Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning Models of Gene Expression from Synthetic DNA Sequences

Learning Models of Gene Expression from Synthetic DNA Sequences Alexander B Rosenberg Chair of the Supervisory Committee: Associate Professor Georg Seelig Electrical Engineering and Computer Science & Engineering Over the past decade, new sequencing technologies have enabled the comprehensive cataloging of human genetic variation, but for most DNA sequence variants we do not even understand the impact on molecular phenotype, let alone human traits and disease. Despite recent advances, the throughput of gene editing technologies is orders of magnitude away from allowing the functional testing of all possible variants. As a result, models are desperately needed to accurately predict the impact of variants on gene expression. In classical genetics, genomes are compared, analyzed, and perturbed to learn the function of the underlying DNA sequences. Here I present a complementary but orthogonal approach, in which fully synthetic DNA sequences are studied. This thesis is a collection of three chapters exploring this approach. In the first chapter, noise buffering at the protein level is explored by constructing feed-forward loops with different engineered miRNA targets. In the second chapter, a model of alternative splicing is learned from millions of random DNA sequences. The resulting model outperforms all other models that we investigated on the task of predicting the effects of human exonic variants on alternative splicing, even though our model was never trained on human DNA sequences. In the third chapter, the same approach is extended to model the impact of the 5’ untranslated region on translation in yeast. After training on measurements of ~500,000 synthetic 4 5’ untranslated regions (5’ UTR), the resulting model accurately predicts the effects of both synthetic and native yeast 5’ UTRs on translational efficiency. This thesis is by no means a comprehensive exploration of gene expression models that can be learned from synthetic DNA sequences, but rather a starting point. The throughput of both DNA sequencing and DNA synthesis have increased at such a rapid pace that we can now make millions of gene expression measurements in parallel. Given that most genomes only have thousands of genes, we should leverage this additional capacity to test synthetic sequences and improve our models of gene expression.
ROLE OF COASTAL SEDIMENT ON SOIL NUTRIENT AVAILABILITY AND OIL PALM YIELD AT PEATLANDS

Peatlands which is limited in chemical, physical and ecology require appropriate management for oil palm plantation. Coastal sediment as an ameliorant in peatlands increased productivity some crops. This study aims determining the effect of the doses of coastal sediment as ameliorant on peatlands to the availability of N, P, K, Ca, Mg and Na oil palm plantations. This research was performed in the area of oil palm plantation in Kubu Raya district, Borneo, Indonesia. Experimental design employed randomized block design with 4 levels of coastal sediment doses (L), i.e. L0 = 0 t ha -1 ; L1 = 20 t ha -1 ; L2 = 40 t ha -1 ; L3 = 60 t ha -1 with three replication. The results showed that the application of coastal sediment at 40 t ha -1 in oil palm plantations significantly increased soil pH, availability of N, K, Ca and Mg, while P was not significantly different
Efficient and Secure NFC Authentication for Mobile Payment Ensuring Fair Exchange Protocol

The standard protocol of near field communication (NFC) has concentrated primarily on the speed of communication while ignoring security properties. Message between an NFC-enabled smartphone and a point of sale are exchanged over the air (OTA), which is a message considered an authentication request for payment, billing, ticketing, loyalty services, identification or access control. An attacker who has an antenna can intercept or manipulate the exchanged messages to take advantage of these. In order to solve this problem, many researchers have suggested authentication methods for NFC communications. However, these remain inadequate transaction security and fairness. In this paper, we will propose a technique that ensures mutual authentication, security properties, and strong fairness. Mutual authentication is a security property that prevents replay attacks and man-in-the-middle attacks. Both fair exchange and transaction security are also significant issues in electronic transactions with regards to creating trust among the parties participating in the transaction. The suggested protocol deploys a secure offline session key generation technique to increase transaction security and, importantly, make our protocol lightweight while maintaining the fairness property. Our analysis suggests that our protocol is more effective than others regarding transaction security, fairness, and lightweight protocol. The proposed protocol checks robustness and soundness using Burrows, Abadi and Needham (BAN) logic, the Scyther tool, and automated validation of internet security protocols and applications (AVISPA) that provide formal proofs for security protocols. Furthermore, our protocol can resolve disputes in case one party misbehaves.
Voltammetric Behaviour of Drug Molecules as a Predictor of Metabolic Liabilities

Electron transfer plays a vital role in drug metabolism and underlying toxicity mechanisms. Currently, pharmaceutical research relies on pharmacokinetics (PK) and absorption, distribution, metabolism, elimination and toxicity (ADMET) measurements to understand and predict drug reactions in the body. Metabolic stability (and toxicity) prediction in the early phases of the drug discovery and development process is key in identifying a suitable lead compound for optimisation. Voltammetric methods have the potential to overcome the significant barrier of new drug failure rates, by giving insight into phase I metabolism events which can have a direct bearing on the stability and toxicity of the parent drug being dosed. Herein, we report for the first time a data-mining investigation into the voltammetric behaviour of reported drug molecules and their correlation with metabolic stability (indirectly measured via t½), as a potential predictor of drug stability/toxicity in vivo. We observed an inverse relationship between oxidation potential and drug stability. Furthermore, we selected and prepared short- (<10 min) and longer-circulation (>2 h) drug molecules to prospectively survey the relationship between oxidation potential and stability.
Molecular and phytochemical evidence for the taxonomic integrity of Salix alba, S. fragilis, and their hybrid S. 3 rubens (Salicaceae) in mixed stands in SE Germany

AFLP fingerprinting, nrDNA sequencing, and HPLC of phenolic compounds from bark samples was used to assess the intensity of hybridisation in two mixed stands of Salix alba, S. fragilis, and their hybrid S. 9 rubens (Salicaceae) along the Danube in the vicinity of Regens- burg (SE Germany). AFLP analyses of 130 individuals from two mixed and two pure strands of the parental spe- cies resulted in a matrix of 337 polymorphic loci that was analysed with Bayesian cluster algorithms implemented in the software programmes Structure and NewHybrids. The results, together with sequence polymorphisms of the nrDNA ITS1 ? 5.8S region, indicate that the three taxa are distinctly separated and that only a few F2-hybrids and no backcrosses to the parental species are present in the sur- veyed mixed stands. These findings were corroborated by HPLC studies of the phenolic compounds from bark sam- ples that were carried out for the same individuals. A multivariate statistical analysis of relative peak areas of chromatograms (PCA, principal component analysis) indicates the clear separation of parental and the interme- diate position of S. 9 rubens individuals.
Quantifying Key Mechanisms That Contribute to the Deviation of the Tropical Warming Profile From a Moist Adiabat

Climate models project tropical warming is amplified aloft relative to the surface in response to increased CO2. Here we show moist adiabatic adjustment overpredicts the multimodel mean 300 hPa temperature response by 16.6–25.3% across the CMIP5 model hierarchy. We show three mechanisms influence overprediction: climatological large‐scale circulation, direct effect of increased CO2, and convective entrainment. Accounting for the presence of a climatological large‐scale circulation and the direct effect of CO2 reduces the CMIP5 multimodel mean overprediction by 0.7–7.2% and 2.8–3.9%, respectively, but does not eliminate it. To quantify the influence of entrainment, we vary the Tokioka parameter in aquaplanet simulations. When entrainment is decreased by decreasing the Tokioka parameter from 0.1 to 0, overprediction decreases by 9.6% and 10.4% with and without a large‐scale circulation, respectively. The sensitivity of overprediction to climatological entrainment rate in the aquaplanet mostly follows the predictions of zero‐buoyancy bulk‐plume and spectral‐plume models.
Epigenome-wide association study on diffusing capacity of the lung

Background Epigenetics may play an important role in the pathogenesis of lung diseases. However, little is known about the epigenetic factors that influence impaired gas exchange at the lung. Aim To identify the epigenetic signatures of the diffusing capacity of the lung measured by carbon monoxide uptake (the diffusing capacity of the lung for carbon monoxide (DLCO)). Methods An epigenome-wide association study (EWAS) was performed on diffusing capacity, measured by carbon monoxide uptake (DLCO) and per alveolar volume (VA) (as DLCO/VA), using the single-breath technique in 2674 individuals from two population-based cohort studies. These were the Rotterdam Study (RS, the “discovery panel”) and the Framingham Heart Study (FHS, the “replication panel”). We assessed the clinical relevance of our findings by investigating the identified sites in whole blood and by lung tissue specific gene expression. Results We identified and replicated two CpG sites (cg05575921 and cg05951221) that were significantly associated with DLCO/VA and one (cg05575921) suggestively associated with DLCO. Furthermore, we found a positive association between aryl hydrocarbon receptor repressor (AHRR) gene (cg05575921) hypomethylation and gene expression of exocyst complex component 3 (EXOC3) in whole blood. We confirmed that the expression of EXOC3 in lung tissue is positively associated with DLCO/VA and DLCO. Conclusions We report on epigenome-wide associations with diffusing capacity in the general population. Our results suggest EXOC3 to be an excellent candidate, through which smoking-induced hypomethylation of AHRR might affect pulmonary gas exchange. Epigenetic changes, including smoking-induced hypomethylation, may affect pulmonary gas exchange https://bit.ly/3k4ZdvH
Prevalence and antimicrobial susceptibility of Brachyspira species in pigs in Korea

The purpose of this study was to investigate the prevalence of Brachyspira species and antimicrobial susceptibility of Brachyspira (B.) hyodysenteriae isolates in Korea. A total of fifty-five Brachyspira species were isolated; five (1.0%) beta-hemolytic Brachyspira species and 50 (10.4%) weak hemolytic Brachyspira species from 116 different diarrheic pig samples and 367 apparently normal pig samples. In farm level, beta hemolytic and weak hemolytic Brachyspira species were detected in 7.4% (5/68) and 19.1% (13/68) of tested pig farms, respectively. By phenotypic and genotypic characterization, all beta hemolytic Brachyspira isolates was classified as group I (B. hyodysenteriae), whereas weak hemolytic Brachyspira species isolates were group III (B. innocens or B. murdochii). B. hyodysenteriae isolates showed high level of minimum inhibition concentrations to macrolide antimicrobials. This study shows that the prevalence of pathogenic B. hyodysenteriae in pigs is low but antimicrobial resistance of the pathogens is high in Korea. This is the first report of the prevalence of Brachyspira group III and antimicrobial susceptibility of B. hyodysenteriae in pigs in Korea. Our results could provide basic data for the management and treatment guidelines of Brachyspira infection.
How Teachers Teach:

Data from across the world have revealed that while school attendance has increased in recent years, hundreds of millions of children are attending school without achieving even basic learning outcomes (World Bank 2018, UNESCO Institute of Statistics 2019). As the scale of this “learning crisis” is revealed, a great deal of policy attention has turned to teaching practices. There has been a general drive in developing countries to shift from rote learning to a more learner-centered education: international organizations have advised on this (United Nations Educational, Scientific and Cultural Organization [UNESCO] 2018); development partners have implemented programs specifically designed to make teaching more learner-centered (for example, Asian Development Bank [ADB] 2019); and a number of developing country governments have committed to moving away from traditional teacher-centered practices (You 2019).
Zinc-Induced Effects on Productivity, Zinc Use Efficiency, and Grain Biofortification of Bread Wheat under Different Tillage Permutations

Zinc (Zn) deficiency is a global concern for human health and causes a decrease in crop production and nutritional characteristics. A two-year field study was planned to evaluate comparative effects of various Zn application approaches in bread wheat under plough tillage (PT) and zero tillage (ZT) system. Cultivation of wheat under ZT improved the soil organic carbon (17%), total soil porosity (11%), soil microbial biomass nitrogen (5%), and carbon (5%) in comparison to PT system averaged across the two years. Various efficiency indices were significantly influenced by Zn application methods during both years of experimentation. However, grain Zn contents were maximum with foliar-applied Zn in PT (31%) and soil-applied Zn under the ZT system (29.85%). Moreover, Zn use also enhanced the bioavailable Zn as lower phytate contents and phytate to Zn molar ratio were recorded. The highest bioavailable Zn was calculated for foliar (30%) and soil application (28%). Under both tillage systems, the maximum net benefits were obtained through Zn seed priming; nevertheless, ZT resulted in higher net benefits than PT due to low associated costs. In conclusion, Zn nutrition through different methods enhanced the productivity, profitability, and grain biofortification of wheat under PT and ZT systems.
Anthracycline Cardiotoxicity in a Patient with Diffuse Large B-Cell Lymphoma: A Case Report

Cardiotoxicity is a relevant side effect of cancer therapy that leads to increased patient morbidity and mortality. It is fundamental to understand and remember it as a cause of disease since accurate and timely diagnosis is crucial. We present the case of a patient who developed chemotherapy-associated cardiac dysfunction after receiving treatment for a diffuse large B-cell lymphoma. Clinical history, echocardiography, and differential diagnosis led us to attribute her condition to heart failure (HF) due to early doxorubicin-induced cardiomyopathy. The patient outcome was favorable. We discuss the pathogenesis and incidence of anthracycline-induced cardiotoxicity as well as strategies for its detection, prevention, and treatment.
Improved artificial immune algorithm for the flexible job shop problem with transportation time

The flexible job shop problem (FJSP), as one branch of the job shop scheduling, has been studied during recent years. However, several realistic constraints including the transportation time between machines and energy consumptions are generally ignored. To fill this gap, this study investigated a FJSP considering energy consumption and transportation time constraints. A sequence-based mixed integer linear programming (MILP) model based on the problem is established, and the weighted sum of maximum completion time and energy consumption is optimized. Then, we present a combinational meta-heuristic algorithm based on a simulated annealing (SA) algorithm and an artificial immune algorithm (AIA) for this problem. In the proposed algorithm, the AIA with an information entropy strategy is utilized for global optimization. In addition, the SA algorithm is embedded to enhance the local search abilities. Eventually, the Taguchi method is used to evaluate various parameters. Computational comparison with the other meta-heuristic algorithms shows that the improved artificial immune algorithm (IAIA) is more efficient for solving FJSP with different problem scales.
Ultrasensitive detection of antigen–antibody interaction and triglycerides in liquid ambient using polysilicon cantilevers

Measurement in liquid media is a major challenge in real-time detection using resonant cantilevers. This is addressed in the present study by fabricating sub-micron thick cantilevers followed by functionalization for biomolecule detection. The fabricated cantilever resonator beams of thickness 165 nm were used for measurements in two systems: (i) human immunoglobulin (HIgG) as the antibody on the cantilever sensing mouse immunoglobulin (MIgG) as corresponding antigen, and (ii) detection of triglyceride (TG) based on the enzymatic hydrolysis with lipase, using tributyrin as a model. In both cases, the beams were functionalized for covalent bonding of the protein receptor. The label-free detection was carried out by measuring the shift in resonance frequency at higher modes, using a laser Doppler vibrometer in liquid and in air. The calibration showed a linear correlation between the bioanalyte concentration and change in the resonance frequency. Notably, detection of antigen mass as low as 434 ± 59fg and triglyceride concentration in the nM range with limit of detection as 7 nM in liquid interface was achieved, greatly improving the sensitivity of bioanalyte detection in liquid samples. Although frequency-based methods are highly sensitive, the issues with measurement liquid medium limit their application. In the present report, these issues were addressed by fabricating sub-micron thick cantilever beam, choosing an appropriate functionalization method without affecting the sensitivity, and measurement at higher modes. These have resulted in circumventing issues like damping and hydrodynamic loading thus improving its potential as real-time sensor.
Textual Analysis as a Method of Identifying Museum Attributes Perceived by Tourists: An Exploratory Analysis of Thyssen-Bornemisza National Museum in Spain

Objective: The identification of museum attributes is essential when analyzing the different factors that attract visitors and studying it in order to improve efficiency in museums, as this could affect the use of funds for developing a marketing campaign to attract visitors. This paper offers a literature review that considers museum visits and museum attributes before proposing a methodology. <br><br>Methodology: The use of big data applied to tourism research is vital, as it allows for the consideration of the opinions of museum visitors. The case study in this paper is the Thyssen-Bornemisza National Museum in Madrid, Spain. The method for identifying the attributes consists of a textual analysis of TripAdvisor reviews written in English (2500) and Spanish (2500). The information is captured using WebHarvy and is analysed using Nvivo12. <br><br>Results: After analyzing the thousand words that were used most frequently, the main attributes were detected, as well as whether the perception of these attributes was positive or negative. The museum’s location and the building itself were the most highly valued attributes. Other attributes that were valued positively were the peripheral services of the museum, such as its food and beverage services. <br><br>Limitations: The main limitation is that TripAdvisor is not an entirely reliable source of information, so it will be necessary to obtain more reviews to analyse. <br><br>Practical implications: The identification of attributes allows for improved decision making,<br>as well as facilitating a better understanding of the museum’s visitors’ perceptions. <br>Being aware of these aspects enables the modification of the museum’s services through<br>proposals for changes and improvements.
Strange loops, oedipal logic, and an apophatic ecology: Reimagining critique in environmental education

Abstract There are currently two broad forms of critique undergirding environmental education theories: the first is one of subtraction from perceived reality as it seeks to reveal and remove illusions and ideologies, while the other takes the inverse form of adding to reality in the form of investigating how matter comes to matter. We suggest a third form that explores the paradoxical and uncanny aspects of ecological awareness and assumes an apophatic, self-negating form, which short-circuits and relinquishes all attempts at epistemological closure. In this third form, we are drawing on themes from dark ecology, which maintains that ecological awareness is decidedly ‘weird’ as it assumes the guise of an ‘Oedipal’ logic, a narrative trope in which the protagonist seeking to avoid a tragic fate finds out that avoidance itself is the realization of the tragedy. Using Timothy Morton’s work as a springboard, we unpack the import of such looping temporality onto the onto-epistemological frameworks of environmental education.
Islanding Detection Using a Micro-Synchrophasor for Distribution Systems with Distributed Generation

Distributed Generation (DG) has changed the power generation system to small-scale instead of large-scale generation. The demanding issue with the interconnection of DG is the detection of unintended islanding in a network. Several methods proposed in the literature show drawbacks such as high non-detection zones (NDZ) and higher tripping time. In this paper, the IEEE 13 bus distribution network with DGs like wind and solar power plants is integrated at two buses. Islanding is detected by utilizing data from a micro-synchrophasor located at the distribution grid and the DG. The micro-synchrophasor-based unintended islanding detection algorithm is based on parameters such as voltage, rate of change of voltage, frequency, rate of change of frequency, voltage phase angle difference and the rate of change of the voltage phase angle difference between the utility and the islanded grid. The proposed islanding detection algorithm discriminates between islanding and non-islanding conditions and is highly efficient under zero power mismatch conditions. The proposed method has null NDZ and satisfies the IEEE 1547 standard for DG tripping time. The effectiveness of the proposed IDM was verified when there are multiple DGs in the islanded grid. Also, the proposed method does not require additional hardware as it can be incorporated in digital relays with synchrophasor functionality.