.
Emergence of Resistance to Ceftazidime-Avibactam in a Pseudomonas aeruginosa Isolate Producing Derepressed blaPDC in a Hollow-Fiber Infection Model

Ceftazidime (CAZ)-avibactam (AVI) is a β-lactam/β-lactamase inhibitor combination with activity against type A and type C β-lactamases. Resistance emergence has been seen, with multiple mechanisms accounting for the resistance. We performed four experiments in the dynamic hollow-fiber infection model, delineating the linkage between drug exposure and both the rate of bacterial kill and resistance emergence by all mechanisms. ABSTRACT Ceftazidime (CAZ)-avibactam (AVI) is a β-lactam/β-lactamase inhibitor combination with activity against type A and type C β-lactamases. Resistance emergence has been seen, with multiple mechanisms accounting for the resistance. We performed four experiments in the dynamic hollow-fiber infection model, delineating the linkage between drug exposure and both the rate of bacterial kill and resistance emergence by all mechanisms. The Pseudomonas aeruginosa isolate had MICs of 1.0 mg/liter (CAZ) and 4 mg/liter (AVI). We demonstrated that the time at ≥4.0 mg/liter AVI was linked to the rate of bacterial kill. Linkage to resistance emergence/suppression was more complex. In one experiment in which CAZ and AVI administration was intermittent and continuous, respectively, and in which AVI was given in unitary steps from 1 to 8 mg/liter, AVI at up to 3 mg/liter allowed resistance emergence, whereas higher values did not. The threshold value was 3.72 mg/liter as a continuous infusion to counterselect resistance (AVI area under the concentration-time curve [AUC] of 89.3 mg · h/liter). The mechanism involved a 7-amino-acid deletion in the Ω-loop region of the Pseudomonas-derived cephalosporinase (PDC) β-lactamase. Further experiments in which CAZ and AVI were both administered intermittently with regimens above and below the AUC of 89.3 mg · h/liter resulted in resistance in the lower-exposure groups. Deletion mutants were not identified. Finally, in an experiment in which paired exposures as both continuous and intermittent infusions were performed, the lower value of 25 mg · h/liter by both profiles allowed selection of deletion mutants. Of the five instances in which these mutants were recovered, four had a continuous-infusion profile. Both continuous-infusion administration and low AVI AUC exposures have a role in selection of this mutation.
Morphology evolution of urchin-like NiCo2O4 nanostructures and their applications as psuedocapacitors and photoelectrochemical cells

Urchin-like NiCo2O4 nanostructures were synthesized on a large scale via a simple hydrothermal method free of any template and catalyst. As-synthesized NiCo2O4 urchins have uniform diameters of 5 μm with numerous small nanorods radially grown from the center. Typical nanorods have diameters of 100–200 nm and lengths of about 2 μm. Studies found that urea plays an important role to determine the morphology of the products and a “rods-to-straw-bundles-to-urchins” mechanism was proposed. With a porous structure and a large surface area of 99.3 m2 g−1, the prepared NiCo2O4 urchins exhibited superior specific capacitance of 1650 and 1348 F g−1 at current densities of 1 and 15 A g−1, respectively. The capacitance loss after 2000 cycles is only 9.2% at the current density of 8 A g−1, indicating their excellent cycling stability. Photoelectrochemical cells were also fabricated on the urchin-like NiCo2O4 nanostructures with the features of fast photocurrent response and excellent stability. A high photocurrent response of about 70 μA cm−2 was observed.
Genetic polymorphism in HSPB6 gene and their association with heat tolerance traits in Indian Karan Fries (Bos taurus x Bos indicus) cattle

Abstract Heat shock proteins (HSPs) act as a chaperone activity ensuring the folding, unfolding, and refolding of denatured proteins, which help in a protective role during thermal stress in dairy cattle. This study aimed to detect genetic variations of the HSPB6 gene and to determine their association with heat tolerance traits in Karan Fries cattle. Five single nucleotide polymorphisms (SNPs) (SNP 1–5) were reported in the Karan Fries cattle, which included three transitions viz. SNP1-g.161G > A, SNP2-g.436G > A, and SNP4-g.2152A > G and two transversions viz. SNP3-g.1743C > G, SNP5-g.2417A > T. The association analysis revealed that the three SNPs loci i.e., SNP1-g.161G > A, SNP2-g.436G > A, and SNP3-g.1743C > G were significantly (p < 0.01) associated with the respiration rate (RR) and rectal temperature (RT) (°C) traits. Furthermore, in the case of heat tolerance coefficient (HTC) trait was found significantly associated (p < 0.01) with SNPs loci i.e., SNP1-g.161G > A, SNP2-g.436G > A, and SNP3-g.1743C > G. The Hap 4 (GACAT) was found to more adaptable than cattle of other haplotypes as reflected by lower values of RR, RT and HTC. This study provides the first association analyses between the SNPs and haplotypes of HSPB6 gene and heat tolerance traits in Karan Fries cattle, which could be used as effective SNP markers in genetic selection for heat tolerance in cattle breeding program.
The effect of Ga‐doping on the defect chemistry of RE3Al5O12 garnets

It has been recently shown that the addition of Ga to Lu3Al5O12 garnet (LuAG) removes the electron trapping associated with cation antisite defects. In this paper, we show via atomic scale simulations that the replacement of Al with Ga in LuAG actually lowers the energy of the antisite disorder process. Thus, we predict that Ga additions will lead to an increase of the antisite defect concentration and, in the absence of the electronic structure changes, would actually degrade the performance of the material. Since there are two crystallographically distinct Al sites in the garnet structure, we not only present results for complete replacement of Al with Ga, but also partial replacement for 40% (on 16a) and 60% (on 24d) of the Al with Ga. Our results support the explanation for Ga‐doping leading to improvement in garnet scintillator performance that relies on variations of the electronic structure rather than reduction of the antisite defect concentration.
Determining the Safety Threshold for the Passage of a Ureteral Access Sheath in Clinical Practice Using a Purpose-Built Force Sensor

Purpose: Ureteral injury is a frequent complication of ureteral access sheath deployment. We sought to define the safe threshold of force for the passage of a ureteral access sheath using a novel ureteral access sheath force sensor. Materials and Methods: Ureteral access sheath-force sensor measurements were recorded in 210 renal units. A 16Fr ureteral access sheath was deployed initially based on a prior porcine study. If 6 N was reached, the surgeon was advised to downsize the 16Fr ureteral access sheath. In each case, a post-ureteroscopic lesion scale was recorded. Regression models were used to estimate the impact of adjusted variables on post-ureteroscopic lesion scale grade, 16Fr ureteral access sheath deployment, and peak force. Results: A 16Fr ureteral access sheath was deployed in 127 (61%) renal units with a mean peak force of 5.7 N. Two high-grade ureteral injuries occurred; in both cases >6 N of force was recorded. Post-ureteroscopic lesion scale grade correlated directly with peak insertion force (p <0.01). Bacteriuria within 60 days of the procedure (OR 2.009, p=0.034), combination of preoperative stent plus oral tamsulosin (OR 2.998, p=0.045), and prior ipsilateral stone surgery (OR 2.13, p=0.01) were independent predictors of successful 16Fr ureteral access sheath deployment. Among patients with neither prior ipsilateral stone surgery nor preoperative stent, preoperative tamsulosin facilitated passage of a 16Fr ureteral access sheath (OR 2.750, p=0.034). Conclusions: Ureteral access sheath associated ureteral injury can be averted by limiting the insertion force to ≤6 N. Prior stone surgery, preoperative indwelling ureteral stent plus oral tamsulosin, and recently treated bacteriuria favored passage of a 16Fr ureteral access sheath. In the naïve, unstented patient, preoperative tamsulosin favored deployment of a 16Fr ureteral access sheath.
Indigenous Fungivorous Nematodes Affect the Biocontrol Efficacy of Trichoderma harzianum through Reducing the Hyphal Density

Indigenous fungus-feeding nematodes may adversely affect the growth and activity of introduced biocontrol fungi. Alginate pellets of the biocontrol fungus Trichoderma harzianum ThzID1-M3 and sclerotia of the fungal plant pathogen Sclerotinia sclerotiorum were added to nonsterile soil at a soil water potential of -50 or -1,000 kPa. The biomass of ThzID1-M3, nematode populations, and extent of colonization of sclerotia by ThzID1-M3 were monitored over time. The presence of ThzID1-M3 increased the nematode population under both moisture regimes (p < 0.05), and fungivores comprised 69–75% of the nematode population. By day 5, the biomass of ThzID1-M3b and its colonization of sclerotia increased and were strongly correlated (R2 = 0.98), followed by a rapid reduction, under both regimes. At -50 kPa (the wetter of the two environments), fungal biomass and colonization by ThzID1-M3 were less, in the period from 5 to 20 days, while fungivores were more abundant. These results indicate that ThzID1-M3 stimulated the population growth of fungivorous nematodes, which in turn, reduced the biocontrol ability of the fungus to mycoparasitize sclerotia. However, colonization incidence reached 100% by day 5 and remained so for the experimental period under both regimes, although hyphal fragments disappeared by day 20. Our results suggest that indigenous fungivores are an important constraint for the biocontrol activity of introduced fungi, and sclerotia can provide spatial refuge for biocontrol fungi from the feeding activity of fungivorous nematodes.
Protein diffusion in porous gel filtration chromatography media studied by pulsed field gradient NMR spectroscopy

Ovalbumin intradiffusion (or tracer diffusion) coefficients within commercially available polymeric gel filtration particles have been determined by pulsed field gradient NMR (PFGNMR) as a function of ovalbumin concentration. The results are well correlated with behavior in tree solution by a tortuosity factor of 2.2±0.4 for the entire concentration range studied. A method for restricting diffusing species to individual particles, to observe intraparticle behavior rather than interparticle transport, is described. PFGNMR is shown to be a powerful experimental technique for selectively observing diffusion of protein or other tracer species within opaque, porous particles
Fast kNN Search in Weighted Hamming Space With Multiple Tables

Hashing methods have been widely used in Approximate Nearest Neighbor (ANN) search for big data due to low storage requirements and high search efficiency. These methods usually map the ANN search for big data into the <inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula>-Nearest Neighbor (<inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula>NN) search problem in Hamming space. However, Hamming distance calculation ignores the bit-level distinction, leading to confusing ranking. In order to further increase search accuracy, various bit-level weights have been proposed to rank hash codes in weighted Hamming space. Nevertheless, existing ranking methods in weighted Hamming space are almost based on exhaustive linear scan, which is time consuming and not suitable for large datasets. Although Multi-Index hashing that is a sub-linear search method has been proposed, it relies on Hamming distance rather than weighted Hamming distance. To address this issue, we propose an exact <inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula>NN search approach with Multiple Tables in Weighted Hamming space named WHMT, in which the distribution of bit-level weights is incorporated into the multi-index building. By WHMT, we can get the optimal candidate set for exact <inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula>NN search in weighted Hamming space without exhaustive linear scan. Experimental results show that WHMT can achieve dramatic speedup up to 69.8 times over linear scan baseline without losing accuracy in weighted Hamming space.
The use of ultraviolet resonance Raman intensities to test proposed molecular force fields for nucleic acid bases

The harmonic molecular force fields for the nucleic acid bases, cytosine, and guanine, that have been previously published by several investigators are tested by the calculation of the relative intensities of the in‐plane modes in the ultraviolet resonance Raman (UVRR) effect from the two lowest lying absorption bands using a theoretical approach devised previously.1–3 Since only a fraction of the 2N – 3 in‐plane vibrations of a molecule are active in the UVRR, the two criteria that are taken for the adjustment of the force constant are: (1) the closest possible agreement between the observed and calculated frequencies of the 2N – 3 in‐plane vibrations, and (2) the closest possible agreement between the calculated and observed intensities of those few vibrations that are strongly active in the ultraviolet resonance Raman effect. In particular it is necessary that the force constants be adjusted to avoid the calculation of intense Raman lines with frequencies that are not observed in the UVRR spectrum. Using this criteria, a new force field has been developed that appears to give better agreement with the observed UVRR intensities than previously published ones. It is suggested that this calculation of the UVRR intensities can be used to refine molecular force fields in combination with other methods such as isotopic replacement currently in use to refine force constants.
Spectroelectrochemical Studies on Dissolution and Passivation of Zinc Electrodes in Alkaline Solutions

Electrochemical oxidation of zinc electrodes has been studied in 1.0 M KOH solutions employing cyclic voltammetric and in situ spectroelectrochemical techniques. The results indicate that three different processes, i.e., dissolution, prepassivation, and passivation, take place in different potential regions. Two optically different solution species absorbing at 250 and 290 nm, which are assigned to Zn(OH){sub 4}{sup 2{sup {minus}} and Zn(OH){sub 3}{sup minus}}, respectively, are produced initially during anodic oxidation of zinc at different potentials to different extents with different respective ratios. These species undergo a series of consecutive chemical reactions to eventually lead to passive films on the surface. The film compositions were identified to be ZnO{sub 1{minus}x}(OH){sub 2x}OH{sup {minus}}-doped ZnO, and Zn-doped ZnO depending on the potential regime and aging. Details of the electrochemistry and chemistry taking place during electrolysis in these three regions are discussed based on the cyclic voltammetric and spectroelectrochemical data.
Data, time, change and land-system dynamics

ABSTRACT Time-related information in land-change studies is reviewed using case studies in JLUS and LAND. An explicit focus on time has potential for exploring process-based perspectives. We report how time is represented and patterns in pre-analytical choices are detected, identifying practices to enhance the relevance and impact of land-change studies. Results show 40% of the studies use two datasets; the modal timespan and interval between datasets are 10 years; 79% are durations up to 30 years; 73% are changes since 1972. Modal start dates are 1990 and 2000. Dates ending in 0 and 5 are over-represented and lack explicit justification. The prevalence of a ‘two-date approach’ restricts measuring and analyzing change, identifying temporal non-stationarity is precluded, and modelling change pathways and responses to underlying system dynamics are limited. An improved focus on time in dataset choice to developimproved understanding of dynamics and change offers broader insights into land-system functions.
Viruses, cancer and non-self recognition

Virus–host interactions form an essential part of every aspect of life, and this review is aimed at looking at the balance between the host and persistent viruses with a focus on the immune system. The virus–host interaction is like a cat-and-mouse game and viruses have developed ingenious mechanisms to manipulate cellular pathways, most notably the major histocompatibility (MHC) class I pathway, to reside within infected cell while evading detection and destruction by the immune system. However, some of the signals sensing and responding to viral infection are derived from viruses and the fact that certain viruses can prevent the infection of others, highlights a more complex coexistence between the host and the viral microbiota. Viral immune evasion strategies also illustrate that processes whereby cells detect and present non-self genetic material to the immune system are interlinked with other cellular pathways. Immune evasion is a target also for cancer cells and a more detailed look at the interfaces between viral factors and components of the MHC class I peptide-loading complex indicates that these interfaces are also targets for cancer mutations. In terms of the immune checkpoint, however, viral and cancer strategies appear different.
Testing the multiple stressor hypothesis: chlorothalonil exposure alters transmission potential of a bumblebee pathogen but not individual host health

Numerous threats are putting pollinator health and essential ecosystem pollination services in jeopardy. Although individual threats are widely studied, their co-occurrence may exacerbate negative effects, as posited by the multiple stressor hypothesis. A prominent branch of this hypothesis concerns pesticide–pathogen co-exposure. A landscape analysis demonstrated a positive association between local chlorothalonil fungicide use and microsporidian pathogen (Nosema bombi) prevalence in declining bumblebee species (Bombus spp.), suggesting an interaction deserving further investigation. We tested the multiple stressor hypothesis with field-realistic chlorothalonil and N. bombi exposures in worker-produced B. impatiens microcolonies. Chlorothalonil was not avoided in preference assays, setting the stage for pesticide–pathogen co-exposure. However, contrary to the multiple stressor hypothesis, co-exposure did not affect survival. Bees showed surprising tolerance to Nosema infection, which was also unaffected by chlorothalonil exposure. However, previously fungicide-exposed infected bees carried more transmission-ready spores. Our use of a non-declining bumblebee and potential higher chlorothalonil exposures under some scenarios could mean stronger individual or interactive effects in certain field settings. Yet, our results alone suggest consequences of pesticide co-exposure for pathogen dynamics in host communities. This underlies the importance of considering both within- and between-host processes when addressing the multiple stressor hypothesis in relation to pathogens.
Complexity of Zoning Management in Biosphere Reserves: The Case of the Yangambi Biosphere Reserve in DRC

HIGHLIGHTS The Yangambi Biosphere Reserve (YBR) in DRC is highly threatened through unsustainable activities undertaken by riparian communities in the reserve. Restrictions imposed on access to resources by the zoning of the YBR have forced riparian populations into over-exploitation of village lands. Zoning applied to the reserve did not take into account the social dynamics nor the participation of riparian communities in the Yangambi region. Variations in the reserve boundaries have led to substantial uncertainty and were found to be at the root of clashes and latent conflicts between the local population and the YBR managers. To reduce the pressure on the resources of the YBR, we suggest an improvement in agricultural techniques coupled with the participatory delimitation of village exploitation zones, as well as a revitalization of participatory structures. SUMMARY Riparian communities activities threaten conservation in biosphere reserves in the Democratic Republic of Congo (DRC). The Yangambi Biosphere Reserve (YBR) is no exception to this degradation. Thus, the objective of the presents study was to elucidate the local factors underlying the high pressure on natural resources and analyze the complexity of biosphere reserve zoning management using an interdisciplinary approach combining document review, field surveys and semi-structured interviews. Our results revealed that the zoning applied to the YBR did not take into account social dynamics. With population growth, the riparian community is doomed to remain in restricted areas, leading to over-exploitation of the space and land degradation, forcing the population to travel long distances to reach fertile plots into the protected area. Also, the lack of employment and the absence of participatory zoning also exacerbate tensions between the manager and the riparian community. For an effective management of the YBR, political authorities should become more involved in the participatory zoning of conservation areas and village exploitations. In addition, they should improve farming techniques to mitigate soil degradation.