Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Panel Sequencing of DNA Variants in cf-, ev- and tumorDNA for Pancreatic Ductal Adenocarcinoma Patients

Simple Summary Pancreatic ductal adenocarcinoma (PDAC) has still a dismal prognosis. To improve treatment, personalized medicine uses next-generation DNA sequencing to monitor disease and guide treatment decisions. Tumor samples for sequencing are usually obtained by invasive fine-needle biopsy. Recently, the focus has been increasingly shifting to blood-based liquid biopsies, including circulating free (cf)DNA or DNA isolated from extracellular vesicles (evDNA). To evaluate the detection performance of DNA alterations, we directly compared tumor-, cf- and evDNA from patients with advanced PDAC upon panel sequencing. Copy number variations (CNVs), single nucleotide variants (SNVs) and insertions and deletions (indels) were compared for their concordance with tumorDNA. Compared to cfDNA, evDNA contained significantly larger DNA fragments, which improved the concordance of SNVs and indels with tumorDNA. In line with previous observations, CNV detection was mostly uninformative for cf- and evDNA. However, the combination of both liquid biopsy analytes was clearly superior for SNV detection, pointing to potentially improved actionable variant prediction. Abstract Pancreatic ductal adenocarcinomas (PDACs) are tumors with poor prognosis and limited treatment options. Personalized medicine aims at characterizing actionable DNA variants by next-generation sequencing, thereby improving treatment strategies and outcomes. Fine-needle tumor biopsies are currently the gold standard to acquire samples for DNA profiling. However, liquid biopsies have considerable advantages as they are minimally invasive and frequently obtainable and thus may help to monitor tumor evolution over time. However, which liquid analyte works best for this purpose is currently unclear. Our study aims to directly compare tumor-, circulating free (cf-) and extracellular vesicle-derived (ev)DNA by panel sequencing of matching patient material. We evaluated copy number variations (CNVs), single nucleotide variants (SNVs) and insertions and deletions (indels). Our data show that evDNA contains significantly larger DNA fragments up to 5.5 kb, in line with previous observations. Stringent bioinformatic processing revealed a significant advantage of evDNA with respect to cfDNA concerning detection performance for SNVs and a numerical increase for indels. A combination of ev- and cfDNA was clearly superior for SNV detection, as compared to either single analyte, thus potentially improving actionable variant prediction upon further optimization. Finally, calling of CNVs from liquid biopsies still remained challenging and uninformative.
A practical approach to assessing existing evidence for specific conservation strategies

There is currently a great deal of work being undertaken to collect, analyze, and synthesize available evidence about the effectiveness of conservation strategies. But substantial challenges still remain in enabling practitioners to assess and apply this evidence to their conservation work in an efficient manner. To solve these challenges, there is growing recognition of the need to use situation assessments and theory of change pathways to detail a set of analytical questions and specific assumptions that can be assessed against the evidence base to “make the case” for a proposed strategy and to identify gaps in knowledge. In this study, we first provide updated definitions of some key terms. We then present and provide examples of an approach to enable practitioners to evaluate the evidence base for the critical assumptions that underlie their specific conservation strategies and to wisely use evidence coming from different knowledge systems. This practical approach, which was developed through a series of pilot tests with Parks Canada projects, involves four iterative steps: (1) identify critical questions and assumptions requiring evidence; (2) assemble and assess the specific and generic evidence for each assumption; (3) determine confidence in evidence and its implications; and (4) validate the assessment and iteratively adapt as needed. Ideally, this approach can be integrated into existing decision‐making frameworks and can also facilitate better cooperation between researchers who synthesize evidence and practitioners who use evidence to make conservation both more effective and efficient.
DNA Methylation and Detoxification in the Earthworm Lumbricus terrestris Exposed to Cadmium and the DNA Demethylation Agent 5-aza-2′-deoxycytidine

Earthworms are well-established model organisms for testing the effects of heavy metal pollution. How DNA methylation affects cadmium (Cd) detoxification processes such as the expression of metallothionein 2 (MT2), however, is largely unknown. We therefore exposed Lumbricus terrestris to 200 mg concentrations of Cd and 5-aza-2′-deoxycytidine (Aza), a demethylating agent, and sampled tissue and coelomocytes, cells of the innate immune system, for 48 h. MT2 transcription significantly increased in the Cd- and Cd-Aza-treated groups. In tissue samples, a significant decrease in MT2 in the Aza-treated group was detected, showing that Aza treatment inhibits basal MT2 gene activity but has no effect on Cd-induced MT2 levels. Although Cd repressed the gene expression of DNA-(cytosine-5)-methyltransferase-1 (DNMT1), which is responsible for maintaining DNA methylation, DNMT activity was unchanged, meaning that methylation maintenance was not affected in coelomocytes. The treatment did not influence DNMT3, which mediates de novo methylation, TET gene expression, which orchestrates demethylation, and global levels of hydroxymethylcytosine (5hmC), a product of the demethylation process. Taken together, this study indicates that Aza inhibits basal gene activity, in contrast to Cd-induced MT2 gene expression, but does not affect global DNA methylation. We therefore conclude that Cd detoxification based on the induction of MT2 does not relate to DNA methylation changes.
Projecting Future Fire Regimes in a Semiarid Watershed of the Inland Northwestern United States: Interactions Among Climate Change, Vegetation Productivity, and Fuel Dynamics

Fire regimes are influenced by both exogenous drivers (e.g., increases in atmospheric CO2 and climate change) and endogenous drivers (e.g., vegetation and soil/litter moisture), which constrain fuel loads and fuel aridity. Herein, we identified how exogenous and endogenous drivers can interact to affect fuels and fire regimes in a semiarid watershed in the inland northwestern United States throughout the 21st century. We used a coupled ecohydrologic and fire regime model to examine how climate change and CO2 scenarios influence fire regimes. In this semiarid watershed, we found an increase in burned area and burn probability in the mid‐21st century (2040s) as the CO2 fertilization effect on vegetation productivity outstripped the effects of climate change‐induced fuel decreases, resulting in greater fuel loading. However, by the late‐21st century (2070s), climatic warming dominated over CO2 fertilization, thus reducing fuel loading and burned area. Fire regimes were shown to shift from flammability‐ to fuel‐limited or become increasingly fuel‐limited in response to climate change. We identified a metric to identify when fire regimes shift from flammability‐ to fuel‐limited: the ratio of the change in fuel loading to the change in its aridity. The threshold value for which this metric indicates a flammability versus fuel‐limited regime differed between grasses and woody species but remained stationary over time. Our results suggest that identifying these thresholds in other systems requires narrowing uncertainty in exogenous drivers, such as future precipitation patterns and CO2 effects on vegetation.
Digital Twin - Cyber Replica of Physical Things: Architecture, Applications and Future Research Directions

The Internet of Things (IoT) connects massive smart devices to collect big data and carry out the monitoring and control of numerous things in cyber-physical systems (CPS). By leveraging machine learning (ML) and deep learning (DL) techniques to analyze the collected data, physical systems can be monitored and controlled effectively. Along with the development of IoT and data analysis technologies, a number of CPS (smart grid, smart transportation, smart manufacturing, smart cities, etc.) adopt IoT and data analysis technologies to improve their performance and operations. Nonetheless, directly manipulating or updating the real system has inherent risks. Thus, creating a digital clone of a real physical system, denoted as a Digital Twin (DT), is a viable strategy. Generally speaking, a DT is a data-driven software and hardware emulation platform, which is a cyber replica of physical systems. Meanwhile, a DT describes a specific physical system and tends to achieve the functions and use cases of physical systems. Since DT is a complex digital system, finding a way to effectively represent a variety of things in timely and efficient manner poses numerous challenges to the networking, computing, and data analytics for IoT. Furthermore, the design of a DT for IoT systems must consider numerous exceptional requirements (e.g., latency, reliability, safety, scalability, security, and privacy). To address such challenges, the thoughtful design of DTs offers opportunities for novel and interdisciplinary research efforts. To address the aforementioned problems and issues, in this paper, we first review the architectures of DTs, data representation, and communication protocols. We then review existing efforts on applying DT into IoT data-driven smart systems, including the smart grid, smart transportation, smart manufacturing, and smart cities. Further, we summarize the existing challenges from CPS, data science, optimization, and security and privacy perspectives. Finally, we outline possible future research directions from the perspectives of performance, new DT-driven services, model and learning, and security and privacy.
One size doesn’t fit all: forms of social technology differentially predict distress

ABSTRACT The current study explored diverse forms of social technology and their corresponding links to distress and well-being during the COVID-19 pandemic. A multinational sample of 302 adults in the United States, Mexico, and Japan self-reported on their use of various forms of social technology, psychological distress, and happiness. Results revealed cultural differences in the amount of social technology use (Mexicans highest, Japanese lowest). While total social technology use positively predicted both distress and happiness, specific forms of social technology differentially predicted distress and happiness. Videoconferencing was associated with lower distress and greater happiness, whereas social media was associated with greater distress and lower happiness. Findings also showed that the use of dating apps was a marginally significant negative predictor of both distress and happiness. These findings suggest that forms of social technology that better mirror in-person interaction may confer greater mental health benefits compared to those that are less naturalistic.
Introduction: critiquing the onto-epistemic coloniality of modernity in/beyond education

When we proposed to do this special issue for Discourse almost three years ago, our intention was to historicize the happenings of epistemic colonialism in transnational/cultural knowledge translation and transfer. During the working process, we found that the seven pieces pushed us further with nuances that form along three lines. First, the notion of colonialism needs to be differentiated from coloniality. As proposed by Quijano (2000) and reiterated through Andreotti (2021),
Thermochemical Characterization of Eight Seaweed Species and Evaluation of Their Potential Use as an Alternative for Biofuel Production and Source of Bioactive Compounds

Algae are underexplored resources in Western countries and novel approaches are needed to boost their industrial exploitation. In this work, eight edible seaweeds were subjected to their valorization in terms of nutritional characterization, thermochemical properties, and bioactive profile. Our results suggest that seaweeds present a rich nutritional profile, in which carbohydrates are present in high proportions, followed by a moderate protein composition and a valuable content of ω-3 polyunsaturated fatty acids. The thermochemical characterization of seaweeds showed that some macroalgae present a low ash content and high volatile matter and carbon fixation rates, being promising sources for alternative biofuel production. The bioactive profile of seaweeds was obtained from their phenolic and carotenoid content, together with the evaluation of their associated bioactivities. Among all the species analyzed, Porphyra purpurea presented a balanced composition in terms of carbohydrates and proteins and the best thermochemical profile. This species also showed moderate anti-inflammatory activity. Additionally, Himanthalia elongata extracts showed the highest contents of total phenolics and a moderate carotenoid content, which led to the highest rates of antioxidant activity. Overall, these results suggest that seaweeds can be used as food or functional ingredient to increase the nutritional quality of food formulations.
A Modular Approach To Teaching “Wireless Communications And Systems” For Ecet Students

Recent development in wireless technologies has generated a high demand for wireless communications professionals. Rigorous math background is needed for students to fully understand wireless communications system fundamentals. However, Electrical and Computer Engineering Technology (ECET) students generally do not have such a math background to digest concepts and analyze issues associated with wireless communications. It is a better approach to focus on a point-to-point wireless system through experiential exploration, and extend the knowledge to wireless communications systems in general. There are different educational training stations available to help achieve educational goals in wireless communications. However, these educational trainers have their obvious shortcomings, which include: (1) most of them transmit at relatively low frequencies (in one hundred MHz range), while most of contemporary communications systems transmit in GHz range; (2) most of them are built as systems and it is hard for students to test module parameters; (3) most of them are costly and it is not affordable for many schools to purchase enough units to satisfy their lab needs. This article presents our on-going efforts of developing a modular approach to teaching a senior level “Wireless Communications and Systems” course. Mini-Circuits R (cid:13) RF modules are used for function block testing and system implementation. The emphasis is on the Radio Frequency (RF) modules of a communications system such as modulator, demodulator, Voltage-Controlled-Oscillator (VCO) and Frequency Mixer. The operating frequency is set at 900 MHz. Performance issues speciﬁc to wireless communications such as large and small scale fading effects are also addressed.
Novel integrated design techniques for biorefineries

Utilisation of biomass is identified as one of the promising solutions to reduce society’s dependence on fossil fuels and mitigate climate change caused by the exploitation of fossil fuels. By using the concept of biorefinery, biomass can be converted into value-added products such as biofuels, biochemical products and biomaterials in a greener and sustainable way. To enhance the efficiency of biorefinery, the concept of integrated biorefinery which focuses on the integration of various biomass conversion technologies is utilised. To date, various biomass conversion pathways are available to convert biomass into a wide range of products. Due to the substantial amount of potential products and conversion technologies, determining of chemical products and processing routes in an integrated biorefinery have become more challenging. Hence, there is a need for a methodology capable of evaluating the integrated process in order to identify the optimal products as well as the optimal conversion pathways that produce the identified products. This thesis presents a novel approach which integrates process with product design techniques for integrated biorefineries. In the proposed approach, integration between synthesis of integrated biorefinery and computer-aided molecular design (CAMD) techniques is presented. By using CAMD techniques, optimal chemical product in terms of target properties which fulfils the required product needs is designed. On the other hand, in order to identify the conversion pathways that produce the identified optimal chemical product in an integrated biorefinery, chemical reaction pathway map (CRPM) and superstructural mathematical optimisation approach have been utilised. Furthermore, this thesis also presents various chemical product design approaches. In order to solve chemical design problems where multiple product needs are required to be considered and optimised, a novel multi-objective optimisation approach for chemical product design has been presented. By using fuzzy optimisation approach, the developed multi-objective optimisation approach identifies optimal chemical product based on multiple product properties. In addition, fuzzy optimisation approach has been further extended to address chemical product design problems where the accuracy of property prediction model is taken into account. A robust chemical product design approach is developed to design optimal chemical products with consideration of accuracy of property prediction model. Furthermore, together with CAMD techniques and superstructural mathematical optimisation approach, the developed multi-objective optimisation approach has been utilised for the design of mixtures in an integrated biorefinery. For this purpose, a systematic optimisation approach has been developed to identify optimal mixture based on multiple desired product needs as well as the optimal conversion pathways that convert biomass into the optimal mixture. Finally, possible extensions and future opportunities for the realm of the research work have been highlighted in the later part of this thesis.
Awareness of Nuclear Medicine Physicians in Romania Regarding the Diagnostic of Cardiac Amyloidosis—A Survey-Based Study

Amyloidosis is a heterogeneous group of diseases caused by the extracellular deposition of amyloid insoluble fibrils in multiple organs, resulting in various clinical manifestations. Cardiac amyloidosis (CA) occurs mainly in primary light-chain (AL) amyloidosis, hereditary transthyretin (ATTRv) amyloidosis and senile or wild-type transthyretin (ATTRwt) amyloidosis. Knowing that myocardial uptake at bone scintigraphy is an essential step in the ATTR-CA diagnostic algorithm, the level of awareness among nuclear medicine physicians (NMPs) using bone tracer scintigraphy is of great importance. The objective of the study was to evaluate NMPs’ awareness of scintigraphy with bisphosphonates for the detection of CA. We conducted an online survey among NMPs from Romania to assess their current awareness and state of knowledge of nuclear techniques used in CA. Among the total 65 Romanian NMPs, 35 (53%) responded to this questionnaire. Approximately three-quarters of participants (74%) found a diffuse accumulation of bisphosphonates in the heart on scintigraphy performed for bone pathology as an incidental discovery. Detection of myocardial uptake of 99mTc-labeled bisphosphonates on scintigraphy suggests CA-AL for 3% of participants and for 9% of respondents, the appearance is of uncertain cardiac amyloidosis, while 5% of participants observed cardiac uptake but did not report it as CA. Even if more than half of those who responded to this survey (54%) found abnormal cardiac uptake and interpreted it as CA-ATTR, only 14% contacted the referring physician to draw attention to the incidental discovery to refer the patient to a specialist in rare genetic cardiomyopathy. Regarding the knowledge about the categories of bisphosphonates recommended in the diagnosis of CA-ATTR, 54% answered inadequately that methylene diphosphonate (MDP) could be used. Romanian nuclear physicians are partially familiar with CA diagnosis by scintigraphy, but its diagnostic potential and standardization, recommended radiotracers and acquisition times and interpretation algorithms are known in varying proportions. Therefore, there is a need to enhance knowledge through continuing medical education programs in order to standardize the protocols for the acquisition, processing and interpretation of bisphosphonate scintigraphy for the detection of cardiac ATTR amyloidosis.
A Comparative Evaluation of the Radiopacity of Contemporary Restorative CAD/CAM Blocks Using Digital Radiography Based on the Impact of Material Composition

Purpose The main purpose of this study was to assess the radiopacity of contemporary restorative computer-aided design (CAD)/computer-aided manufacturing (CAM) materials and the impact of material composition as measured by energy-dispersive X-ray spectrophotometry (EDX) on radiopacity. Materials and Methods Ten specimens of six CAD/CAM materials with 1 mm thickness were produced and then digitally radiographed with an aluminum (Al) step-wedge (SW) and 1 mm thick tooth slice. The specimen mean gray values (MGVs) were recorded in pixels and compared to an Al-SW, dentin, and enamel of equal thickness. For the elementary analysis of the composition of the materials, EDX was performed. Results The recorded MGVs ranged between 21.20 ± 4.94 and 238.5 ± 13.61 pixels. Materials were sorted according to the MGVs descendingly, Prettau, Vita Suprinity, Vita Enamic, Shofu, Pekkton, and BioHPP. Prettau and Vita Suprinity had significantly higher MGV than dentin and 1 mm thick Al. In comparison, Vita Enamic had a slightly higher value than dentin and 1 mm thick Al. Although Pekkton and BioHPP had MGV significantly lower than dentin and 1 mm thick Al, Shofu had a significantly lower value than dentin and nonsignificantly lower than 1 mm thick Al (p < 0.05). According to EDX analysis, the examined materials contained several components in varying quantities of radiopacity. Conclusions The radiopacity of only three studied materials exceeded the International Organization for Standardization's minimum standards (ISO).
A Weak Precipitation Sensitivity of Glacier Runoff

A clear understanding of the influence of glaciers on the climate sensitivity of catchment runoff is critical to unravel the ongoing and future changes in runoff regimes of glacierized catchments in a warming climate. We demonstrate that irrespective of the climate setting, annual glacier runoff is relatively insensitive to the precipitation variability. A temperature‐dependent runoff from the glaciers and a precipitation‐dependent runoff from the non‐glacierized parts determine the climate response of the runoff of glacierized catchments at different time scales. The buffering effect of glaciers against extreme droughts and the multidecadal runoff peak in catchments with shrinking glaciers, both follow from the above properties of glacier runoff. The empirically observed “glacier‐compensation effect” is caused by an inhibited (amplified) response of the catchment runoff to the interannual precipitation (temperature) variability due to the glaciers present in the catchment.