Miracle-dz/UniFAR-FTUs huggingface dataset:
Trimetazidine Inhibits Renal Tubular Epithelial Cells to Mesenchymal Transition in Diabetic Rats via Upregulation of Sirt1

Trimetazidine (TMZ), as a metabolic regulator, is effective in treatment of coronary atherosclerotic heart disease with rare side effects in the clinic for long years. Interestingly, studies have shown that TMZ protects against several acute kidney injuries (AKI). However, the effect of TMZ on chronic kidney diseases (CKD) remains unknown. This study aimed to investigate the role of TMZ in diabetic nephropathy (DN) and its potential mechanisms. A rat model of DN was established in male Sprague-Dawley rats by streptozotocin (STZ) intraperitoneal injection. Experimental rats were separated into three groups: control, DN and DN + TMZ treatment. Metabolic parameters, pathological features and renal function markers were evaluated after 20 weeks of diabetes induction. In vitro experiments, the effect of TMZ on high fat and high glucose (HFG) induced or TGFβ1-induced epithelial-to-mesenchymal transition (EMT) was examined in HK-2 cells. Our results showed that TMZ could maintain renal function without affecting hemodynamic and plasma metabolic levels in diabetic rats. The effect was associated with a reversion of pathological progression of DN, especially for tubulointerstitial fibrosis. EMT is an important contributor to renal fibrosis. In this study, we investigated the role of TMZ in the process of EMT in DN. Mechanistically; TMZ attenuated HFG-induced EMT by relieving oxidative stress via deacetylation forkhead box O1 (FoxO1) in a Sirt1-dependent pathway. And it suppressed TGFβ1-induced EMT by deacetylating Smd4 in a Sirt1-dependent manner. Moreover, our study found that TMZ upregulated Sirt1 expression by increasing the expression of nicotinamide phosphoribosyl transferase (Nampt), which is a rate limiting enzyme for nicotinamide adenine dinucleotide (NAD+) generation by salvage pathway. And the increased NAD+ promoted Sirt1 expression. In conclusion, TMZ can prevent renal dysfunction and pathogenesis of tubulointerstitial fibrosis in DN, partly by inhibition of EMT via FoxO1/ROS pathway and TGFβ/Smad pathway in a Nampt/NAD+/Sirt1 dependent manner.
A Comprehensive Study of Load Balancing Approaches in the Cloud Computing Environment and a Novel Fault Tolerance Approach

The past few years have witnessed the emergence of a novel paradigm called cloud computing. CC aims to provide computation and resources over the internet via dynamic provisioning of services. There are several challenges and issues associated with implementation of CC. This research paper deliberates on one of CC main problems i.e. load balancing (LB). The goal of LB is equilibrating the computation on the cloud servers such that no host is under/ overloaded. Several LB algorithms have been implemented in literature to provide effective administration and satisfying customer requests for appropriate cloud nodes, to improve the overall efficiency of cloud services, and to provide the end user with more satisfaction. An efficient LB algorithm improves efficiency and asset’s usage through effectively spreading the workload across the system’s different nodes. This review research paper objective is to present critical study of existing techniques of LB, to discuss various LB parameters i.e. throughput, performance, migration time, response time, overhead, resource usage, scalability, fault tolerance, power savings, etc. The research paper also discusses the problems of LB in the CC environment and identifies the need for a novel LB algorithm that employs FT metrics. It has been found that traditional LB algorithms are not good enough and they do not consider FT efficiency metrics for their operation. Hence, the research paper identifies the need for FT efficiency metric in LB algorithms which is one of the main concerns in cloud environments. A novel algorithm that employs FT in LB is therefore proposed.
Comparison of four different methods for egg cholesterol determination

Abstract Eggs were collected from 48-wk-old, Single Comb White Leghorn hens fed a wheat and soybean meal-based laying hen ration. Yolks were separated, and five yolk samples were prepared by pooling three yolks per sample. Yolk samples were saponified and extracted with hexane. The hexane extracts were assayed for cholesterol by four different methods: colorimetric, enzymatic, gas chromatographic (GC), and HPLC. The traditional colorimetric method was found to overestimate the yolk cholesterol concentration when compared with the enzymatic, GC, or HPLC methods. No free fatty acids or triglycerides was detected in hexane extracts; therefore, the overestimation by the colorimetric method could not be attributed to contamination by free fatty acids or triglycerides. Cholesterol contents determined by enzymatic, GC, and HPLC methods were not significantly different from each other. All three methods had excellent precision.
Sequencing the Genome of Indian Flying Fox, Natural Reservoir of Nipah Virus, Using Hybrid Assembly and Conservative Secondary Scaffolding

Indian fruit bats, flying fox Pteropus medius was identified as an asymptomatic natural host of recently emerged Nipah virus, which is known to induce a severe infectious disease in humans. The absence of P. medius genome sequence presents an important obstacle for further studies of virus–host interactions and better understanding of mechanisms of zoonotic viral emergence. Generation of the high-quality genome sequence is often linked to a considerable effort associated to elevated costs. Although secondary scaffolding methods have reduced sequencing expenses, they imply the development of new tools for the integration of different data sources to achieve more reliable sequencing results. We initially sequenced the P. medius genome using the combination of Illumina paired-end and Nanopore sequencing, with a depth of 57.4x and 6.1x, respectively. Then, we introduced the novel scaff2link software to integrate multiple sources of information for secondary scaffolding, allowing to remove the association with discordant information among two sources. Different quality metrics were next produced to validate the benefits from secondary scaffolding. The P. medius genome, assembled by this method, has a length of 1,985 Mb and consists of 33,613 contigs and 16,113 scaffolds with an NG50 of 19 Mb. At least 22.5% of the assembled sequences is covered by interspersed repeats already described in other species and 19,823 coding genes are annotated. Phylogenetic analysis demonstrated the clustering of P. medius genome with two other Pteropus bat species, P. alecto and P. vampyrus, for which genome sequences are currently available. SARS-CoV entry receptor ACE2 sequence of P. medius was 82.7% identical with ACE2 of Rhinolophus sinicus bats, thought to be the natural host of SARS-CoV. Altogether, our results confirm that a lower depth of sequencing is enough to obtain a valuable genome sequence, using secondary scaffolding approaches and demonstrate the benefits of the scaff2link application. The genome sequence is now available to the scientific community to (i) proceed with further genomic analysis of P. medius, (ii) to characterize the underlying mechanism allowing Nipah virus maintenance and perpetuation in its bat host, and (iii) to monitor their evolutionary pathways toward a better understanding of bats’ ability to control viral infections.
L’évaluation des représentations vectorielles de mots en utilisant WordNet (Evaluating word representations using WordNet)

Les méthodes d’évaluation actuelles des représentations vectorielles de mots utilisent généralement un jeu de données restreint et biaisé. Pour pallier à ce problème nous présentons une nouvelle approche, basée sur la similarité entre les synsets associés aux mots dans la volumineuse base de données lexicale WordNet. Notre méthode d’évaluation consiste dans un premier temps à classer automatiquement les représentions vectorielles de mots à l’aide d’un algorithme de clustering, puis à évaluer la cohérence sémantique et syntaxique des clusters produits. Cette évaluation est effectuée en calculant la similarité entre les mots de chaque cluster, pris deux à deux, en utilisant des mesures de similarité entre les mots dans WordNet proposées par NLTK (wup _similarity). Nous obtenons, pour chaque cluster, une valeur entre 0 et 1. Un cluster dont la valeur est 1 est un cluster dont tous les mots appartiennent au même synset. Nous calculons ensuite la moyenne des mesures de tous les clusters. Nous avons utilisé notre nouvelle approche pour étudier et comparer trois méthodes de représentations vectorielles : une méthode traditionnelle, WebSOM et deux méthodes récentes, word2vec (Skip-Gram et CBOW) et GloVe, sur trois corpus : en anglais, en français et en arabe.
coIOMMU: A Virtual IOMMU with Cooperative DMA Buffer Tracking for Efficient Memory Management in Direct I/O

Direct assignment of I/O devices (Direct I/O) is the best per-formant I/O virtualization method. However, it requires the hypervisor to statically pin the entire guest memory, thereby hindering the efficiency of memory management. This problem can be fixed by presenting a virtual IOMMU (vIOMMU). Emulation of its DMA remapping capability carries sufficient information about guest DMA buffers, allowing the hypervisor to do fine-grained pinning of guest memory. However, established vIOMMUs are not widely used by commodity guests due to the emulation cost, thus cannot reliably eliminate static pinning in direct I/O. We propose and implement coIOMMU , a new vIOMMU architecture for efficient memory management with a cooperative DMA buffer tracking mechanism. The new mechanism provides a dedicated interface for hypervisor and guest to exchange DMA buffer information over a shared DMA tracking table (DTT), orthogonal to the costly DMA remapping interface. We also explore two techniques: smart pinning and lazy unpinning, to minimize the impact on the performance of direct I/O. Our evaluation results show that coIOMMU dramatically improves the efficiency of memory management in wide direct I/O usages with negligible cost. Moreover, the desired semantics of DMA remapping can be sustained when cooperative tracking is enabled alongside. Overall, we believe that coIOMMU can serve as a reliable solution for efficient memory management in direct I/O.
The effect of an exterior electric field on the instability of dielectric plates

We investigate the theoretical nonlinear response, Hessian stability, and possible wrinkling behaviour of a voltage-activated dielectric plate immersed in a tank filled with silicone oil. Fixed rigid electrodes are placed on the top and bottom of the tank, and an electric field is generated by a potential difference between the electrodes. We solve the associated incremental boundary value problem of superimposed, inhomogeneous small-amplitude wrinkles, signalling the onset of instability. We decouple the resulting bifurcation equation into symmetric and antisymmetric modes. For a neo-Hookean dielectric plate, we show that a potential difference between the electrodes can induce a thinning of the plate and thus an increase of its planar area, similar to the scenarios encountered when there is no silicone oil. However, we also find that, depending on the material and geometric parameters, an increasing applied voltage can also lead to a thickening of the plate, and thus a shrinking of its area. In that scenario, Hessian instability and wrinkling bifurcation may then occur spontaneously once some critical voltages are reached.
Abstract #3235: Efficacy and toxicity of an anti-mesothelin antibody drug conjugate

Mesothelin is a glycoprotein expressed by cells which form the mesothelial lining of the peritoneal and pleural cavities. It exists as both a secreted protein as well as a cell surface protein that is anchored via a GPI linkage. A soluble splice variant of the 40 kDa peptide (termed soluble mesothelin/MFP-related protein or SMR) has been found in the sera of patients with ovarian carcinoma and mesothelioma. Mesothelin is over-expressed on all mesotheliomas, many ovarian cancers and numerous other cancers. As mesothelin has limited expression on normal tissues and high expression on a number of cancers, it is an attractive candidate for targeted therapeutics such as an anti-mesothelin antibody-drug-conjugate (ADC). A fully human anti-mesothelin antibody (MDX-1382) was conjugated to a potent DNA alkylating agent related to Duocarmycin (MED2460). This ADC shows anti-tumor activity in xenograft models of ovarian, lung and pancreatic cancer at doses as low as 0.3 \#956;mole/kg. MDX-1382 does not bind to the mouse mesothelin protein such that toxicity assessments in mouse are limited to \#8220;off target\#8221; effects. However, a rat anti-mouse mesothelin antibody was generated and conjugated to MED2460 to assess the effects of targeting mesothelin in mice. In this model, doses of 0.3 \#956;mole/kg did not result in overt signs of toxicity. In addition, MDX-1382 binds to cynomolgus monkey mesothelin with similar affinity and tissue distribution as in humans. The intravenous administration of 0.4 \#956;mole/kg was well tolerated in cynomolgus monkeys and did not result in overt clinical or histological signs of toxicity. Citation Information: In: Proc Am Assoc Cancer Res; 2009 Apr 18-22; Denver, CO. Philadelphia (PA): AACR; 2009. Abstract nr 3235.
Synthesis and characterization of geminis and implications of their micellar solution on ninhydrin and metal amino acid complex

In our study, three gemini dicationic surfactants with different methylene group spacer (16-6-16, 16-5-16 and 16-4-16) have been synthesized and characterized in solution by 1H NMR spectroscopic technique. The implications of gemini micellar solution on ninhydrin and metal amino acid complex ([Cu(II)-Trp]+) were performed by the means of single-beam UV–visible spectroscopy. The absorbance was noted at regular time intervals and values of rate constant (kψ) were determined by using a computer-based program. Synthesized surfactants proved as an efficient catalyst on the interaction of ninhydrin with metal amino acid complex as compared with conventional surfactant and aqueous systems. The required description regarding the implications of gemini dicationic surfactants are provided in the text in detail. The conductivity technique was applied in order to get critical micelle concentration (cmc) of geminis in the presence and absence of reactants. Catalytic results developed in gemini dicationic surfactant system were explained effectively by pseudo-phase model. Various thermodynamic quantities, viz., activation energy, Ea, activation enthalpy, ΔH#, and activation entropy, ΔS#, were obtained on interaction of ninhydrin with [Cu(II)-Trp]+ in gemini systems by applying Eyring equation. A detailed explanation about these evaluated parameters was also made.
High-Performance Vertical III-V Nanowire MOSFETs on Si With gm > 3 mS/μm

Vertical III-V nanowire MOSFETs have demonstrated excellent performance including high transconductance and high <inline-formula> <tex-math notation="LaTeX">${I}_{\text {on}}$ </tex-math></inline-formula>. One main bottleneck for the vertical MOSFETs is the large access resistance arising from the contacts and ungated regions. We demonstrate a process to reduce the access resistance by combining a gate-last process with ALD gate-metal deposition. The devices demonstrate fully scalable <inline-formula> <tex-math notation="LaTeX">${g}_{\text {m}}$ </tex-math></inline-formula> down to <inline-formula> <tex-math notation="LaTeX">${L}_{\text {g}} =25$ </tex-math></inline-formula> nm. These vertical core/shell InAs/InGaAs MOSFETs demonstrate <inline-formula> <tex-math notation="LaTeX">${g}_{m} =3.1$ </tex-math></inline-formula> mS/<inline-formula> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">${R}_{\text {on}} = 190\,\,\Omega \mu \text{m}$ </tex-math></inline-formula>. This is the highest <inline-formula> <tex-math notation="LaTeX">${g}_{\text {m}}$ </tex-math></inline-formula> demonstrated on Si. Transmission line measurement verifies a low contact resistance with <inline-formula> <tex-math notation="LaTeX">${R}_{\text {C}} = 115\,\,\Omega \mu \text{m}$ </tex-math></inline-formula>, demonstrating that most of the MOSFET access resistance is located in the contact regions.
Local translation in synaptic mitochondria influences synaptic transmission

Mitochondria possess a small genome that codes for core subunits of the oxidative phosphorylation system, and whose expression is essential for energy production. Information on the regulation and spatial organization of mitochondrial gene expression in the cellular context has been difficult to obtain. Here we addressed this by devising an imaging approach to analyze mitochondrial translation, by following the incorporation of clickable non-canonical amino acids. We applied this method to multiple cell types, including hippocampal neurons, where we found ample evidence for mitochondrial translation in both dendrites and axons. Translation levels were surprisingly heterogeneous, were typically stronger in axons, and were independent of their distance from the cell soma, where mitochondria presumably descent from. Presynaptic mitochondrial translation correlated with local synaptic activity, and blocking mitochondria translation reduced synaptic function. Overall, these findings demonstrate that mitochondrial gene expression in neurons is intimately linked to neuronal function.
Comparative analysis of single-cell RNA Sequencing Platforms and Methods

Single-cell RNA sequencing (scRNA-seq) offers great new opportunities for increasing our understanding of complex biological processes. In particular, development of an accurate Human Cell Atlas is largely dependent on the rapidly advancing technologies and molecular chemistries employed in scRNA-seq. These advances have already allowed an increase in throughput for scRNA-seq from 96 to 80,000 cells on a single instrument run by capturing cells within nano-liter droplets. While this increase in throughput is critical for many experimental questions, a thorough comparison between microfluidic-, plate-, and droplet-based technologies or between multiple available platforms utilizing these technologies is largely lacking. Here, we report scRNA-seq data from SUM149PT cells treated with the histone deacetylase inhibitor TSA vs. untreated controls across several scRNA-seq platforms (Fluidigm C1, WaferGen iCell8, 10X Genomics Chromium Controller, and Illumina/BioRad ddSEQ). The primary goal of this project was to demonstrate RNA sequencing (RNA-seq) methods for profiling the ultra-low amounts of RNA present in individual cells, and this report discusses the results of the study as well as technical challenges/lesson learned and present general guidelines for best practices in sample preparation and analysis.
Accurate and sensitive detection of microbial eukaryotes from metagenomic shotgun sequencing

Microbial eukaryotes are found alongside bacteria and archaea in natural microbial systems, including host-associated microbiomes. While microbial eukaryotes are critical to these communities, they are often not included in metagenomic analyses. Here we present EukDetect, a bioinformatics method to identify eukaryotes in shotgun metagenomic sequencing data. Our approach uses a database of universal marker genes, which we curated from all 2,571 currently available fungal, protist, worm and other diverse eukaryotic genomes. EukDetect is accurate and sensitive, has a broad taxonomic coverage of microbial eukaryotes, and is resilient against bacterial contamination in eukaryotic genomes. Using EukDetect, we describe the spatial distribution of eukaryotes along the human gastrointestinal tract, showing that fungi and protists are present in the lumen and mucosa throughout the large intestine. We discover that there is a succession of eukaryotes that colonize the human gut during the first years of life, similar to patterns of developmental succession observed in gut bacteria. By comparing DNA and RNA sequencing of paired samples from human stool, we find that many eukaryotes continue active transcription after passage through the gut, while others do not, suggesting they are dormant or nonviable. Finally, we observe eukaryotes in Arabidopsis leaf samples, many of which are not identifiable from public protein databases. Thus, EukDetect provides an automated and reliable way to characterize eukaryotes in shotgun sequencing datasets from diverse microbiomes.
Nutrient Removal and Uptake by Native Planktonic and Biofilm Bacterial Communities in an Anaerobic Aquifer

Managed aquifer recharge (MAR) offers a collection of water storage and storage options that have been used by resource managers to mitigate the reduced availability of fresh water. One of these technologies is aquifer storage and recovery (ASR), where surface water is treated then recharged into a storage zone within an existing aquifer for later recovery and discharge into a body of water. During the storage phase of ASR, nutrient concentrations in the recharge water have been shown to decrease due, presumably via the uptake by the native aquifer microbial community. In this study, the native microbial community in an anaerobic carbonate aquifer zone targeted for ASR storage was segregated into planktonic and biofilm communities then challenged with NO3-N, PO4-P, and acetate as dissolved organic carbon (DOC) to determine their respective removal and uptake rates. The planktonic community removed NO3-N at a rate of 0.059 mg L–1d–1, PO4-P at 5.73 × 10–8–1.03 × 10–7 mg L–1d–1 and DOC at 0.015–0.244 mg L–1d–1. The biofilm community was significantly more proficient, removing NO3-N at 0.116 mg L–1d–1 (1.6–9.0 μg m–2d–1), PO4-P at 4.20–5.91 × 10–5 mg L–1d–1 (2.47–9.88 ng m–2d–1) and DOC at 0.301–0.696 mg L–1d–1 (29.0–71.0 μg m–2d–1). Additionally, the PO4-P sorption rate onto the carbonate aquifer matrix ranged from 1.64 × 10–7 to 9.25 × 10–7 mg PO4-P m–2 day–1. These rates were applied to field data collected at an ASR facility in central Florida and from the same aquifer storage zone from which the biofilm communities were grown. With only 10% of the available surface area within the storage zone being colonized by biofilms, typical concentrations of NO3-N, PO4-P, and DOC in the recharged filtered surface waters would be reduced to below detection limits, and by 81.4 and 91.1%, respectively, during a 150 days storage period.
Co-Expression of Mitochondrial Genes and ACE2 in Cornea Involved in COVID-19

The Coronavirus disease 2019 (COVID-19) pandemic severely challenges public health and necessitates the need for increasing our understanding of COVID-19 pathogenesis, especially host factors facilitating virus infection and propagation. Here, the co-expression network was constructed by mapping the well-known ACE2, TMPRSS2 and host susceptibility genes implicated in COVID-19 GWAS onto a cornea, retinal pigment epithelium and lung. We found a significant co-expression module of these genes in the cornea, revealing that cornea is potential extra-respiratory entry portal of SARS-CoV-2. Strikingly, both co-expression and interaction networks show a significant enrichment in mitochondrial function, which are the hub of cellular oxidative homeostasis, inflammation and innate immune response. We identified a corneal mitochondrial susceptibility module (CMSM) of 14 mitochondrial genes by integrating ACE2 co-expression cluster and SARS-CoV-2 interactome. Gene ECSIT, as a cytosolic adaptor protein involved in inflammatory responses, exhibits the strongest correlation with ACE2 in CMSM, which has shown to be an important risk factor for SARS-CoV-2 infection and prognosis. Our co-expression and protein interaction network analysis uncover that the mitochondrial function related genes in cornea contribute to the dissection of COVID-19 susceptibility and potential therapeutic interventions.