Miracle-dz/UniFAR-FTUs huggingface dataset:
CSE 190A Research Proposal: Super-Resolution

Super-resolution seeks to create a high-quality image of a scene from several lowquality images of the same scene. Though a literature of super-resolution applications exists, implementing super resolution successfully is apparently quite difficult. In fact, a student unsuccessfully attempted to implement super-resolution in a previous offering of this course. I will attempt the same task, but using a different approach that should yield better compartmentalization of bugs and inaccuricies than was enjoyed by the unsuccessful student. 1 Project description Multiple-image super-resolution seeks to combine the information from several low-quality photographs of a scene to create a single high-quality picture. The field is mature enough that there exists an iPhone application, ClearCam by Occipital, that takes 6 images in quick succession, and then uses them to perform super resolution with about 40 seconds of processing on the iPhone’s processor. Another approach to super resolution uses a single image and prior information about the scene to guess the values of missing pixels. This approach is called “hallucination”, and will not be addressed in this project. In multiple-image super-resolution, the low quality pictures may be of low resolution, be subject to blurring caused by poor focus, and have noisy pixel values. David Capel’s thesis [2] and a follow-up paper [1] describe a framework for performing super-resolution. In the first step, image registration, corresponding points in the low quality images are identified. This algorithm is described concisely in Figure 4 of [1]. These corresponding points are used to compute geometric and photometric transformations between the images. Here, a geometric transformation accounts for a change in the point of view of the camera, and a photometric transformation accounts for changes in illumination and exposure between shots. Once the corresponding points are identified, the main step in super-resolution is performed. The pixel values from the low quality images are represented as the results of a process that creates low quality images from image scenes, and inference is performed to find the ML or MAP value of pixels in the image scene given the low quality pixels. In the winter 2006 offering of CSE 190A, Jesse Cirimele attempted to implement super-resolution [3]. He first implemented image registration as a prerequisite to performing super-resolution on real images, and appears not to have succeeded in implementing super-resolution by the end of the quarter. Given Jesse’s lack of success, and the general difficulty of the problem as described to me by Serge Belongie, I plan to start with a simple subproblem of super-resolution before tackling the full problem. In particular, I plan to start with synthetic images, the corresponding points of which I control, so that I may test my super-resolution implementation independent of a potentially unreliable image registration subroutine. Once this simpler problem is solved, I will extend the implementation to deal with real images.
Characterization of a commercial lower-cost medium-precision non-dispersive infrared sensor for atmospheric CO2 monitoring in urban areas

Abstract. CO2 emission estimates from urban areas can be obtained with a network of in situ instruments measuring atmospheric CO2 combined with high-resolution (inverse) transport modelling. Because the distribution of CO2 emissions is highly heterogeneous in space and variable in time in urban areas, gradients of atmospheric CO2 (here, dry air mole fractions) need to be measured by numerous instruments placed at multiple locations around and possibly within these urban areas. This calls for the development of lower-cost medium-precision sensors to allow a deployment at required densities. Medium precision is here set to be a random error (uncertainty) on hourly measurements of ±1 ppm or less, a precision requirement based on previous studies of network design in urban areas. Here we present tests of newly developed non-dispersive infrared (NDIR) sensors manufactured by Senseair AB performed in the laboratory and at actual field stations, the latter for CO2 dry air mole fractions in the Paris area. The lower-cost medium-precision sensors are shown to be sensitive to atmospheric pressure and temperature conditions. The sensors respond linearly to CO2 when measuring calibration tanks, but the regression slope between measured and assigned CO2 differs between individual sensors and changes with time. In addition to pressure and temperature variations, humidity impacts the measurement of CO2, with all of these factors resulting in systematic errors. In the field, an empirical calibration strategy is proposed based on parallel measurements with the lower-cost medium-precision sensors and a high-precision instrument cavity ring-down instrument for 6 months. The empirical calibration method consists of using a multivariable regression approach, based on predictors of air temperature, pressure and humidity. This error model shows good performances to explain the observed drifts of the lower-cost medium-precision sensors on timescales of up to 1–2 months when trained against 1–2 weeks of high-precision instrument time series. Residual errors are contained within the ±1 ppm target, showing the feasibility of using networks of HPP3 instruments for urban CO2 networks. Provided that they could be regularly calibrated against one anchor reference high-precision instrument these sensors could thus collect the CO2 (dry air) mole fraction data required as for top-down CO2 flux estimates.
Structure of the Escherichia coli DNA Polymerase III ϵ-HOT Proofreading Complex*

The ϵ subunit of Escherichia coli DNA polymerase III possesses 3′-exonucleolytic proofreading activity. Within the Pol III core, ϵ is tightly bound between the α subunit (DNA polymerase) and θ subunit. Here, we present the crystal structure of ϵ in complex with HOT, the bacteriophage P1-encoded homolog of θ, at 2.1 Å resolution. The ϵ-HOT interface is defined by two areas of contact: an interaction of the previously unstructured N terminus of HOT with an edge of the ϵ central β-sheet as well as interactions between HOT and the catalytically important helix α1-loop-helix α2 motif of ϵ. This structure provides insight into how HOT and, by implication, θ may stabilize the ϵ subunit, thus promoting efficient proofreading during chromosomal replication.
Bayes' theorem and its applications in animal behaviour

Bayesian decision theory can be used to model animal behaviour. In this paper we give an overview of the theoretical concepts in such models. We also review the biological contexts in which Bayesian models have been applied, and outline some directions where future studies would be useful. Bayesian decision theory, when applied to animal behaviour, is based on the assumption that the individual has some sort of "prior opinion" of the possible states of the world. This may, for example, be a previously experienced distribution of qualities of food patches, or qualities of potential mates. The animal is then assumed to be able use sampling information to arrive at a "posterior opinion", concerning e.g. the quality of a given food patch, or the average qualities of mates in a year. A correctly formulated Bayesian model predicts how animals may combine previous experience with sampling information to make optimal decisions. We argue that the assumption that animals may have "prior opinions" is reasonable. Their priors may come from one or both of two sources: either from their own individual experience, gained while sampling the environment, or from an adaptation to the environment experienced by previous generations. This means that we should often expect to see "Bayesian-like" decision-making in nature.
Fatty acid starvation activates RelA by depleting lysine precursor pyruvate

Bacteria experiencing nutrient starvation induce the ubiquitous stringent response, a profound physiological change that reprograms cell physiology from fast to slow growth and stress survival. The stringent response is mediated by the secondary messengers pppGpp and ppGpp collectively referred to as (p)ppGpp or “alarmone”. In Escherichia coli, two paralogs, RelA and SpoT, synthesize (p)ppGpp. RelA is activated by amino acid starvation whereas SpoT, which can also degrade (p)ppGpp, responds to fatty acid (FA), carbon and phosphate starvation. Here, we discover that FA starvation leads to rapid activation of RelA and reveal the underlying mechanism. We show that fatty acid starvation leads to depletion of lysine that, in turn, leads to the accumulation of uncharged tRNAlys and activation of RelA. SpoT was also activated by fatty acid starvation but to a lower level and with a delayed kinetics. Next, we discovered that pyruvate, a precursor of lysine, is depleted by FA starvation. We also propose a mechanism that explains how FA starvation leads to pyruvate depletion. Together our results indicate that many responses to nutrient depletion may ultimately result indirectly from depletion of amino acids and thereby activating RelA. Interestingly, FA starvation provoked a ~100-fold increase in relA dependent ampicillin tolerance.
Improvement of reading frame maintenance is a common function for several tRNA modifications

Transfer RNAs from all organisms contain many modified nucleosides. Their vastly different chemical structures, their presence in different tRNAs, their occurrence in different locations in tRNA and their influence on different reactions in which tRNA participates suggest that each modified nucleoside may have its own specific function. However, since the frequency of frameshifting in several different mutants [mnmA, mnmE, tgt, truA (hisT), trmD, miaA, miaB and miaE] defective in tRNA modification was higher compared with the corresponding wild‐type controls, these modifications have a common function: they all improve reading frame maintenance. Frameshifting occurs by peptidyl‐tRNA slippage, which is influenced by the hypomodified tRNA in two ways: (i) a hypomodified tRNA in the ternary complex may decrease the rate by which the complex is recruited to the A‐site and thereby increasing peptidyl‐tRNA slippage; or (ii) a hypomodified peptidyl‐tRNA may be more prone to slip than its fully modified counterpart. We propose that the improvement of reading frame maintenance has been and is the major selective factor for the emergence of new modified nucleosides.
Using parallel architectures in speech recognition

The speed of modern processors has remained constant over the last few years and thus, to be scalable, applications must be parallelized. In addition to the main CPU, almost every computer is equipped with a Graphics Processors Unit (GPU) which is in essence a specialized parallel processor. This paper explores how performances of speech recognition systems can be enhanced by using GPU for the acoustic computations and multi-core CPUs for the Viterbi search in a large vocabulary application. The multi-core implementation of our speech recognition system runs 1.3 times faster than the single-threaded CPU implementation. Addition of the GPU for dedicated acoustic computations increases the speed by a factor of 2.8, leading to a word accuracy improvement of 16.6% absolute at real-time, compared to the the single-threaded CPU implementation.
Occupational protein contact dermatitis from coriander

Case Report A 22-year-old chef had no atopic skin or respiratory problems in infancy, but started to develop rhinoconjunctivitis at 5–6 years. Since then he had also developed oral symptoms, i.e., itching of the lips and palate, and swelling of the throat, from apples, pears and nuts. He had had no skin symptoms before he started training as a chef. In his current job, he had developed itchy hand dermatitis, related to the handling of raw potatoes, tomatoes, carrots, and curry. Dermatitis also occasionally developed on the face, especially if juices of any of the above vegetables or spices splashed onto his face. When seen by us, he had been on sick leave, and was symptomless, except for mild paronychia. Patch testing was performed according to the recommendations of ICDRG with a modified European standard series (allergens mainly from Chemotechnique, Malmö, Sweden, and Trolab, Reinbek/Hamburg, Germany), a series of antimicrobials (Chemotechnique), spices (8), flours, diallylsulfide and allicin. All patch tests were negative. Prick testing was performed as described earlier (9). The following positive prick tests were found: in a series of environmental allergens including natural rubber latex (NRL), birch (13 mmπpseudopodia), alder (10 mm); in a series of vegetables, potato (9 mm), carrot (5 mm), apple (9 mm), parsnip (5 mm) and parsley (5 mm); in a series of spices and nuts, coriander (10 mmπps), almond (9 mm) and hazelnut (9 mm). All other components of curry were negative. Series of storage mites, molds and flours were negative. The control test with histamine 10 mg/ml had a diameter of 8 mm. Total IgE was close to normal (116 kU/l; normal ,110 kU/l). RASTs (Pharmacia, Sweden) to potato, carrot, tomato, onion and garlic were negative. We concluded that our patient had occupational protein contact dermatitis from coriander, raw potato and carrot. Protein contact dermatitis has previously been reported from potato and carrot (Table 1). Our patient also had symptoms of immediate allergy to curry and, based on prick testing, it was concluded that the spice in curry causing the symptoms was coriander. His specific sensitization had developed in less than 1 year from occupational exposure to coriander and vegetables. Based on clinical follow-up, we concluded that the patient could not continue in his job, and re-training has been recommended.
Genetic Analysis of Lipooligosaccharide Core Biosynthesis in Campylobacter jejuni 81-176

ABSTRACT We report isolation and characterization of Campylobacter jejuni 81-176 lgtF and galT lipooligosaccharide (LOS) core mutants. It has been suggested that the lgtF gene of C. jejuni encodes a two-domain glucosyltransferase that is responsible for the transfer of a β-1,4-glucose residue on heptosyltransferase I (Hep I) and for the transfer of a β-1,2-glucose residue on Hep II. A site-specific mutation in the lgtF gene of C. jejuni 81-176 resulted in expression of a truncated LOS, and complementation of the mutant in trans restored the core mobility to that of the wild type. Mass spectrometry and nuclear magnetic resonance of the truncated LOS confirmed the loss of two glucose residues, a β-1,4-glucose on Hep I and a β-1,2-glucose on Hep II. Mutation of another gene, galT, encoding a glycosyltransferase, which maps outside the region defined as the LOS biosynthetic locus in C. jejuni 81-176, resulted in loss of the β-(1,4)-galactose residue and all distal residues in the core. Both mutants invaded intestinal epithelial cells in vitro at levels comparable to the wild-type levels, in marked contrast to a deeper inner core waaC mutant. These studies have important implications for the role of LOS in the pathogenesis of Campylobacter-mediated infection.
Cost of fetal alcohol spectrum disorder in Canada.

QUESTION I have heard that thousands of Canadian kids are affected by fetal alcohol spectrum disorders. Has there been any attempt to estimate what it costs our society? ANSWER In a recent Canadian study, the lifetime cost of fetal alcohol spectrum disorders was estimated at $1 million per case. With an estimated 4000 new cases yearly, this translates to $4 billion annually.
The control mechanisms on precipitation over northern Africa during a dust outbreak

Precipitation in northern Africa occurs mainly during the monsoon season. It arises from the interaction of atmospheric processes across a wide range of scales, making its prediction challenging. The control mechanisms on precipitation are examined during a well-documented case study of dust emission and transport on 9-14 June 2006. The same method for cloud detection and tracking was applied on satellite observations and several numerical simulations (with explicit or parameterized convection) to investigate the precipitating systems. Among the various types of systems identified, mesoscale convective systems (MCSs) yield most of the total precipitation, with an observed contribution of 66%. The greatest precipitation producers are the long-lived MCSs (i.e., that last more than 6 h), at the origin of 55% of precipitation. These MCSs become more organized, i.e., larger, longer-lived and faster, as they propagate westward. The convection-permitting simulations capture the rainfall partition, but do not fully reproduce the organization of the long-lived MCSs. The simulation with parameterized convection fails to correctly represent the rain partition. This shows the added-value provided by the convection-permitting simulations. The radiative effect of dust is then analyzed, by comparing two convection-permitting simulations, with and without dust-radiation interaction. The direct effects are a mid-level warming and a near-surface cooling mainly in the western parts of northern Africa, which tend to stabilize the lower atmosphere. One semi-direct effect is a decrease in precipitation. This rainfall drop is explained by a too low number of long-lived MCSs which, nevertheless, are longer-lived and more efficient in terms of precipitation production. The diminution in the number of long-lived MCSs is due to the stabilization of the atmosphere inhibiting the triggering of convection.
The evolution of inequality of opportunity in Europe

ABSTRACT The paper tests whether inequality of opportunity (IO) in Europe has increased between 2004 and 2010. IO is understood as unfair inequality due to circumstances beyond individual control (such as family background, race or sex). We show that over 2004–2010 IO increased significantly in Austria, Greece and Spain, while it decreased in Poland and Portugal. Relative IO (ratio of IO to overall income inequality) has grown in Austria, Belgium, Greece and Norway. In Greece, several social groups with an immigrant background have experienced sizable declines an opportunity for income acquisition.
Konditionale Mutagenese des IRAG Gens in der Maus

Die intrazellulare Kalziumkonzentration in glatten Gefasmuskelzellen ist von groser Bedeutung fur den Tonus von Blutgefasen. Sie spielt eine wichtige Rolle bei der Kontraktion und Relaxierung der Gefasmuskulatur und wird durch verschiedene Mechanismen reguliert. Eine moglicherweise entscheidende Rolle bei der Relaxierung konnte das kurzlich identifizierte IRAG ubernehmen. In dieser Arbeit wurden Mauslinien mit einer konventionellen oder konditionalen Mutation des IRAG Gens erzeugt. Dies bietet Moglichkeiten zur Aufklarung der physiologischen und patho-physiologischen Funktion des IRAG Gens.
The LTAP trigger gateway for LDAP directories

LDAP (Lightweight Directory Access Protocol) directories are being rapidly deployed on the web. They are currently used to store data like white pages information, user profiles, and network device descriptions. LDAP directories offer scalability advantages over current database technologies, as well as being more flexible. However, as users begin to use them for Directory Enabled Networking tasks such as provisioning network services, allocating resources, reporting, managing end‐to‐end security, and offering mobile users customized features that follow them, LDAP's limited functionality becomes a significant barrier to progress. For example, LDAP directories do not have active database functionality (i.e., triggers). However, triggers are necessary for monitoring changes to directories and taking appropriate actions, just as they are for databases. Such functionality is crucial to take full advantage of proposals such as the Directory Enabled Network (DEN) initiative. Currently, trigger functionality is non‐standardized for LDAP and each vendor's solution is non‐portable. We built the Lightweight Trigger Access Process (LTAP) gateway to provide a portable way to add triggers to a LDAP directory. We describe the trigger language, the gateway's implementation, as well as our experiences gained both during implementation and from our users. LTAP is currently being used in several projects. LTAP can be downloaded at http://ltap.bell‐labs.com. Copyright © 2000 John Wiley & Sons, Ltd.
The Distribution of the Combined Length of Spanned Cycles in a Random Permutation

For a random permutation π on {1,2,…,n} for fixed n, and for M⊆{1,2,…,n}, we analyse the distribution of the combined length L=L(π,M) of all cycles of π that contain at least one element of M. We give a simple, explicit formula for the probability of every possible value for L (backed by three proofs of distinct flavours), as well as closed-form formulae for its expectation and variance, showing that less than 1/(|M|+1) of the elements 1,…,n are expected to be contained in cycles of π that are disjoint from M, with low probability for a large deviation from this fraction. We furthermore give a simple explicit formula for all rising-factorial moments of L. These results are applicable to the study of manipulation in matching markets.
An advanced small-signal model of multi-terminal MMC-HVDC for power systems stability analysis based on dynamic phasors

This paper proposes an advanced small-signal of multi-terminal MMC-HVDC for large-scale systems stability analysis based on dynamic phasors and state-space, and this advanced model. In accordance with active and passive network control strategies for multi-terminal MMC-HVDC, the matchable small-signal stability models contained higher harmonics are conducted, and related theoretical derivation is carried out. The comparison of the advanced small-signal model, electromagnetic-transient model, and traditional small-signal state-space model is performed under a typical multi-terminal MMC-HVDC network with offshore wind generation. According to simulation, the advanced small-signal model can successfully follow the electromechanical transient response with small errors and predict the damped oscillations. Consequently, the validity and applicability of the proposed model are well confirmed.
ADAR1 and MicroRNA; A Hidden Crosstalk in Cancer

The evolution of cancer cells is believed to be dependent on genetic or epigenetic alterations. However, this concept has recently been challenged by another mode of nucleotide alteration, RNA editing, which is frequently up-regulated in cancer. RNA editing is a biochemical process in which either Adenosine or Cytosine is deaminated by a group of RNA editing enzymes including ADAR (Adenosine deaminase; RNA specific) or APOBEC3B (Apolipoprotein B mRNA Editing Enzyme Catalytic Subunit 3B). The result of RNA editing is usually adenosine to inosine (A-to-I) or cytidine to uridine (C-to-U) transition, which can affect protein coding, RNA stability, splicing and microRNA-target interactions. The functional impact of these alterations is largely unclear and is a subject of extensive research. In the present review, we will specifically focus on the influence of ADARs on carcinogenesis via the regulation of microRNA processing and functioning. This follows a brief review of the current knowledge of properties of ADAR enzyme, RNA editing, and microRNA processing.