Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistics of large scale sequence searching

MOTIVATION Database search programs such as FASTA, BLAST or a rigorous Smith-Waterman algorithm produce lists of database entries, which are assumed to be related to the query. The computation of statistical significance of similarity scores is well established for single pairs of sequences and using purely random models. However, the multi-trial context of a database search poses new problems. The credibility of a certain score obtained in a database search decreases with the amount of data that is compared. To improve p-value computation for database search experiments, statistical properties of the databases, such as the distribution of sequence length and effects induced by frequently repeated sequence patterns, need to be taken into account. RESULTS We investigated the SWISS-PROT protein database Release 31.0 running extensive simulations of database searches. A discrepancy is observed between the theoretical predictions and the empirical distribution. To correct for this, we evaluate the statistical significance of scores in the context of a database search by a contrasting semi-random model. This model enhances purely random models by one additional parameter reflecting individual statistical properties of real databases. We call this parameter the effective size of the database. CONTACT r.spang@dkfz-heidelberg.de;m.vingron@dkfz-hei del berg.de
What is Your Diagnosis?

A 3-month-old, sexually intact male domestic goose (Anser anser) was presented to the Louisiana State University Veterinary Teaching Hospital (Baton Rouge, LA, USA) with a 2-day history of progressive lethargy, anorexia, and neurologic signs. The neurologic signs observed by the owner consisted of intermittent circling, stargazing, and neck tremors occurring 4–5 times daily with normal, mentally appropriate behavior noted between episodes. The goose was housed outdoors in a shared enclosure with 1 other goose and 7 ducks. A separate enclosure that contained 12 chickens was also on the property but was not in direct contact with the ducks and geese. Over the past 3–4 weeks, several of the ducks were presented to the primary veterinarian with similar clinical signs. All the ducks died or were humanely euthanized following treatment based on their clinical condition. Additional diagnostic testing and postmortem examination of the ducks were not performed. On physical examination, the goose was depressed, with a thin body condition score (3/9), and weighed 3.1 kg. A bilateral serous discharge from the nares was present, and the goose had a mildly increased respiratory effort with an intermittent cough during examination. On neurologic evaluation, the goose ambulated with an intoed and ataxic gait and intermittently stargazed and walked into corners. The patient also displayed intention tremors of the head and neck and maintained the neck in a retracted position throughout the examination. A small volume of watery green diarrhea was also noted, although the remainder of the physical examination was unremarkable. A blood sample was collected for a complete blood count (CBC) and plasma biochemistry profile. Results of the CBC revealed a packed cell volume of 37% (reference interval 38–58%), and the only abnormality in the plasma biochemistry panel was an increased gamma-glutamyl transferase of 15 U/L (reference 0–5 U/L). Full-body radiographic imaging was performed and revealed numerous pinpoint mineral opacities within the ventriculus consistent with grit. Overall, there were no significant radiographic findings on the images obtained of the patient. Additional blood and fecal samples were acquired for heavy metal testing (lead and zinc); viral disease testing, including eastern equine encephalitis (EEE) and West Nile virus (WNV) serology; and a fecal direct examination and flotation.
Approximate Bayesian Model Selection for Local Cortical Networks at Cellular Resolution

Seven models of local cortical processing were examined and adapted to known circuit constraints of layer 4 of mouse primary somatosensory cortex. To test these hypotheses, an Approximate Bayesian Computation – Sequential Monte Carlo (ABC-SMC) model selection method for local cortical neuronal networks is proposed. For practical application, the pyABC framework together with a method for automated population size selection for ABC–SMC is developed. The method is evaluated for simulated noisy reconstruction conditions. Its robustness is demonstrated and a concrete cortical reconstruction experiment is designed.
A fast intra mode skip decision algorithm based on adaptive motion vector map

We propose a fast intra mode skip decision algorithm for H.264/AVC video encoding. Although intra macroblock encoding algorithm based on various prediction methods in the pixel domain increases compression ratio, it requires a significant increase in the computational complexity. To reduce the processing time for the inter frame encoding, we propose a fast intra mode skip decision scheme based on an adaptive motion vector map (AMVM) algorithm for H.264/AVC video encoding. We verified that the proposed algorithm generates generally good performances in PSNR, bit rates, and processing time.
Inflation Expectations and Choices of Households

Do household in ation expectations affect consumption-savings decisions? We link survey data on quantitative in ation expectations to administrative data on income and wealth. We document that households with higher in ation expectations save less. Estimating panel data models with year and household fixed effects, we find that a one percentage point increase in a household's in ation expectation over time is associated with a 250-400 euro reduction in the household's change in net worth per year on average. We also document that households with higher in ation expectations are more likely to acquire a car and acquire higher-value cars. In addition, we provide a quantitative model of household-level in ation expectations.
Time gestures : time conceptualisation in English with evidence from gestures in a multimodal corpus

This thesis is the first large-scale, corpus-based analysis of time conceptualisation using multimodal ‘big’ data. It exploits the NewsScape Library, an extensive television database, to investigate co-speech gestures for temporal expressions in English. This research investigates time conceptualisation by studying gesture patterns that co-occur with temporal linguistic expressions. While much has been written about time conceptualisation based on linguistic evidence, there has been comparatively little based on other modalities. Non-linguistic data has the capacity to help triangulate existing findings if found to be congruent with linguistic data or, conversely, could offer new insights into the way time is conceptualised. Gestures are an invaluable tool for the study of cognition due to their key role in human communication. Gesture is a universal phenomenon, largely unconscious and less monitored than speech and thus it can reveal information not present in language. In this thesis, I investigate three features of co-speech gestures: axis and direction; language-gesture congruency; and extent or distance. The dataset comprises gestures that co-occur with temporal linguistic expressions which can be further divided into three groups: non-spatial language (e.g. earlier than); spatial, directional language (e.g. back in those days); and spatial, non-directional language (e.g. far in the future). This research confirms that the lateral axis is frequently employed when gesturing about time, but it also suggests that spatial language usesthe sagittal axis more frequently that non-spatial language. Moreover, gestures that co-occur with spatially grounded temporal language tend to be congruent with the canonical direction of time, while this does not occur with non-spatially grounded temporal language. Finally, it seems that temporal distance expressed linguistically is usually analogous to spatial distance expressed through co-speech gestures. The thesis also reflects on theoretical and methodological issues for gesture studies and some possible steps forward in the study of gesture.
Graded and All-or-None Electrogenesis in Arthropod Muscle

Graded electrically excited responsiveness of Romalea muscle fibers is converted to all-or-none activity by Ba++, Sr++, or Ca++, the two former being much the more effective in this action. The change occurs with as little as 7 to 10 per cent of Na+ substituted by Ba++. The spikes now produced have overshoots and may be extremely prolonged, lasting many seconds. During the spike the membrane resistance is lower than in the resting fiber, but the resting resistance and time constant are considerably increased by the alkali-earth ions. The excitability is also increased, spikes arising neurogenically from spontaneous repetitive discharges in the axon as well as myogenically from spontaneous activity in the muscle fibers. Repetitive responses frequently occur on intracellular stimulation with a brief pulse. The data indicate that the alkali-earth ions exert a complex of effects on the different action components of electrically excitable membrane. They may be described in terms of the ionic theory as follows: The resting K+ conductance is diminished. The sodium inactivation process is also diminished, and sodium activation may be increased. Together these changes can act to convert graded responsiveness to the all-or-none variety. The alkali-earth ions can also to some degree carry inward positive charge during activity, since spikes are produced when Na+ is fully replaced with the divalent ions.
Investigating Opto-Electronic Properties of Surface Plasmon Structure for Spectroscopic Applications

This chapter is proposed with an approach to analyze reflectance as a function of negative index material thickness for different parameters under the surface plasmon condition and extended approach towards the field enhancement of electric field as function of incidence angle and transmittance as function of incidence angle has been analyzed. This chapter can reflect the good comparison between 3 layer medium and n layer medium model. Characteristic impedance of MIM surface plasmon structure is analytically calculated considering the effect of both Faraday inductance and kinetic inductance. Effect of metal layer thickness, insulator thickness, and electron density are tailored to observe the impedance variation with frequency. Wavelength dependence of characteristic impedance and quality factor of MIM (metal-insulator-metal) surface plasmon structure is analyzed. Structural parameters and damping ratio of the structure is tuned within allowable limit to analyze the variation after detailed analytical computation.
Point spread function measurement and analysis of three dimensional optical imaging system

Optical coherence tomography (OCT) and confocal scanning microscopes can perform three dimensional (3D) optical imaging of target objects. They are widely used in many fields because of their non-contact measurement, real-time fast imaging and high resolution. This paper is dedicated to evaluating the resolution of 3D optical imaging systems, enabling third-party metrology assessment, assuring periodic quality, and comparing different systems. An improved standard test method based on the system 3D point spread function (PSF) is proposed in this paper. The standard diameter microspheres were embedded in the robust PSF phantoms as scattering particles. An OCT and a confocal scanning microscope were used to acquire the 3D PSF images. Different from previous studies, this paper proposes a new preparation process for PSF phantoms. In addition, new mathematical model was built based on statistical methods to analyze the PSF that includes hundreds of scattered data. Combining the imaging principles of OCT and confocal microscopy, the imaging resolution of the two optical systems was compared. Finally, a stability experiment was performed to further verify the feasibility of using the PSF to evaluate the resolution performance of the imaging system. The results showed that the resolution based on PSF analysis is in good agreement with the theoretically calculated value, and this method can be used to reliably evaluate the resolution of 3D optical imaging system in the future.
Livelihood Risk, Culture, and the HIV Interface: Evidence from Lakeshore Border Communities in Buliisa District, Uganda

Background While studies have focused on HIV prevalence and incidence among fishing communities, there has been inadequate attention paid to the construction and perception of HIV risk among fisher folk. There has been limited research with respect to communities along Lake Albert on the border between Uganda and the Democratic Republic of Congo (DRC). Methods We conducted a qualitative study on three landing sites of Butiaba, Bugoigo, and Wanseko on the shores of Lake Albert along the border of Uganda and the Democratic Republic of Congo. Data were collected using 12 Focus Group Discussions and 15 key informant interviews. Analysis was done manually using content and thematic approaches. Results Lakeshore livelihoods split families between men, women, and children with varying degrees of exposure to HIV infection risk. Sustaining a thriving fish trade was dependent on taking high risks. For instance, profits were high when the lake was stormy. Landing sites were characterized by widespread prostitution, alcohol consumption, drug abuse, and child labour. Such behaviors negatively affected minors and in many ways predisposed them to HIV infection. The lake shore-border heterogeneity resulted in a population with varying HIV knowledge, attitudes, behavior, and competencies to risk perception and adaptation amidst negative masculinities and negative resilience. Conclusion The susceptibility of lakeshore communities to HIV is attributable to a complex combination of geo-socio, the available (health) services, economic, and cultural factors which converged around the fishing livelihood. This study reveals that HIV risk assessment is an interplay of plural rationalities within the circumstances and constraints that impinge on the daily lives by different actors. A lack of cohesion in a multiethnic setting with large numbers of outsiders and a large transient population made the available HIV interventions less effective.
Kinematic analysis and positioning performance evaluation of a structurally stability-enhanced ballbot

Ballbots are advanced mobile robots which actively balance on a single spherical ball, and has the benefits of (a) omni-directionality (b) single contact point with the ground and (c) dynamic stability. Ballbot models which have been previously developed used an inverted mouse-ball drive and a three omni-wheel system to transmit power to the ball. The earliest design used four rollers located at the lower half of the ball while the later designs used omni-wheels located at the upper half of the ball to drive the ballbot. In this paper, a novel design of ballbot is suggested. In the proposed model, the omni-wheels are relocated to the bottom half of the ball, reducing the overall height of the mobile robot. The ball of the ballbot makes contact with other elements at five points out of which three points are used for actuation. In the ballbot, the rotational movement of the omni-wheels was transformed into planar movement. The velocity kinematics of the robot was derived using differential motion transformation. The positioning performance of the ballbot was evaluated using a coordinate measuring machine and reference ball setup and the positioning error was determined.
A perceptual framework for contrast processing of high dynamic range images

Image processing often involves an image transformation into a domain that is better correlated with visual perception, such as the wavelet domain, image pyramids, multiscale-contrast representations, contrast in retinex algorithms, and chroma, lightness, and colorfulness predictors in color-appearance models. Many of these transformations are not ideally suited for image processing that significantly modifies an image. For example, the modification of a single band in a multiscale model leads to an unrealistic image with severe halo artifacts. Inspired by gradient domain methods, we derive a framework that imposes constraints on the entire set of contrasts in an image for a full range of spatial frequencies. This way, even severe image modifications do not reverse the polarity of contrast. The strengths of the framework are demonstrated by aggressive contrast enhancement and a visually appealing tone mapping, which does not introduce artifacts. In addition, we perceptually linearize contrast magnitudes using a custom transducer function. The transducer function has been derived especially for the purpose of HDR images, based on the contrast-discrimination measurements for high-contrast stimuli.
Certified reconstruction of convex curves using radial basis functions

The reconstruction of a curve or surface from an unorganized set of points is a well known problem. It is important in image analysis, but also in computeraided design and the reverse engineering of surfaces. One of the methods for solving the surface reconstruction problem uses radial basis functions to construct an implicit surface interpolating each point of the input set. There are, however, no theoretical guarantees concerning the topological correctness of such an approximation. This master's thesis deals with the reconstruction of convex curves in the plane using radial basis functions. In this case, an implicit curve is constructed as the collection of points where a function evaluates to zero. The function is constructed as a linear combination of radial basis functions centered at the input points. A linear system results from the requirement that each input point belongs to the curve. Using the solution to the linear system the function is found and the curve can be reconstructed from the set of points where the function evaluates to zero. For samplings of a circle and the identity as the radial basis function, it is proven that the reconstruction is a topologically correct approximation of a circle. The same result is achieved for general convex curves under a general condition on the coefficients of the linear system.
ROHub - A Digital Library for Sharing and Preserving Research Objects

ROHub is a digital library system, enhanced with Semantic Web technologies, which supports the storage, lifecycle management, sharing and preservation of research objects - semantic aggregations of related scientific resources, their annotations and research context. ROHub includes a set of features to help scientists throughout the research lifecycle to create and maintain high-quality research objects that can be interpreted and reproduced in the future, including quality assessment, evolution management, navigation through provenance information and monitoring features. It provides a set of RESTful APIs along with a Web Interface for users and developers. A demo installation is available at: www.rohub. org.
Diagnosis and Management of Paediatric Autoimmune Liver Disease: ESPGHAN Hepatology Committee Position Statement.

Paediatric autoimmune liver disease is characterised by inflammatory liver histology, circulating autoantibodies and increased levels of IgG, in the absence of a known etiology. Three conditions have a likely autoimmune pathogenesis: autoimmune hepatitis (AIH), autoimmune sclerosing cholangitis (ASC), and de novo AIH after liver transplantation. Two types of paediatric AIH are recognized according to seropositivity for smooth muscle and/or antinuclear antibody (SMA/ANA, AIH-1) or liver kidney microsomal type 1 and/or anti-liver cytosol type 1 antibodies (anti-LKM-1/anti-LC-1; AIH-2). Pertinent issues addressing the diagnosis, treatment and long term follow up were formulated by a core group of ESPGHAN members. They have commissioned the first authors with execution of this project. Initially, they have performed a systematic literature search on MEDLINE, ResearchGate and Mendeley databases over the last 30 years and produced a document focusing on prospective and retrospective studies in children. The ESPGHAN core group and ESPGHAN Hepatology Committee members voted on each recommendation, using a formal voting technique.
Change Management Of Hospital Information Systems In Context Of Health Professionals Training

Tibbi sistemlerdeki yenilikler ve degisimler, benzeri gorulmemis bir hizla yeni bilgi teknolojileri (BT) olarak one cikiyor. Hastaneler bu degisiklikleri gelismis bilgi teknolojilerini kullanarak uymaya calismakla zaman icinde hizmetlerini gelistirmektedirler. Projelerin arzu edilen sonuclari icin “Degisim Yonetimi” nin uygulanmasi, degisimin insan tarafini calistiran bir dizi fikir, surec ve beceriden olusmasi bakimindan onemlidir. Bu calisma (farkindaligi artirma, istek, bilgi, beceri gelistirme ve gelistirme), araclari (iletisim, katilim, motivasyon, egitim, liderlik, terfi), faktorleri (demografik, teknolojik, ekonomik, politik, yasal, rekabetci) ve devletler (gecmis, simdiki zaman, gelecek), hastane bilgi sistemlerinde degisim yonetimi stratejileri (lider, uzman, tartismaya acik, egitici, proaktif) konularinda inceler . Degisim sureci basladiginda ve devam ettigi zaman ortaya cikan kulturel, direnc, algi ve davranis sorunlarini gosterir. Son olarak, direnisin ardinda yatan bir takim sebepleri siralar ve onlemleri arar. Yani bu, degisim yonetimi surecine ve kullanicilarin degisime karsi direncinin nedenlerine ve bilgi teknolojilerindeki gelismelerin hastanelerde saglik bilisiminin kullanimina onculuk ettigi onlemlere odaklanan bir tur arastirmadir. Hiyerarsik yapisi, asiri disiplini, kati is tanimlari, yetki ve yetki prensibine dayalilik, iletisim kanallarinin yoklugu, bilgi tecrubelerini paylasmamasi ve ust yonetim taahhudunu yerine getirmemesi, calisanlarin fikir ve fikirlerine deger vermemesi, zayif liderlik ve motivasyon, esneklikigin olmayisinda direncle karsilasir ve degisim yonetimini basarili bir sekilde yonetilmeyebilinir
ETSOI CMOS for system-on-chip applications featuring 22nm gate length, sub-100nm gate pitch, and 0.08µm2 SRAM cell

For the first time we report extremely thin SOI (ETSOI) CMOS with 22 nm gate length (L<inf>G</inf>) and sub-100 nm contacted gate pitch for system-on-chip (SoC) applications. Multi-V<inf>t</inf> transistors are demonstrated with competitive drive currents (NFET/PFET) of 1150/1050 µA/µm at I<inf>off</inf> = 100 nA/µm for high performance (HP) and 920/880 µA/µm at I<inf>off</inf> = 1 nA/µm for low power (LP), respectively, at V<inf>DD</inf> = 1 V. High density 6-T SRAM cells down to 0.08 µm<sup>2</sup> are demonstrated. Compared with a 28nm bulk LP technology, the high drive currents of ETSOI transistors coupled with large capacitance reduction by aggressive L<inf>G</inf> scaling result in 25% improvement in ETSOI ring oscillator (RO) speed. Auxiliary ETSOI devices including epitaxy resistors with high precision and gated diodes with near ideal characteristics are fabricated to complete device menu for early ETSOI SoC design.
Sleeper: A Power-Conserving Service Discovery Protocol

The design of service discovery protocols which limit power consumption of devices has received little consideration but is an important problem because of the growing use of power-limited mobile networked devices. We describe sleeper, a new discovery protocol which uses proxied advertisement and discovery to dynamically offload service discovery workload from power-limited devices. The advertisement structure supports several modes of service discovery including conventional service advertisements, meta discovery, taxonomic-based discovery, location-based discovery and federated discovery. In addition, sleeper supports both push and pull modes of advertisement, but unlike other protocols uses service popularity to select push or pull modality. We describe an implementation of the new protocol and provide an analytical model for comparing response time to other push-based service discovery methods