Miracle-dz/UniFAR-FTUs huggingface dataset:
Tissue-type plasminogen activator-binding RNA aptamers inhibiting low-density lipoprotein receptor family-mediated internalisation

Summary Recombinant tissue-type plasminogen activator (tPA, trade name Alteplase), currently the only drug approved by the US Food and Drug Administration and the European Medicines Agency for the treatment of cerebral ischaemic stroke, has been implicated in a number of adverse effects reportedly mediated by interactions with the low-density lipo-protein (LDL) family receptors, including neuronal cell death and an increased risk of cerebral haemorrhage. The tissue-type plasminogen activator is the principal initiator of thrombolysis in human physiology, an effect that is mediated directly via localised activation of the plasmin zymogen plasminogen at the surface of fibrin clots in the vascular lumen. Here, we sought to identify a ligand to tPA capable of inhibiting the relevant LDL family receptors without interfering with the fibrinolytic activity of tPA. Systematic evolution of ligands by exponential enrichment (SELEX) was employed to isolate tPA-binding RNA aptamers, which were characterised in biochemical assays of tPA association to low density lipoprotein receptor-related protein-1 (LRP-1, an LDL receptor family member); tPA-mediated in vitro and ex vivo clot lysis; and tPA-mediated plasminogen activation in the absence and presence of a stimulating soluble fibrin fragment. Two aptamers, K18 and K32, had minimal effects on clot lysis, but were able to efficiently inhibit tPA-LRP-1 association and LDL receptor family-mediated endocytosis in human vascular endothelial cells and astrocytes. These observations suggest that coadministration alongside tPA may be a viable strategy to improve the safety of thrombolytic treatment of cerebral ischaemic stroke by restricting tPA activity to the vascular lumen.
A review of recent developments and trends in the QuEChERS sample preparation approach

Abstract A comprehensive review is presented on the recent developments and trends in the QuEChERS (quick, easy, cheap, effective, rugged, and safe) sample preparation approach. This technique involves liquid-liquid partitioning using acetonitrile and purifying the extract using dispersive solid-phase extraction (d-SPE). Originally, the QuEChERS was introduced for pesticides residues analysis in high moisture fruits and vegetables, but more recently it is gaining significant popularity in the analysis of broad spectrum of analytes in huge variety of samples. The wide range of the technique applications is possible due to introducing various modifications based on the use of different extraction solvent and salt formulation and buffer additions for salting-out partitioning step and the application of various d-SPE sorbents for clean-up step. Therefore, the QuEChERS approach is useful for analysis of, among others pesticides, veterinary drugs and other pharmaceuticals, mycotoxins, polycyclic aromatic hydrocarbons (PAHs), dyes, acrylamide, synthetic musks and UV filters, bisphenols, polybrominated diphenyl ethers and other flame retardants, endocrine disruptors, and other chemical compounds. Thanks to the QuEChERS approach, high-throughput multiresidue methods operate in a routine contaminant control of food products, feedstuff, and environmental samples. Graphical Abstract
Nonlinear Dynamic of Functionally Graded Cylindrical Shells Under the Thermalmechanical Loads

An analysis on nonlinear vibrations of a simply supported functionally graded materials (FGM) cylindrical shell at its two ends which subjected to the radial excitation in the uniform thermal environment is presented for the first time. Materials properties of the constituents are graded in the thickness direction according to a power-law distribution. In the framework of the First-order shear deformation shell theory, the nonlinear governing equations of motion for the functionally graded materials cylindrical shell is derived by using the Hamilton’s principle. The Galerkin’s method is utilized to discretize the governing equations of motion to a five-degree-of-freedom nonlinear system under combined thermal and external excitations. By using the numerical method, the five-degree-of-freedom nonlinear system is analyzed to find the nonlinear responses of the FGMs cylindrical shell.Copyright © 2009 by ASME
Identification and Assessment of the Dominant Aggregate Size Range (DASR) of Asphalt Mixture (With Discussion)

Coarse aggregate structure or interlock is critical for resistance to rutting, and recent work has shown that it can also play a significant role in resistance to damage and fracture. Therefore, large enough aggregates should engage dominantly in the structure for good mixture performance. This study focused on the development of a conceptual and theoretical approach to evaluate coarse aggregate structure based on gradation. In soil mechanics, it has been well established that the porosity of granular materials in the loose state is approximately constant between 45% and 50%, regardless of size or gradation. This implies that one can use porosity as a criterion to assure contact between large enough particles within the mixture to provide suitable resistance to deformation and fracture. Calculations performed for gradations associated with typical dense graded mixtures indicated that the porosity of particles retained on any single sieve was significantly greater than 50%, even for gradations associated with the maximum density line. Since many dense graded mixtures are known to provide suitable resistance to deformation and fracture, then there must be a range of contiguous coarse aggregate particle sizes that form a network of interactive particles with a porosity of less than 50%. A theoretical analysis procedure was developed to calculate the center to center spacing between specific size particles within a compacted assemblage of particles of known gradation. Calculations performed with this procedure indicated that the relative proportion of two contiguous size particles, as defined by the standard arrangement of Superpave sieves, can be no greater than 70/30 in order to form an interactive network. Thus, the 70/30 proportion can be used to determine whether particles on contiguous Superpave sieves can form an interactive network of particles in continuous contact with each other. The range of particle sizes determined to be interactive was referred to as the dominant aggregate size range (DASR) and its porosity must be no more than 50% for the particles to be in contact with each other. It was concluded that porosity of the DASR may provide a good criterion for determining the suitability of gradation for dense-graded asphalt mixture.
Television viewing and abdominal obesity in young adults: is the association mediated by food and beverage consumption during viewing time or reduced leisure-time physical activity?

BACKGROUND The behavioral pathways through which television (TV) viewing leads to increased adiposity in adults are unclear. OBJECTIVE We wanted to determine whether the association between TV viewing and abdominal obesity in young adults is mediated by food and beverage consumption during TV viewing time or by a reduction in overall leisure-time physical activity (LTPA). DESIGN This study involved a cross-sectional analysis of data from 2001 Australian adults aged 26-36 y. Waist circumference (WC) was measured at study clinics, and TV viewing time, frequency of food and beverage consumption during TV viewing, LTPA, and demographic characteristics were self-reported. RESULTS Women watching TV > 3 h/d had a higher prevalence of severe abdominal obesity (WC: > or = 88 cm) compared with women watching < or = 1 h/d [prevalence ratio (PR): 1.89; 95% CI: 1.32, 2.71]. Moderate abdominal obesity (WC: 94-101.9 cm) was more prevalent in men watching TV > 3 h/d than in men watching < or = 1 h/d (PR: 2.16; 95% CI: 1.37, 3.41). Adjustment for LTPA made little difference, but adjustment for food and beverage consumption during TV viewing attenuated the associations (PR: 1.48; 95% CI: 1.01, 2.17 for women; PR: 1.73; 95% CI: 1.06, 2.83 for men). CONCLUSIONS The association between TV viewing and WC in young adults may be partially explained by food and beverage consumption during TV viewing but was not explained by a reduction in overall LTPA. Other behaviors likely contribute to the association between TV viewing and obesity.
Bangla Emergency Post Classification on Social Media using Transformer Based BERT Models

Text classification is one of the most important tasks in Natural Language Processing. As text data is growing rapidly, it needs more computational power to classify the text in a big dataset. The task is difficult for characteristic-rich languages like Bangla. Having good-quality text data significantly affects the outcome of the model that has been used to classify them. Nowadays, social media can be an important source of information. But there is a huge number of data which are of no use. As the use of social media is increasing day by day, people are posting about events around their surroundings. So, it can be an important propaganda of the media. In this study, various text classification methods were used to classify the texts in Bangla from social media, which can be categorized as emergencies that may need immediate actions from the government, local authority, or law enforcement or even may need international attention. Therefore, 5839 social media posts were collected from Facebook and Twitter, which were written in Bangla along with some mixed English words. Then, after preprocessing, various Machine Learning models, Deep Neural Network models, and Transformer based models were applied to classify them. Among these models, transformer-based XLM-RoBERTa outperformed all the other models with an F1-score of 95.25.
Concentrations of Free ( Ionized ) and Total Calcium and Magnesium in Healthy Captive Asian Elephants ( Elephas maximus ) and Effects of Sample Type and pH on measured Free Calcium and Magnesium Concentrations

ABST RACT The Asian elephant (Elephas maximus) is an endangered species, with an overall low reproduction rate in captivity, and a long, 22-month gestation, mostly with a single calve. Calcium and magnesium are important for the normal progression of gestation and parturition. This study measured blood total and ionized calcium (tCa and iCa, respectively) and total and ionized magnesium (tMg and iMg, respectively) in four healthy, captive Asian elephant cows in the Tisch Family Zoological Gardens, Jerusalem, every alternative month, over a 1-year period, to establish their reference intervals and examine sample pH and sample type effects on measured iCa and iMg concentrations. iCa and iMg were measured using an ion-selective electrode electrolyte analyzer. Calcium and magnesium levels in diet samples were measured. The iCa:tCa and iMg:tMg ratios were 0.44 and 0.73, respectively. Mean iMg concentrations in whole-blood, heparinized plasma and serum were 0.58, 0.65 and 0.66 mmol/L, respectively. iCa and iMg concentrations in the three sample types were highly correlated, with no sample type effect on measured iCa concentration, but significant effect on iMg concentration, with significantly lower whole-blood levels vs. serum and plasma. Serum albumin and both tCa and tMg concentrations positively correlated. Sample pH had no effect on measured iCa or iMg levels. This study is the first to measure iMg in Asian elephants, and assess the effects of sample type and pH on the results. It was concluded that different iMg reference intervals should be established for each sample type.
An alternative surgical approach reduces variability following filament induction of experimental stroke in mice

ABSTRACT Animal models are essential for understanding the pathology of stroke and investigating potential treatments. However, in vivo stroke models are associated, particularly in mice, with high variability in lesion volume. We investigated whether a surgical refinement where reperfusion is not reliant on the Circle of Willis reduced outcome variability. Mice underwent 60 min of transient middle cerebral artery occlusion avoiding ligation of the external carotid artery. During reperfusion, the common carotid artery was either ligated (standard approach), or it was repaired to allow re-establishment of blood flow through the common carotid artery. All mice underwent MRI scanning for assessment of infarct volume, apparent diffusion coefficient and fractional anisotropy, along with terminal assessment of infarct volume by 2,3,5-triphenyltetrazolium chloride (TTC) staining. Repairing the common carotid artery following middle cerebral artery occlusion enhanced reperfusion (P<0.01) and reduced the variability seen in both total (histological analysis, P=0.008; T2-weighted MRI, P=0.015) and core (diffusion tensor MRI, P=0.043) lesion volume. Avoiding external carotid artery ligation may improve animal wellbeing, through reduced weight loss, while using an alternative surgical approach that enabled reperfusion through the common carotid artery decreased the variability in lesion volume seen within groups. Summary: An alternative surgical approach following middle cerebral artery occlusion, which allows reperfusion through the common carotid artery, decreases the variability in lesion volume seen within groups and reduces the number of animals required to detect a treatment effect.
Development of a novel carbon fixation pathway enabled by protein engineering

Development of a novel carbon fixation pathway enabled by protein engineering Amanda Lee Smith Chair of the Supervisory Committee: Frank Jungers Chair of Engineering Mary E. Lidstrom Chemical Engineering Metabolic engineering in conjunction with computational protein design has the ability to expand the range of possible metabolic pathways. As a demonstration of this utility, a novel one-carbon assimilation pathway, the Formolase pathway, was implemented in Escherichia coli using a computationally designed enzyme. This pathway was designed to address a need for more sustainable feedstocks for biochemical production. With the documented ability to produce formate from carbon dioxide, this efficient, linear pathway allows for carbon sequestration and utilization through transformation to chemicals or fuels in industrial hosts that do not naturally fix carbon. The development of formolase, a carboligase, through computational protein design enables this pathway by joining 3-1C molecules into 1-3C molecule that accesses glycolysis via phosphorylation. This glycolytic flux can become any number of biochemical products using well-characterized production pathways. In this work, in vitro function of the formolase pathway is presented and efforts to improve pathway function are detailed. Figure 1: Formolase pathway context and overview. A scheme to convert electrical energy and carbon dioxide into biochemicals. Reducing power in the form of electricity converts carbon dioxide into formate, a molecule that can serve as a cellular energy and carbon source. An engineered microorganism fixes the formate into metabolic intermediates that can serve as biochemical or biofuel precursors.
Ieee Transactions on Information Forensics and Security an Investigation of Local Descriptors for Biometric Spoofing Detection

—Biometric authentication systems are quite vulnerable to sophisticated spoofing attacks. To keep a good level of security, reliable spoofing detection tools are necessary, preferably implemented as software modules. The research in this field is very active, with local descriptors, based on the analysis of micro-textural features, gaining more and more popularity, thanks to their excellent performance and flexibility. This work aims at assessing the potential of these descriptors for the liveness detection task in authentication systems based on various biometric traits: fingerprint, iris and face. Besides compact descriptors based on the independent quantization of features, already considered for some liveness detection tasks, we will study promising descriptors based on the joint quantization of rich local features. The experimental analysis, conducted on publicly available datasets and in fully reproducible modality, confirms the potential of these tools for biometric applications, and points out possible lines of development towards further improvements.
Automatic multi-step attack pattern discovering

Current techniques employed in security alert correlation area for multi-step attack recognition purpose are intricate to be performed due to the complexity of the methods and huge computing workload generated during alert analysis and processing. In this paper, we proposed a new method of alert correlation aiming at providing concentrated security event information and thus finding multi-step attack patterns accordingly. We use a kind of extension time window when aggregate the alerts into high level alerts. We then connect hyper alerts into candidate multistep attack patterns according to their IP address association. The final real multi-step attack patterns are discovered from these connected attack patterns with quantitative correlation calculation method. The method is easy to implement and practical to deploy which is proved by the result of our experiments. The experiment also shows our approach can effectively find real multi-step attack behavior patterns and can be used to identify true attack threats.
Vancomycin Treatment Alters Humoral Immunity and Intestinal Microbiota in an Aged Mouse Model of Clostridium difficile Infection.

BACKGROUND The elderly host is highly susceptible to severe disease and treatment failure in Clostridium difficile infection (CDI). We investigated how treatment with vancomycin in the aged host influences systemic and intestinal humoral responses and select intestinal microbiota. METHODS Young (age, 2 months) and aged (age, 18 months) C57BL/6 mice were infected with VPI 10463 after exposure to broad-spectrum antibiotics. Vancomycin was given 24 hours after infection, and treatment was continued for 5 days. At select time points, specimens of serum and intestinal tissue and contents were collected for histopathologic analysis, to measure antibody levels and the pathogen burden, and to determine the presence and levels of select intestinal microbiota and C. difficile toxin. RESULTS Levels of disease severity, relapse, and mortality were increased, and recovery from infection was slower in aged mice compared to young mice. Serum levels of immunoglobulin M, immunoglobulin A, and immunoglobulin G against C. difficile toxin A were depressed in aged mice, and vancomycin treatment reduced antibody responses in both age groups. While baseline levels of total bacterial load, Bacteroidetes, Firmicutes, and Enterobacteriaceae were mostly similar, aged mice had a significant change in the Firmicutes to Bacteroidetes ratio with vancomycin treatment. CONCLUSIONS Vancomycin treatment decreases the systemic humoral response to CDI. Increased mortality from and recurrence of CDI in the aged host are associated with an impaired humoral response and a greater susceptibility to vancomycin-induced alteration of intestinal microbiota.
Additive manufacture of tissue engineering scaffolds for bone and cartilage

her willingness to meet with me and for her expert feedback. Jeannette Yen have also been very insightful and provided me with invaluable direction during the proposal of my work. I would also like to thank my fellow past and present lab members: Dr. Lastly, I would like to thank my dear fiancée Deena for her love and support during the last part of my PhD. It was her love and kindness that kept me going.
improving dynamic language performance using just in time compilation

Dynamic languages are becoming increasingly popular in today’s world. Javascript has become the ubiquitous language for the web browser, and Python and Ruby have become enormously popular on the server side. As a result efficient execution of these highly dynamic languages becomes paramount. JIT-compilers have been written for each of these languages but with mixed results. We present a simple approach to JIT compilation for dynamic languages (using a trivial dynamic language as working example) to illustrate where the largest performance bottlenecks lie and which optimizations have the most significant benefit. The thesis shows that even straightforward JIT compilation can lead to very efficient programs if some basic properties of a program can be deduced.
A Hybrid Image Fusion Model for Generating High Spatial-Temporal-Spectral Resolution Data Using OLI-MODIS-Hyperion Satellite Imagery

 Abstract — Spatial, Temporal, and Spectral Resolution (STSR) are three key characteristics of Earth observation satellite sensors; however, any single satellite sensor cannot provide Earth observations with high STSR simultaneously because of the hardware technology limitations of satellite sensors. On the other hand, a conflicting circumstance is that the demand for high STSR has been growing with the remote sensing application development. Although image fusion technology provides a feasible means to overcome the limitations of the current Earth observation data, the current fusion technologies cannot enhance all STSR simultaneously and provide high enough resolution improvement level. This study proposes a Hybrid Spatial-Temporal-Spectral image Fusion Model (HSTSFM) to generate synthetic satellite data with high STSR simultaneously, which blends the high spatial resolution from the panchromatic image of Landsat-8 Operational Land Imager (OLI), the high temporal resolution from the multi-spectral image of Moderate Resolution Imaging Spectroradiometer (MODIS), and the high spectral resolution from the hyper-spectral image of Hyperion to produce high STSR images. The proposed HSTSFM contains three fusion modules: (1) spatial-spectral image fusion; (2) spatial-temporal image fusion; (3) temporal-spectral image fusion. A set of test data with both phenological and land cover type changes in Beijing suburb area, China is adopted to demonstrate the performance of the proposed method. The experimental results indicate that HSTSFM can produce fused image that has good spatial and spectral fidelity to the reference image, which means it has the potential to generate synthetic data to support the studies that require high STSR satellite imagery.
Economic Principles and Overview of Valuation Methods for Environmental Impacts

Valuing the services derived from the environment is important because it ‘works’ – i.e. it helps make the case for protecting the environment in an effective way. Indeed it can be, in many cases, a more effective instrument than other methods of protecting the environment – such as lobbying, undertaking direct action and so on. But to be successful it has to be carried out in a credible and professional manner. This chapter provides an overview of the different methods of valuing environmental impacts. Before it can do that, however, it has to provide the conceptual basis for such valuations.