nils-herrmann/clean_scirepeval huggingface dataset:
The mRNA recruiting eIF4 factors involved in protein synthesis and its regulation.
Venue: Biochemistry
Year: 2019

The recruitment of mRNA onto the ribosome not only affects global translation, but also the spatial and temporal fine tuning of eukaryotic translation initiation. The eukaryotic Initiation Factor 4 (eIF4) factors, namely eIF4G, eIF4E, eIF4A and eIF4B facilitates the recruitment of mRNA onto the pre assembled 43S Pre Initiation complex (PIC) thus leading to formation of 48S PIC. Several biochemical and genetic studies have established the roles of eIF4 factors, however, the available structural information about it is limited. While structures of some of the individual components and sub complexes are available, the structural details of activated mRNA bound to eIF4 factors (eIF4 mRNA) is missing. Structural characterization of the eIF4 mRNA in association with the 43S PIC in different organisms is crucial for a detailed understanding of mRNA recruitment and for exploiting the structural differences for possible drug designing.
The web browser factor in traffic analysis attacks
Venue: Secur. Commun. Networks
Year: 2015

Website fingerprinting is a known type of traffic analysis attacks that aims to identify which websites are visited in encrypted traffic traces. Recent work showed that some classifiers can successfully identify 90% of visited websites. Because web browsers use different rendering engines and networking application program interfaces APIs, they tend to resist differently to website fingerprinting attacks. In this paper, we study to which extent popular web browsers can resist such attacks by analyzing the shape of their network traffic when fetching websites. To this end, five fine grained measures are used to point out very subtle differences in the network traffic of each web browser. Empirical analysis showed that, among six studied web browsers Chrome, Firefox, Internet Explorer, Safari, Opera, and Tor Browser, Opera and Safari offer the highest resistance to website fingerprinting. Because most of existing fingerprinting techniques have been evaluated using Firefox web browser, we expect the accuracy results of existing work to be reduced in case Opera or Safari browser is used.
Efficient Routing and Spectrum Allocation Considering QoT in Elastic Optical Network
Year: 2016

In recent years, Orthogonal Frequency Division Multiplexing (OFDM) based elastic optical network (EON) has drawn increasing attention in both academia and industry. Compared to traditional optical Wavelength Division Multiplexing (WDM) network, EON is capable of supporting variable data rate, accommodating traffic demands flexibly with finer provisioning granularity, and utilizing spectrum more efficiently. Accordingly, the resource management in EON is different from that in WDM networks and addresses new challenges in network design and control. In this paper, we study the routing, modulation level and spectrum allocation (RMLSA) problem in EON. We propose an efficient link based mixed integer linear programming (MILP) model with the objective to optimally utilize the spectrum resources while considering the constraint on Quality of Transmission (QoT) Then, the performance of the proposed model is evaluated and analyzed through case study.
Advancement of Routing Protocols and Applications of Underwater Wireless Sensor Network (UWSN) A Survey
Year: 2020

Water covers a greater part of the earth's surface. Even though we know very little about the underwater world as most parts of it remain unexplored. Oceans including other water bodies hold huge natural resources and also the aquatic lives. These are mostly unexplored and very few of those are known due to unsuited and hazardous environments for the human to explore. This vast underwater world can be monitored remotely from a distant location with much ease and less risk. To monitor water bodies remotely in real time, sensor networking has been playing a great role. It is needed to deploy a wireless sensor network over the volume which we want to surveil. For vast water bodies like oceans, rivers and large lakes, data is collected from the different heights of the water level which is sent to the surface sink. Unlike terrestrial communication, radio waves and other conventional mediums can't serve the purpose of underwater communication as they pose high attenuation and very reduced transmission range. Rather an acoustic medium can transmit data more efficiently and reliably in comparison to other mediums. To transmit data reliably from the bottom of the sea to the sinks at the surface, multi hop communication is needed which must involve a certain scheme. For seabed to surface sink communication, leading researchers have proposed different routing protocols. The goal of these routing protocols is to make underwater communication more reliable, energy efficient and delay efficient thus to improve the performance of the overall communication. This paper surveys the advancement and applications of the routing protocols which eventually helps in finding the most efficient routing protocol for the Underwater Wireless Sensor Network (UWSN)
Learning opacity in Stratal Maximum Entropy Grammar*
Venue: Phonology
Year: 2017

Opaque phonological patterns are sometimes claimed to be difficult to learn; specific hypotheses have been advanced about the relative difficulty of particular kinds of opaque processes (Kiparsky 1971, 1973) and the kind of data that is helpful in learning an opaque pattern (Kiparsky 2000) In this paper, we present a computationally implemented learning theory for one grammatical theory of opacity, a Maximum Entropy version of Stratal OT (Bermudez Otero 1999, Kiparsky 2000) and test it on simplified versions of opaque French tense lax vowel alternations and the opaque interaction of diphthong raising and flapping in Canadian English. We find that the difficulty of opacity can be influenced by evidence for stratal affiliation: the Canadian English case is easier if the learner encounters application of raising outside the flapping context, or non application of raising between words (e.g. life with ^I] lie for with [aI]
Coexisting frequency combs spaced by an octave in a monolithic quantum cascade laser.
Venue: Optics express
Year: 2018

Quantum cascade lasers are proving to be instrumental in the development of compact frequency comb sources at mid infrared and terahertz frequencies. Here we demonstrate a heterogeneous terahertz quantum cascade laser with two active regions spaced exactly by one octave. Both active regions are based on a four quantum well laser design and they emit a combined 3 mW peak power at 15 K in pulsed mode. The two central frequencies are 2.3 THz (bandwidth 300 GHz) and 4.6 THz (bandwidth 270 GHz) The structure is engineered in a way that allows simultaneous operation of the two active regions in the comb regime, serving as a double comb source as well as a test bench structure for all waveguide internal self referencing techniques. Narrow RF beatnotes 15 kHz) are recorded showing the simultaneous operation of the two combs, whose free running coherence properties are investigated by means of beatnote spectroscopy performed both with an external detector and via self mixing. Comb operation in a highly dispersive region (4.6 THz) relying only on gain bandwidth engineering shows the potential for broad spectral coverage with compact comb sources.
Review on biomimetic affinity chromatography with short peptide ligands and its application to protein purification.
Venue: Journal of chromatography. A
Year: 2018

Biomimetic affinity chromatography with short peptide ligands, as a promising bioseparation technique, has great potential to protein separation and purification, which is based on highly specific biological interactions between specially designed ligands and target proteins. Generally, short peptide ligands with the chain length ranging from two to nine amino acids could be divided into two types, linear peptide ligands and cyclic peptide ligands. To obtain the desired short peptide ligands, rational design strategies could be applied by knowing the 3 dimensional (3D) information of the receptors or just knowing the surface cavities and the active site of the receptors. Subsequently, several technologies could be used to screen the optimal peptide ligands from the designed peptide ligands, such as combinatorial chemistry, phage display, mRNA display and computer based screening technology. The screening efficiency is dependent on the different technology for individual target proteins. After screening, the chromatographic resin could be prepared by coupling the optimal short peptide ligand onto a matrix with some spacer arms. The suitable matrix and spacer arms are also important to enhance the ability of the peptide ligand for protein purification. With the advantages of high affinity, high adsorption capacity, structural stability, low immunogenicity and low cost, biomimetic affinity chromatography with short peptides as the functional ligands have shown an extensive development and application potentiality to protein purification. In this review, we focused on the strategies of rational designs and screening for short peptide ligands, and some items on the perpetration of new resins and their applications for protein purification would also be discussed.
Tax Compliance of Village Owned Enterprises Based on Government Regulation (PP) No 23 Year of 2018
Year: 2020

Taxes are source of income for a country to finance its activities in providing facilities and infrastructure as well as services to the community, while one of the largest sources of tax revenue comes from Micro, Small and Medium Enterprises, which in this study focus on Village Owned Enterprises (BumDes) Focus This research is with the implementation of Government Regulation No. 23 of 2018 which is an improvement from Government Regulation No. 46 of 2016 concerning tax rates for SMEs which were previously at 1% to 0.5% The purpose of this study is to provide fundamental knowledge about the factors that influence an SME to comply with paying taxes. Operationally, this research has the following objectives: (a) explore factors that influence MSMEs to comply with paying taxes, (b) test tax planning practices for MSMEs, (c) understandings for the government to find out what factors influence MSMEs to comply with paying taxes, (d) knowing the dominant factor for MSMEs as a driver of tax compliance. This research was tested using multiple linear regressions to determine the dominant factor. The results of this study indicate that only understanding, awareness, and sales variables affects the tax compliance, while socialization and trust have insignificant effect.
Exploring Android Studio: Getting Familiar with the IntelliJ IDEA
Year: 2015

Now that you have a comprehensive overview of the new features in Android, including the new Material Design paradigm and other new Android 5 features, this chapter will take a look at the for Android, IntelliJ IDEA. You took care of getting your Development Workstation assembled during Chapter 2, so all that is left to do now is to get you up to speed regarding the ins and outs of the IDE software tool that you will be using from here on out during this book. Once this is out of the way, you can then focus on Java 7 coding or XML markup for the duration of the next 16 chapters in this book.
Flynn effect and its reversal are both environmentally caused
Venue: Proceedings of the National Academy of Sciences
Year: 2018

Using administrative register data with information on family relationships and cognitive ability for three decades of Norwegian male birth cohorts, we show that the increase, turning point, and decline of the Flynn effect can be recovered from within family variation in intelligence scores. This establishes that the large changes in average cohort intelligence reflect environmental factors and not changing composition of parents, which in turn rules out several prominent hypotheses for retrograde Flynn effects. Population intelligence quotients increased throughout the 20th century a phenomenon known as the Flynn effect although recent years have seen a slowdown or reversal of this trend in several countries. To distinguish between the large set of proposed explanations, we categorize hypothesized causal factors by whether they accommodate the existence of within family Flynn effects. Using administrative register data and cognitive ability scores from military conscription data covering three decades of Norwegian birth cohorts (1962 1991) we show that the observed Flynn effect, its turning point, and subsequent decline can all be fully recovered from within family variation. The analysis controls for all factors shared by siblings and finds no evidence for prominent causal hypotheses of the decline implicating genes and environmental factors that vary between, but not within, families.
Knowledge Base Enhanced Topic Modeling
Venue: 2020 IEEE International Conference on Knowledge Graph (ICKG)
Year: 2020

Topic models, such as Latent Dirichlet Allocation (LDA) are successful in learning hidden topics and has been widely applied in text mining. There are many recently developed augmented topic modeling methods to utilize metadata information. However, the effect of topic models is still not comparable to humans. We think one key point is that humans have background knowledge, which is essential for topic understanding. Inspired by this, we propose a knowledge base enhanced topic model in this paper. We take knowledge bases as good presentations of human knowledge, with huge collections of entities and their relations. We assume that documents with related entities tend to have similar topic distributions. Based on this assumption, we compute document similarity information via the linked entities and then use it as a constraint for LDA. More specifically, we embed entities in a low dimensional space via DeepWalk and use Entity Movers Distance to efficiently and effectively measure the similarities between documents. The results of experiments over two real world datasets show that our method boosts the LDA model on the document classification while no supervision information is needed.
Astro 2020 Science White Paper Resolving Galaxy Formation at Cosmic Noon Thematic Area Galaxy Evolution
Year: 2019

Cosmic noon was an active and critical period in the evolution of galaxies. During this epoch, roughly 10 Gyr ago, star formation and black hole accretion were at their highest rates. Key characteristics of today's galaxies, such as regularly rotating disks, bulges, and a population of dead galaxies, were just emerging. We describe opportunities over the next decade to transform our view of galaxy evolution at this important epoch by resolving both early galaxies and their surrounding gaseous media. High angular resolution spectroscopic observations are needed to resolve individual star forming regions, dissect emerging substructures such as disks, clumps, and bulges, map galaxy scale winds, and identify supermassive black holes. On larger scales, deep optical spectroscopy is needed to characterize and resolve the circumand intergalactic media within which galaxies are forming by using dense networks of faint background galaxies to probe gas in absorption. Only extremely large telescopes (ELTs) provide both of these capabilities, thereby delivering an unprecendented density of information over a wide range of scales, spanning 100 pc to 1 Mpc. Multi scale resolved observations will be essential to understand the flow of baryons through galaxies, the mechanics of feedback, and its role in shaping early galaxies' star formation and structural evolution.
Can Celebrities Burst Your Bubble?
Venue: ArXiv
Year: 2020

Polarization is a growing, global problem. As such, many social media based solutions have been proposed in order to reduce it. In this study, we propose a new solution that recommends topics to celebrities to encourage them to join a polarized debate and increase exposure to contrarian content bursting the filter bubble. Using a state of the art model that quantifies the degree of polarization, this paper makes a first attempt to empirically answer the question: Can celebrities burst filter bubbles? We use a case study to analyze how people react when celebrities are involved in a controversial topic and conclude with a list possible research directions.
Effects of clothianidin on aquatic communities: Evaluating the impacts of lethal and sublethal exposure to neonicotinoids
Venue: PloS one
Year: 2017

The widespread usage of neonicotinoid insecticides has sparked concern over their effects on non target organisms. While research has largely focused on terrestrial systems, the low soil binding and high water solubility of neonicotinoids, paired with their extensive use on the landscape, puts aquatic environments at high risk for contamination via runoff events. We assessed the potential threat of these compounds to wetland communities using a combination of field surveys and experimental exposures including concentrations that are representative of what invertebrates experience in the field. In laboratory toxicity experiments, LC50 values ranged from 0.002 ppm to 1.2 ppm for aquatic invertebrates exposed to clothianidin. However, freshwater snails and amphibian larvae showed high tolerance to the chemical with no mortality observed at the highest dissolvable concentration of the insecticide. We also observed behavioral effects of clothianidin. Water bugs, Belostoma flumineum, displayed a dose dependent reduction in feeding rate following exposure to clothianidin. Similarly, crayfish, Orconectes propinquus, exhibited reduced responsiveness to stimulus with increasing clothianidin concentration. Using a semi natural mesocosm experiment, we manipulated clothianidin concentration (0.6, 5, and 352 ppb) and the presence of predatory invertebrates to explore community level effects. We observed high invertebrate predator mortality with increases in clothianidin concentration. With increased predator mortality, prey survival increased by 50% at the highest clothianidin concentration. Thus, clothianidin contamination can result in a top down trophic cascade in a community dominated by invertebrate predators. In our Indiana field study, we detected clothianidin (max 176 ppb) imidacloprid (max 141 ppb) and acetamiprid (max 7 ppb) in soil samples. In water samples, we detected clothianidin (max 0.67 ppb) imidacloprid (max 0.18 ppb) and thiamethoxam (max 2,568 ppb) Neonicotinoids were detected in >56% of soil samples and >90% of the water samples, which reflects a growing understanding that neonicotinoids are ubiquitous environmental contaminants. Collectively, our results underscore the need for additional research into the effects of neonicotinoids on aquatic communities and ecosystems.
Microbiota tryptophan metabolism induces aryl hydrocarbon receptor activation and improves alcohol induced liver injury
Venue: Gut
Year: 2020

Chronic alcohol consumption is an important cause of liver related deaths. Specific intestinal microbiota profiles are associated with susceptibility or resistance to alcoholic liver disease in both mice and humans. We aimed to identify the mechanisms by which targeting intestinal microbiota can improve alcohol induced liver lesions.  We used human associated mice, a mouse model of alcoholic liver disease transplanted with the intestinal microbiota of alcoholic patients and used the prebiotic, pectin, to modulate the intestinal microbiota. Based on metabolomic analyses, we focused on microbiota tryptophan metabolites, which are ligands of the aryl hydrocarbon receptor (AhR) Involvement of the AhR pathway was assessed using both a pharmacological approach and AhR deficient mice.  Pectin treatment modified the microbiome and metabolome in human microbiota associated alcohol fed mice, leading to a specific faecal signature. High production of bacterial tryptophan metabolites was associated with an improvement of liver injury. The AhR agonist Ficz (6 formylindolo (3,2 b) carbazole) reduced liver lesions, similarly to prebiotic treatment. Conversely, inactivation of the ahr gene in alcohol fed AhR knock out mice abrogated the beneficial effects of the prebiotic. Importantly, patients with severe alcoholic hepatitis have low levels of bacterial tryptophan derivatives that are AhR agonists.  Improvement of alcoholic liver disease by targeting the intestinal microbiota involves the AhR pathway, which should be considered as a new therapeutic target.
DIGITAL ECONOMY: HARNESSING THE BENEFITS AND TACKLING THE CHALLENGES FOR SUSTAINABLE DEVELOPMENT IN NIGERIA
Year: 2019

This paper titled "Digital Economy: Harnessing the Benefits and Tackling the Challenges for Sustainable Development in Nigeria" focused on the core concept of digital economy, x rayed its benefits and suggested ways to tackle the inevitable challenges posed by digital economy itself. Historical antecedents of various nations revealed that business economies of different countries were reshaped and restructured from time to time through the application of revolutionary inventions, beginning from the inventions of ABACUS, the first mechanised calculating apparatus in Asia Minor, 5000 years ago which was mostly used for the accounting of business transactions. However, in this 21 st century, the application of Information and Communication Technology (ICT) to business transactions and economic activities stimulated the emergence of e commerce which brought about buying and selling of products over the Internet between sellers and buyers. Digital Economy is thus defined as the use of ICT to interact and communicate in a globalised, high tech economy. The benefits of digital economy cannot be overemphasised as it provides a global market platform upon which people and organisations worldwide interact, communicate, collaborate, search and share information on various topics. This economy as well, enhances rapid business turnover through easy, cheap and direct advertisement of goods on social media this benefits thus prompts rapid business opportunities as it synergises companies and individuals to quickly adapt to the Internet which offers them business opportunities. Harnessing this benefits and tackling inevitable challenges of digital economy is therefore a necessity for a developing country like Nigeria in this 21 st century.