MSIQ: Joint Modeling of Multiple RNA-seq Samples for Accurate Isoform Quantification

Next-generation RNA sequencing (RNA-seq) technology has been widely used to assess full-length RNA isoform abundance in a high-throughput manner. RNA-seq data offer insight into gene expression levels and transcriptome structures, enabling us to better understand the regulation of gene expression and fundamental biological processes. Accurate isoform quantification from RNA-seq data is challenging due to the information loss in sequencing experiments. A recent accumulation of multiple RNA-seq data sets from the same tissue or cell type provides new opportunities to improve the accuracy of isoform quantification. However, existing statistical or computational methods for multiple RNA-seq samples either pool the samples into one sample or assign equal weights to the samples when estimating isoform abundance. These methods ignore the possible heterogeneity in the quality of different samples and could result in biased and unrobust estimates. In this article, we develop a method, which we call "joint modeling of multiple RNA-seq samples for accurate isoform quantification" (MSIQ), for more accurate and robust isoform quantification by integrating multiple RNA-seq samples under a Bayesian framework. Our method aims to (1) identify a consistent group of samples with homogeneous quality and (2) improve isoform quantification accuracy by jointly modeling multiple RNA-seq samples by allowing for higher weights on the consistent group. We show that MSIQ provides a consistent estimator of isoform abundance, and we demonstrate the accuracy and effectiveness of MSIQ compared with alternative methods through simulation studies on D. melanogaster genes. We justify MSIQ's advantages over existing approaches via application studies on real RNA-seq data from human embryonic stem cells, brain tissues, and the HepG2 immortalized cell line

Neyman-pearson classiffication under high-dimensional settings

Most existing binary classification methods target on the optimization of the overall classification risk and may fail to serve some real-world applications such as cancer diagnosis, where users are more concerned with the risk of misclassifying one specific class than the other. Neyman-Pearson (NP) paradigm was introduced in this context as a novel statistical framework for handling asymmetric type I/II error priorities. It seeks classifiers with a minimal type II error and a constrained type I error under a user specified level. This article is the first attempt to construct classifiers with guaranteed theoretical performance under the NP paradigm in high-dimensional settings. Based on the fundamental Neyman-Pearson Lemma, we used a plug-in approach to construct NP-Type classifiers for Naive Bayes models. The proposed classifiers satisfy the NP oracle inequalities, which are natural NP paradigm counterparts of the oracle inequalities in classical binary classification. Besides their desirable theoretical properties, we also demonstrated their numerical advantages in prioritized error control via both simulation and real data studies

Colour Contrast Based On WCAG 2.0

Master in Universal Design of ICTInsufficient contrast between text and the background is a common problem on the web meanwhile very few researchers study the insights of the designers’ design thinking process, how they choose the specific colours from all the colours. WCAG 2.0 addresses the contrast problem, but the requirement is hard to understand for most designers. Therefore, some web designers check their designs with contrast checking tools after the design is finished. If the design does not meet the WCAG 2.0 guidelines the designer will have to go back and make adjustments and check contrast again. The gap between the requirements for designers and the sufficient tool assist them need to be filled. To overcome this problem, a cross culture interview was conducted to identify the factors the designer consider and their actual behavior during the design process. Moreover a colour picker tool is developed that allows designers to select WCAG 2.0 compliant colours during the design process thus eliminating the need for post-design colour adjustments. This dissertation aims to help software developer gain a deeper understanding about designers’ selections and make it easier to achieve readability on the web

Lithium cations mobility in a coarse-grained polymer embedded with Lennard Jones particles using non-equilibrium molecular dynamics

Kompositt faststoffelektrolytter er lovende alternativer til de eksisterende flytende elektrolyttene i litium-batterier fordi de kan brukes med litium-metall som anode. Hovedproblemet med slike polymer-baserte faste elektrolytter er den lave ioniske ledningsevnen. Tilsats av nanopartikler til polymer-matriser dopet med litium-salter har vært foreslått for å øke ionisk ledningsevne ved romtemperatur selv om den eksakte underliggende mekanismen er kompleks og uklar. Dagens eksperimentelle metoder kan ikke brukes til å observere eller gi ledetråder om transport av litium-kationer gjennom slike komplekse kompositt-system. Molekylærdynamiske simuleringer kan derimot åpne en vei til å utforske mikrotilstandene i og gi prediksjoner om litium-kationers mobiliteter ved ikke-likevekts molekylærdynamikk. Det er ikke gjort noe forsøk på å bygge et spesifikt system i dette arbeidet og alle anionenes bevegelser er fryst som er en situasjon som kun er tilgjengelig gjennom simuleringer. Fokuset er på å bygge en grovkornet polymermatrise med passende mengde litium-salt og deretter observere mobiliteten til litium-kationene ved innsetting av en nanopartikkel. Ved å endre partikkelstørrelsen og styrken til interaksjonen mellom partikkel og polymer, så ønsker vi å utforske effekten på polymertetthet og litium-kationers mobilitet. Siden det eneste parvise potensialet til nanopartikkelen er det klassiske Lennard-Jones potensialet, så kaller vi den Lennard-Jones partikkelen i dette arbeidet. Partikler med størrelse 4, 5, 6, 7 Å og interaksjonsstyrke 0,2, 0,35, 0,5, 0,65 kcal/mol har blitt modellert og simulert. Interaksjonsstyrken ble låst ved 0,2 kcal/mol når variabelen var størrelse og størrelsen ble låst ved 7 Å når variabelen var interaksjonsstyrke. Basert på dataene i dette arbeidet, for partikler større enn 4 Å, dess større partikkelen er dess høyere vil polymertettheten bli og dess høyere vil den gjennomsnittlige litium-mobiliteten bli. For partikler med interaksjonsstyrke større enn 0,2 kcal/mol, selv om ingen enkel trend er observert, trenden i litium-mobilitet følger polymertettheten hvor 0,35 kcal/mol systemet er omtrent samme som 0,65 kcal/mol og 0,5 kcal/mol systemet har lavere mobilitet enn begge. Minst fire paralleller ble simulert ved 300 K for hvert system inkludert polymersystemet uten nanopartikkel som referanse. Den gjennomsnittlige mobiliteten for systemet uten partikkelen ble 2,14 · 10-8 m^2/Vs. Av alle parallellene ble den høyeste mobiliteten 7,15 · 10−8 m^2/Vs observert i systemet med nanopartikkel med størrelse 6 Å og interaksjonsstyrke 0,2 kcal/mol. Den laveste mobiliteten 5.62 · 10−9 m^2/Vs ble observert i systemet med nanopartikkel med størrelse 7 Å og interaksjonsstyrke 0,35 kcal/mol.Composite solid-state electrolytes have become a promising alternative to the existing liquid electrolytes in lithium batteries with the potential of utilizing lithium metal as anode directly. The main issue with such polymer based solid electrolyte is the low ionic conductivity. The addition of nanoparticles to lithium salt doped polymer matrixes has been proposed to enhance the room temperature ionic conductivity of the host polymer. However, current experimental methods are not able to observe nor give clues on lithium cations transportation within such complex composite system. Molecular dynamic simulations open a way to explore the microstates within the electrolytes and can be used to predict lithium cations mobility through non-equilibrium molecular dynamics. There is no attempt to build any specific system in this work and all anions’ movements are frozen which is a situation only achievable through simulations. The focus here is to construct a coarse-grained polymer matrix dopped with appropriate amount of lithium salts and then observe the lithium cations mobilities with a nanoparticle embedded in the polymer matrix. By changing the particle size and interaction energy between the particle and the polymer, we seek to explore the effects on polymer density as well as lithium cation mobilities. As the only pair wise potential on this nanoparticle is the classical Lennard Jones potential, we thus call it Lennard Jones particle in this work. The composite systems with particles radius 4, 5, 6, 7 Å and interaction energy 0.2, 0.35, 0.5, 0.65 kcal/mol have been modelled and simulated. Interaction energy is fixed at 0.2 kcal/mol when the variable is radius, and radius is fixed at 7 Å when the variable is interaction energy. Based on data in this work, in terms of size (radius), for particle larger than 4 Å, the larger the particle is the higher the polymer density would be and the higher the average lithium mobility is. Data of average lithium mobility shows that system with size 5 Å particle is 1.94 · 10−8 m^2/Vs, system with size 6 Å particle is 2.92 · 10−8 m^2/Vs and system with size 7 Å particle is 3.47 · 10−8 m^2/Vs. Data of polymer density shows that system with size 5 Å particle is 0.8591 g/cm^3, system with size 6 Å particle is 0.8597 g/cm^3and system with size 7 Å particle is 0.8606 g/cm^3. In terms of interaction energy, for particle with interaction energy larger than 0.2 kcal/mol, the trend in lithium mobility follows that of polymer density where 0.35 kcal/mol system roughly same as 0.65 kcal/mol system and 0.5 kcal/mol system lower than both. Data of average lithium mobility shows that system with energy 0.35 kcal/mol particle is 2.03 · 10−8 m^2/Vs, system with energy 0.5 kcal/mol particle is 1.11 · 10−8 m^2/Vs and system with energy 0.65 kcal/mol particle is 1.51 · 10−8 m^2/Vs. Data of polymer density shows that system with 0.35 kcal/mol particle is 0.8624 g/cm^3, system with 0.5 kcal/mol particle is 0.8617 g/cm^3 and system with 0.65 kcal/mol particle is 0.8629 g/cm^3. Meanwhile, we notice that the polymer density trend in both size and interaction energy cases align with the trend of 1st peak intensity in radial distribution function (RDF). At least four trajectories have been simulated at 300 K for each case including polymer system without the nanoparticle as a reference. The average mobility for system without the particle is 2.14 · 10−8 m^2/Vs. Among all the trajectories, the largest mobility 7.15 · 10−8 m^2/Vs is observed in system where the particle has size 6 Å and interaction energy 0.2 kcal/mol; the smallest mobility 5.62 · 10−9 m^2/Vs is observed in system where the particle has size 7 Å and interaction energy 0.35 kcal/mol

Past and Future Land Use Impacts of Canadian Oil Sands and Greenhouse Gas Emissions

The Canadian oil sands underlie 142,000 km2 of the boreal forest in northeastern Alberta. Oil sands production greenhouse gas (GHG) emissions increased from 15 million tonnes (Mt) to 55 Mt between 1990 and 2011. Their production represents the fastest-growing source of GHG emissions in Canada. A large body of studies show that oil sands industries have large environmental impacts, including effects on climate, land, water, and air quality but GHG emissions from oil sands land use disturbance and future land use impacts have yet to be examined in detail and the associated literature is scarce and incomplete. Our paper examines the historical and potential land use change and GHG emissions associated with oil sands development in Canada. Disturbance occurred between 1985 and 2009 from oil sands development were identified using remote sensing technique and mapped onto spatially explicit soil, biomass and peatlands carbon maps. We found that land use and GHG disturbance of oil sands production, especially in-situ technology that will be the dominant technology of choice for future oil sands development, are greater than previously reported. We estimate additional 500 km2 and 2,400 km2 of boreal forest including carbon-rich peatlands would be disturbed from surface mining and in-situ production, respectively, between 2012 and 2030; releasing additional 107–182 million tonnes of GHG from land use alone. Future efforts to monitor land use impacts of in-situ production are needed to reduce landscape impacts and associated GHG emissions. In addition, land reclamation after oil sands projects needs to be enforced for broad ecological benefits together with GHG benefits

Is Pre-consultation Conducted by the Assistant Physician Effective in Improving Online Healthcare Service Quality and Satisfaction?

To improve online healthcare quality and efficiency, online healthcare communities (OHCs) enabled the pre-consultation function, in which an assistant physician interacts with the patient to understand and document the patient’s health conditions, medical history, and consultation objectives prior to the formal online consultation with the attending physician. Using detailed service data from a Chinese OHC, this study scrutinizes the effect of using pre-consultation on online healthcare service quality and satisfaction. The results show that pre-consultation can significantly increase the attending physician’s response speed, length, and the level of informational support embedded within the response, while maintaining a consistent level of emotional support. Despite the improvement in service quality, pre-consultation leads to decreased patient satisfaction with the consultation service. Furthermore, we find that pre-consultation improves service quality by enhancing the professionalism and comprehensiveness of patient case information and reducing information seeking and clarification of the attending physician with the patient

Uncommon linear systems of two equations

A system of linear equations $L$ is common over $\mathbb{F}_p$ if, as $n\to\infty$, any 2-coloring of $\mathbb{F}_p^n$ gives asymptotically at least as many monochromatic solutions to $L$ as a random 2-coloring. The notion of common linear systems is analogous to that of common graphs, i.e., graphs whose monochromatic density in 2-edge-coloring of cliques is asymptotically minimized by the random coloring. Saad and Wolf initiated a systematic study on identifying common linear systems, built upon the earlier work of Cameron-Cilleruelo-Serra. When $L$ is a single equation, Fox-Pham-Zhao gave a complete characterization of common linear equations. When $L$ consists of two equations, Kam\v{c}ev-Liebenau-Morrison showed that irredundant $2\times 4$ linear systems are always uncommon. In this work, (1) we determine commonness of all $2\times 5$ linear systems up to a small number of cases, and (2) we show that all $2\times k$ linear systems with $k$ even and girth (minimum number of nonzero coefficients of a nonzero equation spanned by the system) $k-1$ are uncommon, answering a question of Kam\v{c}ev-Liebenau-Morrison.Comment: 59 pages, 1 figur

The Effect of Online Follow-up Services on Offline and Online Physician Demand: Evidence from Chronic Disease Physicians

The adoption of online follow-up services by physicians provides their offline patients with an important channel for medical follow-ups. Using detailed service data from a Chinese online healthcare community (OHC), the present study scrutinizes the rarely studied effect of adopting online follow-up services on offline and online physician demand in the context of chronic disease. The results demonstrate that adopting online follow-up services leads to higher offline physician demand. Interestingly, in contrast to the channel substitution effect documented in the literature, we find that providing online follow-up services also increases online physician demand. Furthermore, the results of mechanism tests reveal that online follow-up services affect online demand by boosting physicians’ online exposure and increasing the availability of information on their online service characteristics to patients. Our findings offer strategic guidance for physicians, design implications for OHCs, and insights for healthcare policymakers