Miracle-dz/UniFAR-FTUs huggingface dataset:
ROLE OF RADIATION AS EFFECTIVE INTERVENTION IN Aβ INDUCED OXIDATIVE STRESS IN ANIMAL MODEL OF ALZHEIMER’S DISEASE

Objective: The present study was undertaken to study the therapeutic effects of low dose fractionated cranial X-irradiation on reducing the amyloid-beta (Aβ) induced oxidative stress burden in an animal model of Alzheimer’s disease (AD). Methods: S.D. female rats received an intracerebroventricular injection of Aβ peptide at stereotaxically defined points. Experimental sessions were conducted by randomly dividing animals into four groups, namely sham-operated, Aβ-injected, and Aβ injection followed by cranial X-irradiation and only cranial X-irradiated. Anesthetized animals received 5 μl synthetic Aβ peptide injection with a 10 μl Hamilton microsyringe with the needle kept in place for a period of 2min following injection. Sham-operated group received 5 μl of bidistilled water instead of Aβ peptide. Animals were treated 6 weeks post-surgery with fractionated radiation of 2Gy for 5 days. Neurobehavior studies were undertaken to confirm memory impairment along with biochemical indices involved in the antioxidant defense system.Results: Fractionated cranial X-irradiation proved effective in restoration of activity of enzymes involved in the antioxidant defense system; the lipid peroxidation and catalase levels that showed a significant increase in Aβ-treated group decreased on subsequent X-irradiation. Moreover, the decrease in the superoxide dismutase, glutathione, glutathione-S-transferase, and glutathione reductase levels witnessed an increase post-irradiation, implicating the X-irradiation to be an effective intervention to restore the redox status of the oxidatively stressed brain cells in AD condition.Conclusion: The present study evaluated the therapeutic potential of low dose fractionated cranial X- irradiation by mitigating the amyloid-induced oxidative stress suggesting a novel treatment for AD-associated pathologies.
Ionic liquid supported acid-catalysed esterification of lauric acid [mangkin asid disokong pada cecair ionik sebagai mangkin dalam tindak balas pengesteran asid laurik]

Ionic Liquid (IL) based on 1-n-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BMI.NTf2) under acidic condition was used as catalyst for the esterification reaction of fatty acid. Various acids namely sulphuric acid, perchloric acid, p-toulene sulphonic acid and various chloride salts such as zinc chloride (ZnCl2) and iron(III) chloride (FeCl3) immobilized in ionic liquid BMI.NTf2 gave acidic ILs. These acidic ILs were tested as catalysts for esterification reactions. Esterification of alcohol (methanol) with fatty acid (lauric acid) using ionic liquid BMI.NTf2 combined with H2SO4 (BMI.NTf2(H2SO4)) gave high activity (>85%) and selectivity (100%) observed over a period of 2 hours reaction with reaction temperature 70oC. The ester became easily separated due to IL forming biphasic with product after the reaction where ester accumulated as the upper phase and IL with water produced after reaction at lower phase. Catalytic activities comparison also be studied between acidic ionic liquid BMI.NTf2 with acidic ionic liquid ChCl.2ZnCl2 and conventional acid catalyst. These ILs were characterised by using FTIR, NMR and TGA. Results from FTIR were showed no significant difference between ILs with ILs in acidic condition. The TGA curve show BMI.NTf2 thermal's decomposition is =400°C but when BMI.NTf2 combination with H2SO4, TGA curve show weight loss increase and becomes unstable. The advantages of ILs as catalyst are "clean process" and "green chemistry" due to its behaviour such as non-volatile, no loss of solvent through evaporation and reduced environmentally impact. This ILs-catalyst system can be recycle for futher reaction.
Cytoskeleton Proteins: A Purification Manual

A General. - I User's Instructions. - II General Lab Equipment. - III Preparation of Buffers. - IV Ammonium Sulfate Precipitation. - V Chromatographic Fractionation. - VI Centrifugation. - VII Abbreviations. - B Purification Protocols. - I Actin and Actin-Associated Proteins. - II Tubulin and Microtubule-Associated Proteins. - III Motor Proteins. - IV Intermediate Filament Proteins. - V Plasmamembrane and Organelle-Associated Proteins. - C Suppliers List.
Pathogen diversity drives the evolution of promiscuous peptide binding of human MHC-II alleles

Major histocompatibility complex (MHC) molecules mediate the adaptive immune response against pathogens. Certain MHC alleles are generalists: they present an exceptionally large variety of antigenic peptides. However, the functional implications of such elevated epitope binding promiscuity in the MHC molecules are largely unknown. According to what we term the pathogen-driven promiscuity hypothesis, exposure to a broad range of pathogens favors the evolution of highly promiscuous MHC variants. Consistent with this hypothesis, we found that in pathogen-rich geographical regions, humans are more likely to carry promiscuous MHC class II DRB1 alleles, and the switch between high and low promiscuity levels has occurred repeatedly and in a rapid manner during human evolution. We also show that selection for promiscuous peptide binding shapes MHC genetic diversity. In sum, our study offers a conceptually novel mechanism to explain the global distribution of allelic variants of a key human immune gene by demonstrating that pathogen pressure maintains promiscuous MHC class II alleles. More generally, our work highlights the hitherto neglected role of epitope binding promiscuity in immune defense, with implications for medical genetics and epidemiology.
Hybrid optoelectronics with colloidal nanocrystals

In this work we present spectroscopic studies of the exciton dynamics in colloidal spherical cadmium sulfide CdS nanocrystals (NC) in the vicinity of a single indium gallium nitride InGaN quantum well (QW) in dependence of temperature. QWs of the alloy material InGaN exhibit a dependence of the exciton dimensionality on the thermal energy available. It was demonstrated that this dependence influences the rate for fluorescence resonant energy transfer from the QW to a layer of CdS-NC deposited on top of its capping layer. Investigations of different capping layer thicknesses demonstrated the dependence of the exciton dimensionality on the disorder potential of the QW. Furthermore, spectroscopic measurements of elongated asymmetric cadmium selenide/- cadmium sulfide CdSe/CdS nanorods (NR) under the application of external magnetic and electric fields are discussed. Asymmetric CdSe/CdS-NR represent a special case of elongated NR as the analytical treatment of spherical NC can be combined with numerical methods of calculating the electron and hole energies and wave functions. The results for the excitonic fine structure splitting in these nanomaterials is used to explain the dependence of the exciton dynamics under an external magnetic field. For the first time, a separate measurement of the Zeeman splitting and the magnetic field induced spin admixture in colloidal NR was performed. Electric field mediated carrier separation in asymmetric CdSe/CdS-NR is measured in time resolved luminescence quenching experiments. Retrieval of stored excitations is demonstrated employing a synchronised ultrafast voltage pulse detection scheme.
Novel genes for autism implicate both excitatory and inhibitory cell lineages in risk

We present the largest exome sequencing study to date focused on rare variation in autism spectrum disorder (ASD) (n=35,584). Integrating de novo and case-control variation with an enhanced Bayesian framework incorporating evolutionary constraint against mutation, we implicate 99 genes in ASD risk at a false discovery rate (FDR) ≤ 0.1. Of these 99 risk genes, 46 show higher frequencies of disruptive de novo variants in individuals ascertained for severe neurodevelopmental delay, while 50 show higher frequencies in individuals ascertained for ASD, and comparing ASD cases with disruptive mutations in the two groups shows differences in phenotypic presentation. Expressed early in brain development, most of the risk genes have roles in neuronal communication or regulation of gene expression, and 12 fall within recurrent copy number variant loci. In human cortex single-cell gene expression data, expression of the 99 risk genes is also enriched in both excitatory and inhibitory neuronal lineages, implying that disruption of these genes alters the development of both neuron types. Together, these insights broaden our understanding of the neurobiology of ASD.
A Levenberg–Marquardt Backpropagation Neural Network for Predicting Forest Growing Stock Based on the Least-Squares Equation Fitting Parameters

Traditional field surveys are expensive, time-consuming, laborious, and difficult to perform, especially in mountainous and dense forests, which imposes a burden on forest management personnel and researchers. This study focuses on predicting forest growing stock, one of the most significant parameters of a forest resource assessment. First, three schemes were designed—Scheme 1, based on the study samples with mixed tree species; Scheme 2, based on the study samples divided into dominant tree species groups; and Scheme 3, based on the study samples divided by dominant tree species groups—the evaluation factors are fitted by least-squares equations, and the non-significant fitted-factors are removed. Second, an overall evaluation indicator system with 17 factors was established. Third, remote sensing images of Landsat Thematic Mapper, digital elevation model, and the inventory for forest management planning and design were integrated in the same database. Lastly, a backpropagation neural network based on the Levenberg–Marquardt algorithm was used to predict the forest growing stock. The results showed that the group estimation precision exceeded 90%, which is the highest standard of total sampling precision of inventory for forest management planning and design in China. The prediction results for distinguishing dominant tree species were better than for mixed dominant tree species. The results also showed that the performance metrics for prediction could be improved by least-squares equation fitting and significance filtering of the evaluation factors.
Image-derived Models of Cell Organization Changes During Differentiation of PC12 Cells

Cellular differentiation is a complex process requiring the coordination of many cellular components. PC12 cells are a popular model system to study changes driving and accompanying neuronal differentiation. While significant attention has been paid to changes in transcriptional regulation and protein signaling, much less is known about the changes in cell organization that accompany PC12 differentiation. Fluorescence microscopy can provide extensive information about this, although photobleaching and phototoxicity frequently limit the ability to continuously observe changes in single cells over the many days that differentiation occurs. Here we describe a generative model of differentiation-associated changes in cell and nuclear shape and their relationship to mitochondrial distribution constructed from images of different cells at discrete time points. We show that our spherical harmonic-based model can accurately represent cell and nuclear shapes by measuring reconstruction errors. We then learn a regression model that relates cell and nuclear shape and mitochondrial distribution and observe that the predictive accuracy generally increases during differentiation. Most importantly, we propose a method, based on cell matching and linear interpolation in the shape space, to model the dynamics of cell differentiation using only static images. Without any prior knowledge, the method produces a realistic shape evolution process. Author Summary Cellular differentiation is an important process that is challenging to study due to the number of organizational changes it includes and the different time scales over which it occurs. Fluorescent microscopy is widely used to study cell dynamics and differentiation, but photobleaching and phototoxicity often make it infeasible to continuously observe a single cell undergoing differentiation for several days. In this work, we described a method to model aspects of the dynamics of PC12 cell differentiation without continuous imaging. We constructed accurate representations of cell and nuclear shapes and quantified the relationships between shapes and mitochondrial distributions. We used these to construct a generative model and combined it with a matching process to infer likely sequences of the changes in single cells undergoing differentiation.
SILAGEM DE CAPIM BRACHIARIA PARA TERMINAÇÃO DE BOVINOS EM CONFINAMENTO

RESUMO: O presente trabalho teve como objetivo avaliar o potencial da silagem de capim Brachiaria para a terminação de bovinos em confinamento, bem como determinar a proporção mais adequada do referido volumoso, levando-se em consideração o desempenho produtivo dos animais. Utilizaram-se 32 tourinhos da raça Nelore, desmamados aos sete meses de idade e recriados em pastagem de Brachiaria brizantha cv. Marandu com suplementação mineral, apresentando ao início do experimento 18 meses e 383,5 kg de peso corporal. Os animais foram confinados aos pares em baias (16 m) parcialmente cobertas, equipadas com bebedouros e comedouros individualizados. Os teores de matéria seca (MS) e proteína bruta (PB) foram determinados segundo AOAC (1995). Os teores de fibra em detergente neutro (FDN), fibra em detergente ácido (FDA) e lignina foram determinadas segundo VAN SOEST (1973) e VAN SOEST et al. (1991. Os teores de carboidratos não fibrosos (CNF) e nutrientes digestíveis totais (NDT) foram determinados segundo (SNIFFEN et al., 1992), o teor de nutrientes digestíveis totais foi determinado a partir do ensaio de digestibilidade em que: NDT (%) = PBD + FDND + CNFD + (2,25 x EED). O delineamento experimental utilizado foi o inteiramente casualizado, em que para os dados de consumo as baias constituíram as unidades experimentais (quatro repetições) e, para demais dados, os animais constituíram as repetições. Os dados foram submetidos à análise de variância e regressão polinomial, considerando 5% como nível crítico de significância. PALAVRA-CHAVE: ruminante; pastagem; confinamento
A Review on Major Risk Factors and Current Status of Visceral Leishmaniasis in North India

In India, more than 1,00,000 people are affected every year by Visceral Leishmaniasis (VL). VL is a chronic and fatal disease caused by Leishmania donovani parasites which are transmitted by infected female sand flies, Phlebotomus argentipes. Ninety percent of total cases of the world are reported from India, Bangladesh and Sudan. Several districts of the state Bihar show the occurrence of VL. This is 40-50% of the world cases and 90% of the cases in India. Conversely, information on epidemiology of kala-azar in India remains scanty due to inadequate studies about the various risk factors associated with VL. The present review contributes to the study of the number of cases, deaths, prevalence and incidence caused by VL, spatial distribution, basic epidemiologic features, the vector biology, transmission of the parasite, hosts and most importantly the major risk factors viz. climatic, the physical and biotic factors, the socio-economic conditions, the environmental factors, deforestation due to urbanization, domestic animals and the living standard. For this study we chose five states in India; Bihar, Uttarakhand, Uttar Pradesh, Jharkhand and West Bengal. The study period was from 2010-2017. A decreasing trend was observed in the number of incidences, cases and deaths. But on the contrary, the Post Kala Azar Dermal Leishmaniasis cases (PKDL) showed an increasing trend. The Gram Pradhans (Heads of Villages) and the villagers were also questioned regarding the associated risk factors viz. housing conditions- kaccha (mud) houses, poverty, use of bed nets, cleanliness, damp floors, cooking fuel, vegetation, the rearing of the domestic animals etc. The study suggests that the control measures have been effective in suppressing/eradicating VL but seeing the PKDL trend it also leaves a suspicion that apart from P. argentipus some other flies may also be playing the role as vectors in the transmission of VL. To decrease the transmission of Leishmania donovani and to achieve the goal of total eradication of VL from India in near future, a better understanding of the biology underlying transmission and disease with the major risk factors is the pressing need.
Beyond Accuracy: Investigating the Potential Clinical Utility of Predicting Functional Dependency and Severe Disability or Death in Successfully Reperfused Patients using Machine Learning

Objectives: Machine learning (ML) has been demonstrated to improve the prediction of functional outcome in patients with acute ischemic stroke. However, its value in a specific clinical use case has not been investigated. Aim of this study was to assess the clinical utility of ML models with respect to predicting functional impairment and severe disability or death considering its potential value as a decision-support tool in an acute stroke workflow. Materials and Methods: Patients (n=1317) from a retrospective, non-randomized observational registry treated with Mechanical Thrombectomy (MT) were included. The final dataset of patients who underwent successful recanalization (TICI [≥] 2b) (n=932) was split in order to develop ML-based prediction models using data of (n=745, 80%) patients. Subsequently, the models were tested on the remaining patient data (n=187, 20%). For comparison, baseline algorithms using majority class prediction, SPAN-100 score, PRE score, and Stroke-TPI score were implemented. The ML methods included eight different algorithms (e.g. Support Vector Machines and Random forests), stacked ensemble method and tabular neural networks. Prediction of modified Rankin Scale (mRS) 3-6 (primary analysis) and mRS 5-6 (secondary analysis) at 3 months was performed using 25 baseline variables available at patient admission. ML models were assessed with respect to their ability for discrimination, calibration and clinical utility (decision curve analysis). Results: Analyzed patients (n=932) showed a median age of 74.7 (IQR 62.7-82.4) years with (n=461, 49.5%) being female. ML methods performed better than clinical scores with stacked ensemble method providing the best overall performance including an F1-score of 0.75 {+/-} 0.01, an ROC-AUC of 0.81 {+/-} 0.00, AP score of 0.81 {+/-} 0.01, MCC of 0.48 {+/-} 0.02, and ECE of 0.06 {+/-} 0.01 for prediction of mRS 3-6, and an F1-score of 0.57 {+/-} 0.02, an ROC-AUC of 0.79 {+/-} 0.01, AP score of 0.54 {+/-} 0.02, MCC of 0.39 {+/-} 0.03, and ECE of 0.19 {+/-} 0.01 for prediction of mRS 5-6. Decision curve analyses suggested highest mean net benefit of 0.09 0.19 {+/-} 0.02 at a-priori defined threshold (0.8) for the stacked ensemble method in primary analysis (mRS 3-6). Across all methods, higher mean net benefits were achieved for optimized probability thresholds but with considerably reduced certainty (threshold probabilities 0.24-0.47). For the secondary analysis (mRS 5-6), none of the ML models achieved a positive net benefit for the a-priori threshold probability 0.8. Conclusions: The clinical utility of ML prediction models in a decision-support scenario aimed at yielding a high certainty for prediction of functional dependency (mRS 3-6) is marginal and not evident for the prediction of severe disability or death (mRS 5-6). Hence, using those models for patient exclusion cannot be recommended and future research should evaluate utility gains after incorporating more advanced imaging parameters.
Diverse stepping motions of cytoplasmic dynein revealed by kinetic modeling

Cytoplasmic dynein is a two-headed molecular motor that moves to the minus end of microtubule (MT) using ATP hydrolysis free energy. By employing its two heads (motor domains), cytoplasmic dynein shows various bipedal stepping motions; the inchworm and hand-over-hand motions, as well as non-alternate steps of one head. However, the molecular basis to achieve such diverse stepping manners remains obscure. Here, we propose a kinetic model for bipedal motions of cytoplasmic dynein and performed Gillespie Monte Carlo simulations that reproduces most experimental data obtained to date. The model represents status of each motor domain as five states according to conformations, nucleotide- and MT-binding conditions of the domain. Also, the relative positions of the two domains were approximated by three discrete states. Accompanied by ATP hydrolysis cycles, the model dynein stochastically and processively moved forward in multiple steps via diverse pathways, including inchworm and hand-over-hand motions, same as experimental data. The model reproduced key experimental motility-related parameters including velocity and run-length as functions of ATP concentration and external force. Our model reveals that, in a typical inchworm motion, the leading domain moves via the ATP-dependent power-stroke of the linker coupled with a small change in the stalk angle, whereas the lagging domain moves via diffusion dragged by the leading domain. Moreover, the hand-over-hand motion in the model dynein clearly differs from that of kinesin by the usage of the power-stroke. Author Summary Cytoplasmic dynein is a two-headed molecular motor, which moves linearly and transports intra-cellar organelles along microtubules driven by ATP hydrolysis free energy. In contrast to other better-known molecular motors, such as kinesin, dynein is known to take various stepping motions including motions akin to human walking and inchworm-like motions. However, molecular mechanisms underpinning the diverse stepping motions are unclear. Here, based on recent high-resolution structure information and single-molecule motility assay data, we designed a kinetic model that explicitly include two heads, each of which makes ATP hydrolysis cycles and moves along the microtubules. Using the model, we performed Monte Carlo simulations. The simulation reproduced most of currently available experimental results. More importantly, the simulation suggested molecular mechanisms of various stepping motions. While stepping motions apparently resemble to those proposed before, once looking into details, we found the resulting mechanisms distinct from previously proposed ones in the usage of ATP and protein conformation changes coupled with stepping motions.