Miracle-dz/UniFAR-FTUs huggingface dataset:
An objective IQA framework based on noise clusters estimation for still images

Recently, various objective image quality assessment (IQA) metrics have been proposed for measuring the quality of a captured image. Moreover, IQA databases have been made available to enable researchers develop and test IQA metrics. For instance, the TID2013 database was used in the experiments conducted in this study. It contains many test images obtained from 25 reference images, each having 24 types of distortion and five levels of noise for each distortion. However, estimating a subjective evaluation score for many types of noise is a difficult task. Therefore, this study proposes an objective IQA framework for evaluating noise clusters using image features. Experimental results confirmed the effectiveness of the proposed framework.
The presence of non‐native helical structure in the unfolding of a beta‐sheet protein MPT63

MPT63, a major secreted protein from Mycobacterium tuberculosis, has been shown to have immunogenic properties and has been implicated in virulence. MPT63 is a β‐sandwich protein containing 11 β strands and a very short stretch of 310 helix. The detailed experimental and computational study reported here investigates the equilibrium unfolding transition of MPT63. It is shown that in spite of being a complete β‐sheet protein, MPT63 has a strong propensity toward helix structures in its early intermediates. Far UV‐CD and FTIR spectra clearly suggest that the low‐pH intermediate of MTP63 has enhanced helical content, while fluorescence correlation spectroscopy suggests a significant contraction. Molecular dynamics simulation complements the experimental results indicating that the unfolded state of MPT63 traverses through intermediate forms with increased helical characteristics. It is found that this early intermediate contains exposed hydrophobic surface, and is aggregation prone. Although MPT63 is a complete β‐sheet protein in its native form, the present findings suggest that the secondary structure preferences of the local interactions in early folding pathway may not always follow the native conformation. Furthermore, the Gly25Ala mutant supports the proposed hypothesis by increasing the non‐native helical propensity of the protein structure.
PHONETIC AND GRAPHEMIC SYSTEMS FOR MULTI-GENRE BROADCAST TRANSCRIPTION

State-of-the-art English automatic speech recognition systems typically use phonetic rather than graphemic lexicons. Graphemic systems are known to perform less well for English as the mapping from the written form to the spoken form is complicated. However, in recent years the representational power of deep-learning based acoustic models has improved, raising interest in graphemic acoustic models for English, due to the simplicity of generating the lexicon. In this paper, phonetic and graphemic models are compared for an English Multi-Genre Broadcast transcription task. A range of acoustic models based on lattice-free MMI training are constructed using phonetic and graphemic lexicons. For this task, it is found that having a long-span temporal history reduces the difference in performance between the two forms of models. In addition, system combination is examined, using parameter smoothing and hypothesis combination. As the combination approaches become more complicated the difference between the phonetic and graphemic systems further decreases. Finally, for all configurations examined the combination of phonetic and graphemic systems yields consistent gains.
Plasmatic L-lactate in pet rabbits: association with morbidity and mortality at 14 days.

BACKGROUND The clinical relevance of plasmatic L-lactate concentration (PLLC) is unknown in rabbits. Due to an entirely different metabolism of lactic acid, PLLC in rabbits can reach much higher concentrations than in other species. OBJECTIVES The aim of this study was to establish a reference interval (95% RI) for venous PLLC in pet rabbits and to assess its diagnostic and prognostic significance in ill pet rabbits. METHODS Plasmatic L-lactate concentration was determined by an enzymatic colorimetric method. In the first study, healthy rabbits (n = 140) were the control group. The ill rabbits group (n = 405) included the deceased (n = 108) and the survivors (n = 266), depending on the outcome at day 14. In a second study, variation in the PLLC was determined in 25 boarding (control-serial), 99 hospitalized (deceased-serial [n = 27], and survivors-serial [n = 72]) rabbits sampled at 0, 12, 24 and 48 hours. RESULTS The 95% RI for PLLC in controls was 2.1-15.2 mmol/L. On-arrival PLLC in ill rabbits was not statistically different from those in the control group, but was significantly lower in deceased compared to survivors or controls. The range of PLLC variation differed significantly between control-serial, deceased-serial, and survivors-serial groups. A better prognosis was associated with an increase of 3.3 mmol/L PLLC within 48 hours after arrival. CONCLUSIONS Contrary to the available information in other species, morbidity and mortality is associated with sustained low PLLC in pet rabbits, while a good prognosis is associated with an increase in PLLC. Monitoring PLLC in hospitalized rabbits is advisable.
Automated dataset generation for image recognition using the example of taxonomy

This master thesis addresses the subject of automatically generating a dataset for image recognition, which takes a lot of time when being done manually. As the thesis was written with motivation from the context of the biodiversity workgroup at the City University of Applied Sciences Bremen, the classification of taxonomic entries was chosen as an exemplary use case. In order to automate the dataset creation, a prototype was conceptualized and implemented after working out knowledge basics and analyzing requirements for it. It makes use of an pre-trained abstract artificial intelligence which is able to sort out images that do not contain the desired content. Subsequent to the implementation and the automated dataset creation resulting from it, an evaluation was performed. Other, manually collected datasets were compared to the one the prototype produced in means of specifications and accuracy. The results were more than satisfactory and showed that automatically generating a dataset for image recognition is not only possible, but also might be a decent alternative to spending time and money in doing this task manually. At the very end of this work, an idea of how to use the principle of employing abstract artificial intelligences for step-by-step classification of deeper taxonomic layers in a productive system is presented and discussed.
Adolescents’ knowledge and opinions about smoking: a qualitative study from the Jhaukhel-Duwakot Health Demographic Surveillance Site, Bhaktapur District, Nepal

Abstract Background: The use of tobacco products among adolescents in Southeast Asia represents a major public health burden. Two out of ten adolescents attending school are tobacco users and several factors influence them to initiate tobacco use. Most studies related to tobacco use are quantitative, whereas qualitative studies exploring adolescents’ smoking behavior and their views, knowledge and experiences are scarce. Objective: To gain a deep understanding of Nepalese adolescents’ knowledge and opinions about smoking and reasons for smoking initiation. Subjects: Adolescents from four secondary schools in the Bhaktapur district, Nepal. Methods: Eight focus-group discussions were conducted with 71 adolescents aged 13–16 years and from grades 8–10. Data were analyzed using manifest qualitative content analysis. Results: The participants knew that smoking represents health risks as well as socio-economic risks, but few described the addictive nature of tobacco and health risks related to passive smoking. Most participants related smoking initiation to the smoking behavior of peers and family members, but easy accessibility to cigarettes, ineffective rules and regulations, and exposure to passive smoking also created environments for smoking. Some expressed confidence to resist peer pressure and refuse to start smoking, but also expressed the need for prevention strategies in schools and for governmental initiatives, such as more strict implementation of tobacco control and regulations to prevent and reduce smoking. Conclusion: Curbing the tobacco epidemic in Nepal requires healthy public policies and multifaceted interventions to address the knowledge gap on health consequences associated with smoking among adolescents, teachers and parents/adults.
Finite Element Analysis of Reinforced Concrete Beam Retrofitted with Different Fiber Composites

Most of the reinforced concrete (RC) structures get damaged during earthquakes and they need replacements. Presently several studies have been conducted to investigate the flexural strengths of reinforced concrete members with fiber reinforced composites. This paper presents the finite element analysis of beam retrofitted with different fiber reinforced polymer (FRP) composite sheets carried out using ANSYS software. Three RC beams with different FRP composite sheet specimens were modeled using Pro-E software. The first RC beam wrapped with carbon fiber reinforced polymer (CFRP) sheet, the second with glass fiber reinforced polymer (GFRP) sheet and the third with Kevlar fiber reinforced polymer (KFRP) sheet. The performances of the above three retrofitted beams were compared with the controlled specimen and the results are presented in this paper.
A mobile immersive virtual reality cardiac auscultation app

Cardiac auscultation is a routine examination procedure that allows a medical professional to diagnose the condition of a patient's heart. The ability to interpret heart sounds is key during the diagnosis and only achieved through extensive training. Currently, there is great concern among physicians regarding the loss of cardiac auscultation skills, and the effects on proper diagnoses that may lead to inadequate treatments. Current cardiac auscultation training employs equipment that completes the diagnose without the use of a stethoscope, diminishing the amount of practice trainees obtain with it. However, despite the decreased emphasis on stethoscope training, the stethoscope remains a cost-effective tool and relevant in several examination scenarios. This paper presents the development of a mobile virtual reality prototype for cardiac auscultation training. Our approach employs a virtual reality headset to facilitate training. We analyzed the effect of visual immersion on auscultation training, by comparing its usability perception to a non-VR auscultation training app.
FGF4 and Retinoic Acid Direct Differentiation of hESCs into PDX1-Expressing Foregut Endoderm in a Time- and Concentration-Dependent Manner

Background Retinoic acid (RA) and fibroblast growth factor 4 (FGF4) signaling control endoderm patterning and pancreas induction/expansion. Based on these findings, RA and FGFs, excluding FGF4, have frequently been used in differentiation protocols to direct differentiation of hESCs into endodermal and pancreatic cell types. In vivo, these signaling pathways act in a temporal and concentration-dependent manner. However, in vitro, the underlying basis for the time of addition of growth and differentiation factors (GDFs), including RA and FGFs, as well as the concentration is lacking. Thus, in order to develop robust and reliable differentiation protocols of ESCs into mature pancreatic cell types, including insulin-producing β cells, it will be important to mechanistically understand each specification step. This includes differentiation of mesendoderm/definitive endoderm into foregut endoderm- the origin of pancreatic endoderm. Methodology/Principal Findings Here, we provide data on the individual and combinatorial role of RA and FGF4 in directing differentiation of ActivinA (AA)-induced hESCs into PDX1-expressing cells. FGF4's ability to affect endoderm patterning and specification in vitro has so far not been tested. By testing out the optimal concentration and timing of addition of FGF4 and RA, we present a robust differentiation protocol that on average generates 32% PDX1+ cells. Furthermore, we show that RA is required for converting AA-induced hESCs into PDX1+ cells, and that part of the underlying mechanism involves FGF receptor signaling. Finally, further characterization of the PDX1+ cells suggests that they represent foregut endoderm not yet committed to pancreatic, posterior stomach, or duodenal endoderm. Conclusion/Significance In conclusion, we show that RA and FGF4 jointly direct differentiation of PDX1+ foregut endoderm in a robust and efficient manner. RA signaling mediated by the early induction of RARβ through AA/Wnt3a is required for PDX1 expression. Part of RA's activity is mediated by FGF signaling.
THE EFFECTS OF AUTONOMY , EXPERIENCE , AND PERSON-ORGANIZATION FIT ON JOB SATISFACTION : THE CASE OF PUBLIC SECTOR

Although the past several decades of research on determinants of job satisfaction have generated a plethora of theoretical considerations among private and public management scholars across the globe, scholars has produced many conflicting findings. Research also shows that most of the studies are limited to the work cultures in developed western nations. Utilizing a subset of data from the International Social Survey Program on Work Orientations III module conducted in 2005, I conduct ordinary least squares multiple regression analyses to explore the relationships between job satisfaction and its key determinants in the public sector across 18 countries. For all countries, findings clearly show that organizational commitment explains the most variance in the respondents’ job satisfaction, followed by work experience and autonomy. On the autonomy, while autonomy regarding the control of hours was found to be negatively associated, the other two dimensions--ease of taking time off during working and organization of daily work– were found to be positively and significantly related to job satisfaction. In terms of work experience, the usage of past work experience and skills for the current job and helpfulness of the current work experience for future employment were both found to be positively and significantly related to job satisfaction. Job training, however, was not a significant predictor of job satisfaction.
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data

Motivation: The Illumina Infinium 450 k DNA Methylation Beadchip is a prime candidate technology for Epigenome-Wide Association Studies (EWAS). However, a difficulty associated with these beadarrays is that probes come in two different designs, characterized by widely different DNA methylation distributions and dynamic range, which may bias downstream analyses. A key statistical issue is therefore how best to adjust for the two different probe designs. Results: Here we propose a novel model-based intra-array normalization strategy for 450 k data, called BMIQ (Beta MIxture Quantile dilation), to adjust the beta-values of type2 design probes into a statistical distribution characteristic of type1 probes. The strategy involves application of a three-state beta-mixture model to assign probes to methylation states, subsequent transformation of probabilities into quantiles and finally a methylation-dependent dilation transformation to preserve the monotonicity and continuity of the data. We validate our method on cell-line data, fresh frozen and paraffin-embedded tumour tissue samples and demonstrate that BMIQ compares favourably with two competing methods. Specifically, we show that BMIQ improves the robustness of the normalization procedure, reduces the technical variation and bias of type2 probe values and successfully eliminates the type1 enrichment bias caused by the lower dynamic range of type2 probes. BMIQ will be useful as a preprocessing step for any study using the Illumina Infinium 450 k platform. Availability: BMIQ is freely available from http://code.google. com/p/bmiq/. Contact: a.teschendorff@ucl.ac. uk Supplementary information: Supplementary data are available at Bioinformatics online
knowledge in an attempt to achieve more meaningful decompositions

This paper presents a method for automatic music transcription applied to audio recordings of a cappella performances with multiple singers. We propose a system for multi-pitch detection and voice assignment that integrates an acoustic and a music language model. The acoustic model performs spectrogram decomposition, extending probabilistic latent component analysis (PLCA) using a six-dimensional dictionary with pre-extracted log-spectral templates. The music language model performs voice separation and assignment using hidden Markov models that apply musicological assumptions. By integrating the two models, the system is able to detect multiple concurrent pitches in polyphonic vocal music and assign each detected pitch to a specific voice type such as soprano, alto, tenor or bass (SATB). We compare our system against multiple baselines, achieving state-of-the-art results for both multi-pitch detection and voice assignment on a dataset of Bach chorales and another of barbershop quartets. We also present an additional evaluation of our system using varied pitch tolerance levels to investigate its performance at 20-cent pitch resolution.
A theory of how the brain might work.

I propose a speculative new version of the grandmother cell theory to explain how the brain may work, discuss how the visual system may learn to recognize 3D objects, and relate our theory to existing models of the cerebellum and motor control. The main points are: 1) the brain uses modules for multivariate function approximation as components of several information processing subsystems, 2) these modules are realized as HyperBF networks, and 3) HyperBF networks can be implemented in terms of biologically plausible mechanisms and circuitry. The theory predicts a type of population coding that represents an extension of schemes such as look-up tables.
Dynamic behavior of different quantities of osteoblasts during formation of micromass cultures

Implantation of micromass cultures of osteoblastic cells offers the possibility of scaffold free tissue engineering for example, regeneration of bone defects. However, the details of cell dynamics during the formation of these micromasses are still not well understood. This study aims to investigate and clarify the extent to which cell quantity influences the dynamics of micromass formation of osteoblastic cell cultures. For this purpose, the migration and aggregation during this process are investigated by optical inspection employing image processing software that allows for automated tracking of cell groups using digital image correlation. An exponential time behavior is observed with respect to the velocity of the cells and the distance of the cells to their common center of gravity. Characteristic time constants are derived as quantitative measures of the cell dynamics. The results indicate that the time constants strongly depend on the quantity of cells, that is, will decrease with increasing cell quantity. © 2018 International Society for Advancement of Cytometry
Coded Caching with Heterogeneous Cache Sizes and Link Qualities: The Two-User Case

The centralized coded caching problem is studied under heterogeneous cache sizes and channel qualities from the server to the users, focusing on the two-user case. A server holding $N$ files is considered to be serving two users with arbitrary cache capacities of $M_{1}$ and $M_{2}$, and it is assumed that in addition to a shared common link, each user also has a private link from the server available during the delivery phase. Optimal caching and delivery strategies that minimize the worst-case delivery latency are presented for an arbitrary N. The converse proof benefits from Tian's observation that it suffices to consider file-index symmetric caching schemes, while the achievability is obtained through memory-sharing among certain special $(M_{1}, M_{2})$ pairs. The optimal scheme is shown to exploit the private link capacities by transmitting part of the corresponding user's request in an uncoded fashion. When there are no private links, the results presented here improve upon the two known results in the literature, namely, i) equal cache capacities and arbitrary number of files; and ii) unequal cache capacities and N = 2 files.
A 3D puzzle approach to building protein–DNA structures

ABSTRACT Despite recent advances in structural analysis, it is still challenging to obtain a high-resolution structure for a complex of RNA polymerase, transcriptional factors, and DNA. However, using biochemical constraints, 3D printed models of available structures, and computer modeling, one can build biologically relevant models of such supramolecular complexes.
A Genomic Survey of HECT Ubiquitin Ligases in Eukaryotes Reveals Independent Expansions of the HECT System in Several Lineages

The posttranslational modification of proteins by the ubiquitination pathway is an important regulatory mechanism in eukaryotes. To date, however, studies on the evolutionary history of the proteins involved in this pathway have been restricted to E1 and E2 enzymes, whereas E3 studies have been focused mainly in metazoans and plants. To have a wider perspective, here we perform a genomic survey of the HECT family of E3 ubiquitin-protein ligases, an important part of this posttranslational pathway, in genomes from representatives of all major eukaryotic lineages. We classify eukaryotic HECTs and reconstruct, by phylogenetic analysis, the putative repertoire of these proteins in the last eukaryotic common ancestor (LECA). Furthermore, we analyze the diversity and complexity of protein domain architectures of HECTs along the different extant eukaryotic lineages. Our data show that LECA had six different HECTs and that protein expansion and N-terminal domain diversification shaped HECT evolution. Our data reveal that the genomes of animals and unicellular holozoans considerably increased the molecular and functional diversity of their HECT system compared with other eukaryotes. Other eukaryotes, such as the Apusozoa Thecanomas trahens or the Heterokonta Phytophthora infestans, independently expanded their HECT repertoire. In contrast, plant, excavate, rhodophyte, chlorophyte, and fungal genomes have a more limited enzymatic repertoire. Our genomic survey and phylogenetic analysis clarifies the origin and evolution of different HECT families among eukaryotes and provides a useful phylogenetic framework for future evolutionary studies of this regulatory pathway.