Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of rhamnolipid biosurfactant for bio-detergent formulation

Biosurfactants, also known as biological surface-active agents, are a group of surface-active agents, which are produced by a variety of microorganisms. Biosurfactants possess the characteristic property of lowering surface tension, increase the solubility of poorly soluble compound, low toxicity, non-allergenic, and biodegradable. Growing public awareness about the environmentally friendly health care and associated product has stimulated the search for eco-friendly compounds in laundry detergents. In this research, the application of biosurfactants in the formulation of a washing detergent was investigated. Variation of biosurfactants and its mixture with sodium tripolyphosphate as a builder and sodium sulfate as filler was applied to wash cotton fabric which was contaminated with known amounts of stain (chocolate milk). The effects of various bio-detergent formulations, including the ratio of biosurfactants and builder, was examined. The formulation presented in this study was also compared with some standard detergent for the stains removal efficiency. The results showed that the rhamnolipid biosurfactants have a promising as a substitute for its synthetic counterpart. Based on the colorfastness to wash, color strength (K/S), and color difference (∆E) value, rhamnolipid based bio-detergent have similar washing effectiveness compared to the synthetic detergent. Research result also found that Na-bicarbonate and Na-citrate have the potential as a substitute for phosphate-based detergent builder.
Pretreatment of Hazelnut Shells as a Key Strategy for the Solubilization and Valorization of Hemicelluloses into Bioactive Compounds

Hazelnut industries generate a large amount of byproducts. Among them, waste hazelnut shells (which account for about 50% of the nut weight), are potential raw materials to produce value added products. Hydrothermal pretreatment enables the solubilization of hemicelluloses, while cellulose and lignin remain in the solid phase almost unaltered, allowing their subsequent processing for an integral valorization of the feedstock. When the reaction was performed at the optimal temperature (210 °C), hemicelluloses were mainly converted into soluble substituted oligosaccharides (OS). Further membrane processing of the liquid phase from hydrothermal pretreatment enabled the refining of the OS, which accounted for up to 90.87 wt% of the nonvolatile solutes (NVC) in the refined solution, which also contained 5 g of natural bound phenolics/100 g NVC. The target products showed a dose-dependent antioxidant activity, conferred by the phenolic components. Substituted OS were made up of xylose backbones with a wide degree of polymerization distribution, and showed structures highly substituted by acetyl and uronic groups. The data included in this study provide the basis for assessing the large-scale manufacture of substituted oligosaccharides with bound phenolics as bioactive components of functional use in foods, cosmetics, or pharmaceuticals.
Extrafield Activity Shifts the Place Field Center of Mass to Encode Aversive Experience

Abstract Hippocampal place cells are known to have a key role in encoding spatial information. Aversive stimuli, such as predator odor, evoke place field remapping and a change in preferred firing locations. However, it remains unclear how place cells use positive or negative experiences to remap. We investigated whether CA1 place cells, recorded from behaving rats, remap randomly or whether their reconfiguration depends on the perceived location of the aversive stimulus. Exposure to trimethylthiazoline (TMT; an innately aversive odor), increased the amplitude of hippocampal β oscillations in the two arms of the maze in which TMT exposure occurred. We found that a population of place cells with fields located outside the TMT arms increased their activity (extrafield spiking) in the TMT arms during the aversive episodes. Moreover, in the subsequent post-TMT recording, these cells exhibited a significant shift in their center of mass (COM) towards the TMT arms. The induction of extrafield plasticity was mediated by the basolateral amygdala complex (BLA). Photostimulation of the BLA triggered aversive behavior, synchronized hippocampal local field oscillations, and increased the extrafield spiking of the hippocampal place cells for the first 100 ms after light delivery. Optogenetic BLA activation triggered an increase in extrafield spiking activity that was correlated with the degree of place field plasticity. Furthermore, BLA-mediated increase of the extrafield activity predicts the degree of subsequent field plasticity. Our findings demonstrate that that the remapping of hippocampal place cells during aversive episodes is not random but it depends on the location of the aversive stimulus.
Repeatability, Reproducibility and Agreement of Central Corneal Thickness Measurements by Two Noncontact Pachymetry Devices

This study was designed to assess the repeatability, reproducibility, and agreement of Noncontact Pachymetry (NPC) (Topcan TRK-2P) and the non-contact optical low coherence reflectometer (Lenstar LS 900) devices for measuring Central Corneal Thickness (CCT) of healthy corneas. A total of 82 healthy volunteers were evaluated. The first observer used both the TopconTRK-2P and Lenstar 900 devices while the second observer only used the TopconTRK-2P for the measurements. The measurements with either device were repeated three times for each patient, consecutively. The central corneal thickness measurements with the Topcon TRK-2P revealed mean ± Standard Deviation (SD) values of 553.1 ± 36.1 micrometer (µm) for the first observer and 552.3 ± 35. 9µm for the second observer and the mean ± SD of CCT was 537.3 ± 34. 8µm with the Lenstar 900. The difference between the CCT measurements of the observers using the Topcon TRK-2P (P = 0.142) was insignificant. However, significantly lower measurements were found with the Lenstar 900 compared with the Topcon TRK-2P (P ˂ 0.001). The central corneal thickness measurements obtained by the Topcon TRK-2P were found to have high repeatability for both observers with a lower SD, less than 1% Coefficient of Variation (CV) and higher than 0.99 Intra-Class Correlation Coefficient (ICC) (Observer 1: 3.77 SD, 0.68 CV and 0.995 ICC; the second observer: 3.58 SD, 0.65 CV and 0.995 ICC). There was an excellent inter-observer reproducibility between the two observers for Topcon TRK-2P with 2.71 SD, 0.49 CV, and 0.994 ICC. The Bland-Altman plot showed high agreement between the two devices. These results suggest that the TopconTRK-2P is a reliable device for evaluating CCT in healthy corneas compared with Lenstar 900.
Genome-Wide Identification, Characterization, and Expression Analysis of the Grapevine Superoxide Dismutase (SOD) Family

Superoxide dismutase (SOD) is an essential enzyme of the plant antioxidant system that responds to oxidative damage caused by adverse conditions. However, little is known about the SOD gene family in Vitis vinifera (Vv). In the present study, ten SOD genes, including 6 copper/zinc SODs, 2 iron SODs, and 2 manganese SODs, were identified in the grapevine genome where they were unevenly distributed on 12 chromosomes. Ten VvSOD genes were divided into three main groups based on phylogenetic analysis, subcellular localization, and the distribution of conserved protein motifs. Additionally, many cis-elements related to different stresses were found in the promoters of the 10 VvSOD genes. Syntenic analysis revealed that VvMSD1 and VvMSD2 were derived from segmental duplication, and VvCSD4 and VvCSD5 belong to a pair of tandemly duplicated genes. Gene expression analysis based on microarray data showed that the 10 VvSOD genes were expressed in all the tested tissues. Interestingly, the segmentally duplicated gene pair (VvMSD1 and VvMSD2) exhibited differential expression patterns in various organs. In contrast, the tandemly duplicated gene pair (VvCSD4 and VvCSD5) displayed similar expression patterns in the tested organs. Our results provide a basis for further functional research on the SOD gene family in grapevine.
The COVID-19 Pandemic: Theories to Therapies

Present COVID-19 pandemic has confronted almost every sector of the world creating terrible havoc and impacting day to day life of each individual. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2), identified and reported in Wuhan city, China spread across the globe with an unseen and unpredictable trajectory and limited knowledge of pathogenicity and epidemiology. With the major challenge lying in treatment and vaccine development, researchers and health care workers have come upfront to contribute in terms of knowledge and support. This review presents an overview of the structure, multiplication, and uniqueness of the novel coronavirus focusing on the ongoing treatments and scope of vaccines based on the current studies available in the literature.
InMeRF: prediction of pathogenicity of missense variants by individual modeling for each amino acid substitution

Abstract In predicting the pathogenicity of a nonsynonymous single-nucleotide variant (nsSNV), a radical change in amino acid properties is prone to be classified as being pathogenic. However, not all such nsSNVs are associated with human diseases. We generated random forest (RF) models individually for each amino acid substitution to differentiate pathogenic nsSNVs in the Human Gene Mutation Database and common nsSNVs in dbSNP. We named a set of our models ‘Individual Meta RF’ (InMeRF). Ten-fold cross-validation of InMeRF showed that the areas under the curves (AUCs) of receiver operating characteristic (ROC) and precision–recall curves were on average 0.941 and 0.957, respectively. To compare InMeRF with seven other tools, the eight tools were generated using the same training dataset, and were compared using the same three testing datasets. ROC-AUCs of InMeRF were ranked first in the eight tools. We applied InMeRF to 155 pathogenic and 125 common nsSNVs in seven major genes causing congenital myasthenic syndromes, as well as in VANGL1 causing spina bifida, and found that the sensitivity and specificity of InMeRF were 0.942 and 0.848, respectively. We made the InMeRF web service, and also made genome-wide InMeRF scores available online (https://www.med.nagoya-u.ac.jp/neurogenetics/InMeRF/).
Satellite-derived leaf area index and roughness length information for surface–atmosphere exchange modelling: a case study for reactive nitrogen deposition in north-western Europe using LOTOS-EUROS v2.0

Abstract. The nitrogen cycle has been continuously disrupted by human activity over the past century, resulting in almost a tripling of the total reactive nitrogen fixation in Europe. Consequently, excessive amounts of reactive nitrogen ( Nr ) have manifested in the environment, leading to a cascade of adverse effects, such as acidification and eutrophication of terrestrial and aquatic ecosystems, and particulate matter formation. Chemistry transport models (CTMs) are frequently used as tools to simulate the complex chain of processes that determine atmospheric Nr flows. In these models, the parameterization of the atmosphere–biosphere exchange of Nr is largely based on few surface exchange measurement and is therefore known to be highly uncertain. In addition to this, the input parameters that are used here are often fixed values, only linked to specific land use classes. In an attempt to improve this, a combination of multiple satellite products is used to derive updated, time-variant leaf area index (LAI) and roughness length ( z0 ) input maps. As LAI, we use the Moderate Resolution Imaging Spectroradiometer (MODIS) MCD15A2H product. The monthly z0 input maps presented in this paper are a function of satellite-derived normalized difference vegetation index (NDVI) values (MYD13A3 product) for short vegetation types (such as grass and arable land) and a combination of satellite-derived forest canopy height and LAI for forests. The use of these growth-dependent satellite products allows us to represent the growing season more realistically. For urban areas, the z0 values are updated, too, and linked to a population density map. The approach to derive these dynamic z0 estimates can be linked to any land use map and is as such transferable to other models. We evaluated the sensitivity of the modelled Nr deposition fields in LOng Term Ozone Simulation – EURopean Operational Smog (LOTOS-EUROS) v2.0 to the abovementioned changes in LAI and z0 inputs, focusing on Germany, the Netherlands and Belgium. We computed z0 values from FLUXNET sites and compared these to the default and updated z0 values in LOTOS-EUROS. The root mean square difference (RMSD) for both short vegetation and forest sites improved. Comparing all sites, the RMSD decreased from 0.76 (default z0 ) to 0.60 (updated z0 ). The implementation of these updated LAI and z0 input maps led to local changes in the total Nr deposition of up to ∼30 % and a general shift from wet to dry deposition. The most distinct changes are observed in land-use-specific deposition fluxes. These fluxes may show relatively large deviations, locally affecting estimated critical load exceedances for specific natural ecosystems.
Plasticity of NMDA Receptors at Ventral Hippocampal Synapses in the Infralimbic Cortex Regulates Cued Fear

Visual Abstract The medial prefrontal cortex (mPFC) processes contextual information from the hippocampus to generate appropriate fear responses. In rodents, one path for sending contextual information to the mPFC is via the direct projections from the ventral hippocampus (vHC) to the infralimbic cortex (IL). Plasticity in the synaptic communication from the vHC to the IL could contribute to the behavioral changes produced by the acquisition and extinction of conditioned fear. To examine this possibility, we used optogenetic stimulation of vHC synapses in brain slices from trained rats. We found that fear acquisition reduced NMDA receptor (NMDAR) currents at vHC synapses onto IL pyramidal neurons. The depression of NMDAR currents reversed more efficiently after extinction in the conditioning context than extinction in a novel context. Moreover, a cohort of animals that exhibited poor extinction retrieval failed to reverse the plasticity induced by fear conditioning. In addition, ex vivo application of brain-derived neurotrophic factor (BDNF), which is known to simulate extinction in IL, reversed this conditioning-induced plasticity mimicking extinction. Therefore, we have identified a novel mechanism that modulates conditioned fear via changes in NMDAR current at vHC synapses onto IL pyramidal neurons. Disruption of this mechanism could contribute to the abnormal contextual modulation of fear seen in posttraumatic stress disorder (PTSD).
Impact of Habitual Snoring on Subjective Dental Esthetics in University Population

Objective: The aims of this study were to assess the prevalence of snoring in the University population and to test the null hypothesis that there is no impact of habitual snoring on the self-perceived of dental esthetics. Materials and Methods: Berlin Questionnaire and esthetic component of the index of orthodontic treatment need was given to 700 students and employees aged 17–59 years (22 ± 4.5). Both snorers and nonsnorers were assessed for orthodontic treatment need. Chi-square and Student t-test were used to compare the difference between both groups using SPSS Statistics for Windows, Version 23.0. (IBM Corp, Armonk, NY). Results: The prevalence of snoring was 19.2% (male 11.8% and female 7.4%). Nodded off or fall asleep during driving a car or while waiting at least twice a month were reported in 46%. The prevalence of tiredness and fatigue after sleep from 3 to 4 times a week was 36.9% and during the working time was 33.6%. Based on the Berlin Questionnaire stratification for risk of obstructive sleep apnea (OSA), 8.2% were considered as a high-risk patient for OSA, (males: 3.8% and females: 4.4%). About 38.3% of the participants with habitual snoring have gone through orthodontic treatment, while only 28.5% of nonsnoring participant have done that. About 12.3% of snoring participant consider themselves in need of orthodontic treatment compared to 6.6% of a nonsnoring participant (P < 0.04). Conclusion: The null hypothesis is rejected; snoring has an impact on the self-perceived of dental esthetics. Snoring participant seeks orthodontic treatment more than the nonsnoring participant in our University population.
Restoring Attention Networks

The attention networks of the human brain have been under intensive study for more than twenty years and deficits of attention accompany many neurological and psychiatric conditions. There is more dispute about the centrality of attention deficits to these conditions. It appears to be time to study whether reducing deficits of attention alleviate the neurological or psychiatric disorder as a whole. In this paper we review human and animal research indicating the possibility of improving the function of brain networks underlying attention and their potential clinical role.
Phase Coherent Currents Underlying Neocortical Seizure-Like State Transitions

Abstract In the epileptic brain, phase amplitude cross-frequency coupling (CFC) features have been used to objectively classify seizure-related states, and the inter-seizure state has been demonstrated as being random, in contrast to the seizure state being predictable; however, the excitatory and inhibitory networks underlying their dynamics remain unclear. Therefore, the objectives of this study are to classify the dynamics of seizure sub-states labeling seizure-like event (SLE) onset and termination intervals using CFC features and to obtain their underlying excitatory/inhibitory cellular correlates. SLEs were induced in mouse neocortical brain slices using a low-magnesium perfusate, and were recorded in Layer II/III using simultaneous local field potential (LFP) and whole-cell voltage clamp electrodes. Classification of onset and termination of SLE transitions was investigated using CFC features in conjunction with an unsupervised two-state hidden Markov model (HMM). γ-Distributions of their durations indicated that both are predictable. Furthermore, omitting 4 Hz from the HMM classifier switched both SLE sub-states from statistically deterministic to random without changing the dynamics of the SLE state. These results were generalized to 4-aminopyridine (4-AP)-induced SLEs and human seizure traces. Only during these sub-states, both excitatory and inhibitory currents coupled with the field. Where excitatory currents phase locked to a broad range of frequencies between 1 and 12 Hz, inhibitory currents dominantly phase locked at 4 Hz. We conclude that inhibition underlies the predictability of neocortical CFC-defined SLE transition sub-states.
The Role of Vitamin D in Inflammatory Bowel Disease – Assessing Therapeutic and Preventive Potential of Supplementation and Food Fortification

SUMMARY Inflammatory bowel diseases are a group of chronic inflammatory conditions that affect gastrointestinal tract due to inapt and continuous immune activation in response to a myriad of predisposing factors (most notably genetics, environmental impact and gut microbiota composition). It has been shown that vitamin D status can also play a role in the disease pathogenesis, as its deficiency is commonly observed in two major forms of inflammatory bowel diseases – Crohn’s disease and ulcerative colitis. Mounting evidence supports the concept of intricate relationship between gut dysbiosis and vitamin D metabolism, while suboptimal levels of this vitamin have been linked to increased clinical disease relapse rates, inadequate response to drugs, as well as decreased quality of life in patients with Crohn’s disease and ulcerative colitis. Consequently, the pertinent question is whether increased vitamin D supplementation and (on a population level) food fortification may bring significant benefit to the affected individuals. In this short review we discuss the synthesis, functions, status and food sources of vitamin D, appraise biotechnological facets of vitamin D status analysis and food fortification, and concentrate on novel developments in the field that describe its influence on intestinal microbiota and inflammatory bowel disease.
Antiplatelet therapy in very elderly and comorbid patients with acute coronary syndromes

With population ageing and rise of life expectancy, a progressively increasing proportion of patients presenting with an acute coronary syndrome (ACS) are older adults, including those at extreme chronological age. Increasing amounts of data, including randomized clinical trials, have shown that the benefits of an early revascularization are maintained also at very old age, resulting in improved outcome after an acute coronary event. On the contrary, the optimal antiplatelet therapy (APT) remains unclear in these patients, because of both safety and efficacy concerns. Indeed, age-related multiple organ dysfunction and high prevalence of comorbidities may on the one hand reduce the therapeutic effects of administered drugs; on the other hand, it leads to increased vulnerability to drug toxicity and side effects. Therefore, management of APT is particularly challenging in elderly patients because of higher risk of both ischemic and bleeding events. The aim of the present paper is to review the current evidence, gaps in knowledge and ongoing research regarding APT in the setting of an ACS in elderly and very elderly patients, and in those with significant comorbidities including chronic kidney disease, diabetes mellitus and frailty.