Miracle-dz/UniFAR-FTUs huggingface dataset:
AlzGenPred: A CatBoost based method using network features to classify the Alzheimer’s Disease associated genes from the high throughput sequencing data

Background and Objective AD is a progressive neurodegenerative disorder characterized by memory loss. Due to the advancement in next-generation sequencing technologies, an enormous amount of AD-associated genomics data is available. However, the information about the involvement of these genes in AD association is still a research topic because all these algorithms are based on statistical techniques. Therefore, AlzGenPred is developed to identify the AD-associated genes from a large set of data. Methods To develop the AlzGenPred, we have compiled a benchmark dataset consisting of 1086 AD and non-AD genes and used them as positive and negative datasets. We have generated several features including the fused features and evaluated them through machine learning methods. Then hyperparameter tuning approach was also applied and the final model was selected. The proposed method was validated by using the AlzGene and transcriptomics datasets and proposed as a standalone tool. Results Total 13504 features belonging to eight different encoding schemes of these sequences were generated and evaluated by using 16 ML algorithms. It reveals that network-based features can classify AD genes while sequence-based features are not able to classify them. Then we generated 24 different fused features (6020 D) using sequence-based features and fed them into a two-step lightGBM-based recursive feature selection method. It increased up to 5-7% accuracy. After that selected eight fused features with CKSAAP were used for the hyperparameter tuning. They showed <70% accuracy. Therefore, network-based features were used to generate the CatBoost-based ML method called AlzGenPred with 96.55% accuracy and 98.99% AUROC. The developed method is tested on the AlzGene dataset where it showed 96.43% accuracy. Then the model is validated using the transcriptomics dataset also. Conclusion The validation of AlzGenPred using the AlzGene dataset and transcriptomics dataset obtained from Human, mouse, and ES-derived neural cells revealed that it can classify the omics data and can sort the AD-associated genes. These predicted genes can be directly used in the wet lab for further testing which will reduce labor cost and time expenses. The AlzGenPred is developed as a standalone package and is available for users at https://www.bioinfoindia. org/alzgenpred/ and https://github.com/shuklarohit815/AlzGenPred.
The influence of internal pressure and neuromuscular agents on C. elegans biomechanics: an empirical and multi-compartmental in silico modelling study

The function of a specific tissue and its biomechanics are interdepended, with pathologies or ageing often being intertwined with structural decline. The biomechanics of Caenorhabditis elegans (C. elegans), a model organism widely used in pharmacological and ageing research, has been established as biomarker for healthy ageing, though the mechanics of individual tissues have remained elusive. In this study we investigated the biomechanics of healthy C. elegans cuticle, muscle tissue, and pseudocoelom using a combination of indentation experiments and in silico modelling. Nematode stiffness measurements were performed using an atomic force microscope. The worm’s cylindrical body was approximated using a novel three-compartmental nonlinear finite element model, enabling analysis of how changes in the elasticity of individual compartments affect the bulk stiffness of C. elegans. The parameters of the model were then fine-tuned to match the simulation force-indentation output to the experimental data. To test the finite element model, distinct compartments were modified experimentally. Our in silico results, in agreement with previous studies, suggest that hyperosmotic shock reduced stiffness by decreasing the C. elegans’ internal pressure. Unexpectedly, treatment with the neuromuscular agent aldicarb, traditionally associated with muscle contraction, reduced stiffness by decreasing the internal pressure. It challenges previous assumptions about the effects of aldicarb. Furthermore, our finite element model can offer insights into how drugs, mutations or processes like ageing target individual tissues.
Endonucleosis mediates internalization of cytoplasm into the nucleus in senescent cells

Cellular senescence is driven by diverse effector programs, leading to irreversible growth arrest, DNA damage and complex secretomes. Here we show that, in liver-specific Setd8-KO mice, after mitogen treatment, a significant number of hepatocytes become senescent and display unusual features such as enlarged nuclei, chromosomal hyperploidy and nuclear engulfments progressing to the formation of intranuclear vesicles. These vesicles contain glycogen, cytoplasmic proteins and even entire organelles. We term this process “endonucleosis”. Experiments with Setd8/Atg5 double knockout mice, demonstrated that endonucleosis requires the function of the autophagy machinery. Endonucleosis and hyperploidization are temporary, early features of senescence. Larger vesicles brake down into microvesicles over time and are eventually eliminated. The results reveal a senescence phenotype, which function as part of survival mechanisms to prevent necrotic death.
Formation age,geochemical characteristics of the Ninggang granite body in Jiangxi Province and its tectonic significance

The Ninggang granite body,located at the juncture of Hunan and Jiangxi provinces,is an important member of the Caledonian granite zone with south-north trend.It is mainly composed of monzogranite.LA-ICPMS U-Pb dating of zircons yields an age of 433.8±2.2Ma,suggesting that it was formed in the Caledonian magmatism event.Although Ninggang granite body exhibit obvious variation of SiO_2 contents (67.46%～74.85%),their ACNK values are all bigger than 1.1,potassium larger than sodium(K_2O/Na_2O= 1.36～2.37),CaO/Na_2O ratios larger than 0.3 and enrichment of Rb,Th and Cs,depletion of Nb,Ta,Ba and Sr,strong REE fractionation (LREE/HREE=5.8～12.2) and relative obvious Eu depletion (δEu=0.28～0.61). They also have lower e_(Nd)(t) values (-9.3～-8.6),higher (~(87)Sr/~(86)Sr)_i ratios (0.71172～0.71937) and old Nd model ages (1838～1909Ma). These geoehemical characteristics indicate that the Ninggang granite body belonged to crust sourced type of granite and were derived from the paitial melting of psammitic rock under an extensional tectonic setting which is caused by continent-continent collision between remnant Cathaysia fragments and Yangtze block.
Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment

In the nucleus, biological processes are driven by proteins that diffuse through and bind to a meshwork of nucleic acid polymers. To better understand this interplay, we developed an imaging platform to simultaneously visualize single protein dynamics together with the local chromatin environment in live cells. Together with super-resolution imaging, new fluorescent probes, and biophysical modeling, we demonstrated that nucleosomes display differential diffusion and packing arrangements as chromatin density increases whereas the viscoelastic properties and accessibility of the interchromatin space remain constant. Perturbing nuclear functions impacted nucleosome diffusive properties in a manner that was dependent on local chromatin density and supportive of a model wherein transcription locally stabilizes nucleosomes while simultaneously allowing for the free exchange of nuclear proteins. Our results reveal that nuclear heterogeneity arises from both active and passive process and highlights the need to account for different organizational principals when modeling different chromatin environments.
Effect of Thinning on Growth Quality and Efficiency of Mid-young Plantation of Cunninghamia lanceolata

Cunninghamia lanceolata was a major species for fast-growing timber in Jiangxi.Through different thinning measures were made on 20 years old Cunninghamia lanceolata plantation in Wanhuashan forest farm in Jishui.Their average diameter at breast height,average tree height,timber volume of wood species and economic benefits were investigated and analyzed,which have significant differences.Thinning was made scientifically and timely,the land that with thinning for 2 times,the above factor were higher than that with once thinning and that without thinning,it showed that the forest thinning can improve the lad quality and economic effectively.
Dispersion Analysis of Tsunami Propagation with the Consideration of Water Compressibility and Earth Elasticity for the Improvement of Prediction Accuracy of Far-field Tsunamis

The discrepancy of tsunami arrival time between the tsunami simulation and the real observation has been widely recognized since the 27 February 2010 Chile tsunami and the 11 March 2011 Japan tsunami. The effect of ocean-water compressibility and earth elasticity on tsunami propagation speed was analyzed on the basis of a multilayered earth model. A correction term of these effects was introduced to ordinary linear long wave equations. Calculated waveforms with the correction were quantitatively compared with observed ones of the two tsunamis. The accuracy of far-field tsunami simulation was significantly improved without any arbitrary parameter.
All outputs in CentAUR are protected by Intellectual Property

Background: Cardiovascular diseases (CVDs) are the greatest cause of death globally, and their reduction is a key public-health target. High blood pressure (BP) affects 1 in 3 people in the United Kingdom, and previous studies have shown that milk consumption is associated with lower BP. Objective: We investigated whether intact milk proteins lower 24-h ambulatory blood pressure (AMBP) and other risk markers of CVD. Design: The trial was a double-blinded, randomized, 3-way–crossover, controlled intervention study. Forty-two participants were randomly assigned to consume 2 3 28 g whey protein/d, 2 3 28 g Ca caseinate/d, or 2 3 27 g maltodextrin (control)/d for 8 wk separated by a 4-wk washout. The effects of these interventions were examined with the use of a linear mixed-model ANOVA. Results: Thirty-eight participants completed the study. Significant reductions in 24-h BP [for systolic blood pressure (SBP): 23.9 mm Hg; for diastolic blood pressure (DBP): 22.5 mm Hg; P = 0.050 for both)] were observed after whey-protein consumption compared with control intake. After whey-protein supplementation compared with control intake, peripheral and central systolic pressures [25.7 mm Hg (P = 0.007) and 25.4 mm Hg (P = 0.012), respectively] and mean pressures [23.7 mm Hg (P = 0.025) and 24.0 mm Hg (P = 0.019), respectively] were also lowered. Flowmediated dilation (FMD) increased significantly after both wheyprotein and calcium-caseinate intakes compared with control intake [1.31% (P , 0.001) and 0.83% (P = 0.003), respectively]. Although both whey protein and calcium caseinate significantly lowered total cholesterol [20.26 mmol/L (P = 0.013) and 20.20 mmol/L (P = 0.042), respectively], only whey protein decreased triacylglycerol (20.23 mmol/L; P = 0.025) compared with the effect of the control. Soluble intercellular adhesion molecule 1 and soluble vascular cell adhesion molecule 1 were reduced after whey protein consumption (P = 0.011) and after calcium-caseinate consumption (P = 0.039), respectively, compared with after control intake. Conclusions: The consumption of unhydrolyzed milk proteins (56 g/d) for 8 wk improved vascular reactivity, biomarkers of endothelial function, and lipid risk factors. Whey-protein supplementation also lowered 24-h ambulatory SBP and DBP. These results may have important implications for public health. This trial was registered at clinicaltrials.gov as NCT02090842. Am J Clin Nutr doi: 10.3945/ajcn.116. 137919.
Microbial (Microalgal-Bacterial) Biomass Grown on Municipal Wastewater for Sustainable Biofuel Production

xiv Research Publications . xvi Chapter 1: Introduction . 1 1.1 Background . 1 1.2 Conventional Biofuels . 2 1.3 Sustainable Biofuels from Microalgae. 2 1.4 Microbial Biomass Consortia . 4 1.4.1 Microalgae . 4 1.4. 2 Bacteria . 6 1.4. 3 Microbial Nutrition . 6 1.4. 4 Microbial (Microalgal-Bacterial) Floc Dynamics and Characteristics . 7 1.4. 5 Wastewater Treatment . 8 1.4. 6 Factors Affecting Large-Scale Microbial Biofuel Production . 10 1.4. 6.1 Biomass Productivity in Photobioreactors and High-Rate Algal Ponds . 10 1.4. 6.2 Biomass Harvesting . 12 1.4. 6.3 Biochemical Composition. 14 1.4. 6.4 Economics . 15 1.5 Research Drivers . 16 1.6 Research Hypotheses, Objectives, and Organisation . 16 Chapter 2: Materials and Methods . 18 2.1 Source Water Characteristics . 18 2.1.1 Microbial Inocula . 18 2.1.2 Wastewater Feeds . 19 2.2 Laboratory Growth System Specifications . 20 2.2.1 Glass Reactors . 20 2.2.2 Steel Reactors . 21 2.3 Sampling Logistics. 25 2.3.1 Mixture . 25 2.3.2 Supernatant . 25 2.3.3 Settleable Biomass . 25 2.3.4 Total Biomass . 26 2.4 Analytical Methods . 26 2.4.1 pH, DO, Water Temperature, and PAR . 26 2.4. 2 Biomass and Dry Weight . 26 2.4. 3 Sedimentation and Settleability . 27 2.4. 4 COD and Nitrogen Species . 28 2.4. 5 Turbidity . 29 2.4. 6 Chl a . 29 2.4. 7 Energy . 30 2.4. 8 Lipids . 30 2.4. 9 TKN and TP . 30 2.4.10 TC and TOC . 31 2.4.11 Microalgal and Microfaunal Taxonomy . 31 v 2.4.12 Bacterial Taxonomy . 31 2.5 Quality Assurance/Quality Control . 31 2.6 Climate Data . 32 2.6.1 Ambient Climate Laboratory Conditions . 32 2.6.2 Controlled Climate Laboratory Conditions . 32 2.7 Statistical Analyses . 33 2.8 Health and Safety Approach . 34 Chapter 3: Preliminary Experiments Using Ambient Climate Laboratory Reactors . 35 3.1 Batch Experiments . 35 3.1.1 Microalgal Inoculum Selection Experiment . 35 3.1.2 Activated Sludge Addition Experiments . 36 3.1.2.1 Effects on Microalgal Growth . 36 3.1.2.2 Effects on Microalgae Harvesting . 38 3.2 Continuous Stirred Tank Reactor Experiment . 41 3.2.1 Experimental Design . 41 3.2.2 pH and DO Concentrations . 41 3.2.3 Biomass Production and Settleability . 42 3.2.4 Biomass Harvesting . 43 3.3 Sequencing Batch Reactor Experiment . 43 3.3.1 Experimental Design . 43 3.3.2 Wastewater Treatment . 44 3.3.2.1 Ammonia Concentrations . 44 3.3.2.2 pH and DO Concentrations . 45 3.3.3 Biomass Production and Settleability . 47 3.3.3.1 COD and TSS Concentrations. 47 3.3.3.2 Microalgal Growth and Settleability . 47 3.3.3.3 Supernatant Characteristics . 50 3.3.4 Biomass Stabilisation Experiment . 51 3.3. 5 Related Work . 52 3.4 Summary. 52 Chapter 4: Municipal Feed Water Selection Experiments Using Controlled Climate Laboratory SBRs . 54 4.1 Experimental Design . 54 4.1.1 Inoculum Standardisation . 54 4.1.2 Culture Acclimation and Operation . 55 4.1.3 Difficulties Encountered .
The unusual 28 December 2014 dike‐fed paroxysm at Mount Etna: Timing and mechanism from a multidisciplinary perspective

Between 2011 and 2013, there were 43 lava fountain episodes from Mount Etna's New South‐East summit crater (NSEC). In 2014, this intense activity was supplanted by sporadic Strombolian explosions and the opening of an eruptive fissure between July and August. The only lava fountaining episode of the year occurred on 28 December; this was characterized by the emplacement of a shallow dike that, at the surface, fed two distinct lava flows from an ENE‐WSW trending eruptive fissure. Here we provide a detailed picture of the onset of the dike emplacement, as well as the mechanism driving its migration, using a multidisciplinary data set based on seismic, geodetic, geochemical, and volcanological observations. The dike emplacement was preceded by a pressurization of the magmatic plumbing system recorded from August 2014 on. This pressurization has been modeled as a vertically elongated magmatic source located beneath the summit craters at ~4.5 km below sea level. From September to October, magma rising was also detected by seismic and geochemical data that highlighted pressurization of the shallower portion of the plumbing system. We suggest that the 28 December 2014 dike emplacement resulted from a modification of the preexisting NSEC shallow plumbing system, largely due to drainage of the main shallow conduit during the July–August 2014 eruptive fissure activity. Such a structural modification might have created the conditions for magma emplacement as a dike‐like structure.
Hintless Single-Server Private Information Retrieval

We present two new constructions for private information retrieval (PIR) in the classical setting where the clients do not need to do any preprocessing or store any database dependent information, and the server does not need to store any client-dependent information. Our ﬁrst construction HintlessPIR eliminates the client preprocessing step from the recent LWE-based SimplePIR (Henzinger et. al., USENIX Security 2023) by outsourcing the “hint” related computation to the server, leveraging a new concept of homomorphic encryption with composable preprocessing . We realize this concept on RLWE encryption schemes, and thanks to the composibility of this technique we are able to pre-process almost all the expensive parts of the homomorphic computation and reuse across multiple executions. As a concrete application, we achieve very eﬃcient matrix vector multiplication that allows us to build HintlessPIR . For a database of size 8GB, HintlessPIR achieves throughput about 3.7GB/s without requiring any client or server state. We additionally formalize the matrix vector multiplication protocol as LinPIR primitive, which may be of independent interests. In our second construction TensorPIR we reduce the communications of HintlessPIR from square root to cubic root in the database size. We show how to use RLWE encryption with preprocessing to outsource LWE de-cryption for ciphertexts generated by homomorphic multiplications. This allows the server to do more complex processing using a more compact query under LWE. We implement and benchmark HintlessPIR which achieves better concrete costs than TensorPIR for a large set of databases of interest. We show that it improves the communication of recent preprocessing
MIT Open Access Articles Automated Home-Cage Behavioural Phenotyping of Mice

Neurobehavioral analysis of mouse phenotypes requires the monitoring of mouse behavior over long periods of time. Here, we describe a trainable computer vision system enabling the automated analysis of complex mouse behaviors. We provide software and an extensive manually annotated video database used for training and testing the system. Our system performs on par with human scoring, as measured from ground-truth manual annotations of thousands of clips of freely behaving mice. As a validation of the system, we characterized the home-cage behaviors of two standard inbred and two non-standard mouse strains. From this data we were able to predict in a blind test the strain identity of individual animals with high accuracy. Our video-based software will complement existing sensor based automated approaches and enable an adaptable, comprehensive, high-throughput, fine-grained, automated analysis of mouse behavior.
Luminescent Composites Based on Nanocellulose and K3Tb(PO4)2Phosphor - Preparation and Properties

The study of new nanocomposite materials based on the micro/nanocellulose matrices filled with K3Tb(PO4)2phosphor is herein presented. The prepared composites and their initial components have been characterized by means of optical and scanning electron microscopy, UV-VIS and photoluminescence spectroscopies. The scanning electron microscopy confirmed that the cellulose nanocomposites films comprise multi-domain regions with the oxide and matrix components. The luminescence of K3Tb(PO4)2or cellulose particles can be observed depending on the excitation wavelength indicating the possibility of the composites luminescence properties tailoring through changes in the relative content of matrix and filler. The studied cellulose-based composites can be considered as luminescent ink materials for 3D printing devices.
Complex Frequency Eigenvalue Problem for Circular Dielectric Rod Partially Covered with Graphene

We consider the two-dimensional electromagnetic complex-frequency eigenvalue problem for the natural modes of circular dielectric rod with partial graphene cover. The surface impedance of graphene is characterized by the quantum-theory Kubo equations. To reduce the problem to a well-conditioned determinantal equation, we use the method of analytical regularization based on explicit inversion of the static part of the problem. To find the roots of truncated determinantal equation, we apply the residual inverse iteration method. This analysis reveals the presence of the plasmon modes of the curved strip of graphene and the modes of the circular dielectric rod, perturbed by the presence of the strip. If the rod radius is measured in micrometers, the real parts of all these eigenfrequencies are comparable, however, the plasmon mode Q-factors are higher.
Liddicoatite Tourmaline From Anjanabonoina, Madagascar

28 LIDDICOATITE FROM MADAGASCAR GEMS & GEMOLOGY SPRING 2002 three lithium tourmalines with the general formula (Ca,Na,K, )(Li,Al)3Al6Si6O18(BO3)3(OH)3(OH,F), which are defined on the basis of their X-site occupancy: Ca = liddicoatite, Na = elbaite, and a vacant ( ) X site = rossmanite. Elbaite is the most abundant gem tourmaline, whereas rossmanite has so far been identified from few localities (Johnson and Koivula, 1998b; Selway et al., 1998), and typically is not of gem quality. However, neither can be separated from liddicoatite without quantitative chemical analysis. Therefore, in this article we use the group name tourmaline to refer to material that has not been chemically analyzed. Although liddicoatite is well characterized mineralogically, little has been published about the history, sources, and gemology of this tourmaline species in particular. This article focuses on liddicoatite from Madagascar—which is the principal historic source— and in particular on the Anjanabonoina pegmatite, By Dona M. Dirlam, Brendan M. Laurs, Federico Pezzotta, and William B. (Skip) Simmons
Non-myopic agents can stabilize cooperation in feedback-evolving games

Individuals make decisions that affect a shared environment, and in turn, a changing environment shapes incentives for future action. In this paper, we investigate the impact that non-myopic agents can have in altering environmental outcomes in scenarios where cooperation improves the environment and defection degrades it. The non-myopic agents considered here make choices that optimize future payoffs, based on projections of the future environmental states. We thus break with traditional assumptions in evolutionary game theory that all agents are myopic, basing decisions only on immediately available rewards. We show that the presence of non-myopic types can stabilize interior fixed points that were originally unstable in a fully myopic population. However, non-myopic types cannot de-stabilize fixed points that constitute a tragedy of the commons (TOC), i.e. configurations where all agents defect. We provide conditions on i) how non-myopic agents need to be, and ii) what fraction of non-myopic types in the population are necessary such that these results hold.
A spatial analysis of dengue fever and an analysis of dengue control strategies in Jeddah City, Saudi Arabia

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