Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanism of cargo-directed Atg8 conjugation during selective autophagy

Selective autophagy is mediated by cargo receptors that link the cargo to the isolation membrane via interactions with Atg8 proteins. Atg8 proteins are localized to the membrane in an ubiquitin-like conjugation reaction, but how this conjugation is coupled to the presence of the cargo is unclear. Here we show that the S. cerevisiae Atg19, Atg34 and the human p62, Optineurin and NDP52 cargo receptors interact with the E3-like enzyme Atg12~Atg5-Atg16, which stimulates Atg8 conjugation. The interaction of Atg19 with the Atg12~Atg5-Atg16 complex is mediated by its Atg8-interacting motifs (AIMs). We identify the AIM-binding sites in the Atg5 subunit and mutation of these sites impairs selective autophagy. In a reconstituted system the recruitment of the E3 to the prApe1 cargo is sufficient to drive accumulation of conjugated Atg8 at the cargo. The interaction of the Atg12~Atg5-Atg16 complex and Atg8 with Atg19 is mutually exclusive, which may confer directionality to the system. DOI: http://dx.doi. org/10.7554/eLife.18544. 001
Phonon Transport and Thermal Conductivity Percolation in Random Nanoparticle Composites

In this paper, we investigated the effective thermal conductivity of three dimen- sional nanocomposites composed of randomly distributed binary nanoparticles with large differ- ences (contrast ratio) in their intrinsic (bulk) ther- mal conductivity. When random composites are made from particles with very different thermal conductivity (large contrast ratio), a continuous phase of high thermal conductivity constituent is formed when itsvolumetric concentrationreaches beyond the percolation threshold. Such a contin- uous phase of material can provide a potentially low resistance pathway for thermal transport in random composites. The percolation theory pre- dicts the thermal conductivityof the random com- positesto increase according to a scaling law with increasing concentration of the high thermal con- ductivity constituent after percolation. However, when the characteristic size of the particles in the nanocomposites is comparable to or smaller than the phonon mean free path, the phonon scattering at interfaces between two materials can introduce significant thermal resistance in the highly con- ductive phononpathway. Such interfacial thermal resistance can reduce the thermal conductivity of the nanoparticle composites. The thermal con- ductivity of the random nanoparticle composites thus deviates significantly from the predictions of the percolation theory. In this study, the Monte Carlo simulation was employed to generate ran- dom distribution of nanoparticles and to simulate the phonontransportinrandomnanoparticlecom- posites. The effects of particle size, thermal con-
Reliability and Factorial Validity of the Standard Progressive Matrices among Kuwaiti Children Ages 8 to 15 Years

The Raven Standard Progressive Matrices was administered to a sample of 6,529 children in Kuwait ranging in age from 8 to 15 years. Test-retest reliability (N = 968) ranged between . 69 and . 85, while Cronbach coefficients alpha ranged from . 88 to . 93, showing from acceptable to good temporal stability and from good to high internal consistency. The loadings of the five sets of matrices on the only salient factor ranged from . 73 to . 89 indicating the good factorial validity of the scale. The test seems useful in the Kuwaiti context.
Models and empirical data for the production of referring expressions

This paper introduces a special issue of Language, Cognition and Neuroscience dedicated to Production of Referring Expressions: Models and Empirical Data, focusing on models of reference production that make empirically testable predictions, as well as on empirical work that can inform the design of such models. In addition to introducing the volume, this paper also gives an overview of recent experimental and modelling work, focusing on two principal aspects of reference production, namely, choice of anaphoric referential expression and choice of semantic content for referential noun phrases. It also addresses the distinction between dialogue and non-dialogue settings, focussing especially on the impact of a dialogue setting on referential choice and the evidence for audience design in the choices speakers make.
The proteasome inhibitor MG-132 protects hypoxic SiHa cervical carcinoma cells after cyclic hypoxia/reoxygenation from ionizing radiation.

INTRODUCTION Transient hypoxia and subsequent reoxygenation are common phenomena in solid tumors that greatly influence the outcome of radiation therapy. This study was designed to determine how varying cycles of hypoxia/reoxygenation affect the response of cervical carcinoma cells irradiated under oxic and hypoxic conditions and whether this could be modulated by proteasome inhibition. MATERIALS AND METHODS Plateau-phase SiHa cervical carcinoma cells in culture were exposed to varying numbers of 30-minute cycles of hypoxia/reoxygenation directly before irradiation under oxic or hypoxic conditions. 26S Proteasome activity was blocked by addition of MG-132. Clonogenic survival was measured by a colony-forming assay. RESULTS Under oxic conditions, repeated cycles of hypoxia/reoxygenation decreased the clonogenic survival of SiHa cells. This effect was even more pronounced after the inhibition of 26S proteasome complex. In contrast, under hypoxic conditions, SiHa cells were radioresistant, as expected, but this was increased by proteasome inhibition. CONCLUSIONS Proteasome inhibition radiosensitizes oxygenated tumor cells but may also protect tumor cells from ionizing radiation under certain hypoxic conditions.
The TRANSFAC system on gene expression regulation

The TRANSFAC database on transcription factors and their DNA-binding sites and profiles (http://www.gene-regulation.de/) has been quantitatively extended and supplemented by a number of modules. These modules give information about pathologically relevant mutations in regulatory regions and transcription factor genes (PathoDB), scaffold/matrix attached regions (S/MARt DB), signal transduction (TRANSPATH) and gene expression sources (CYTOMER). Altogether, these distinct database modules constitute the TRANSFAC system. They are accompanied by a number of program routines for identifying potential transcription factor binding sites or for localizing individual components in the regulatory network of a cell.
Cluster Analysis Through Model Selection

Clustering is an important and challenging statistical problem for which there is an extensive literature. Modelling approaches include mixture models and product partition models. Here we develop a product partition model and search algorithm driven by Bayes factors from intrinsic priors. The priors we develop for the partitions, and the number of clusters in the partition, lead to finding partitions with a smaller number of clusters, which does not happen if a uniform prior is used. We argue that this is desirable, since one reason for doing a cluster analysis is to find a small number of clusters that can help to understand underlying structure. Moreover, we are also able to establish that our procedure is consistent, and hence will find the true underlying structure as the sample size increases. We illustrate our cluster algorithm with both simulated and real examples. Distinguished Professor, Department of Statistics, University of Florida, Gainesville, FL 32611. Supported by National Science Foundation Grants DMS-0631632 and SES-0631588, and NIH grant 1R01GM081704. Email: casella@stat.ufl. edu. Professor, Department of Statistics, University of Málaga. Email: fj giron@uma.es. Professor, Department of Statistics, University of Granada, 18071, Granada, Spain. Supported by Ministerio de Ciencia y Tecnoloǵıa, Grant SEJ-65200 and Junta de Andalućıa Grant SEJ-02814. Email: emoreno@ugr.es.
A Descriptor based on Intensity Binning for Image Matching

This paper proposes a method for extracting image descriptors using intensity binning. It is based on the fact that, when the intensities of the interest regions are quantized, the pixels retain their bin labels under common image deformations, up to a certain degree of perturbation. Consequently, the spatial configuration and the shape of the connected regions of pixels belonging to each bin become resilient to noise, which, as a whole, capture the topography of the intensity map pertaining to that region. We examine the effect of classical image deformations on this representation and seek to find a compact yet robust representation which remains unperturbed in the presence of noise and image deformations. We use Oxford dataset in our experiments and the results show that the proposed descriptor gives a better performance than the existing methods for matching two images under common image deformations.
GENETIC STRUCTURE OF NORWAY SPRUCE (PICEA ABIES): CONCORDANCE OF MORPHOLOGICAL AND ALLOZYMIC VARIATION

This study describes the population structure of Norway spruce (Picea abies) as revealed by protein polymorphisms and morphological variation. Electrophoretically detectable genetic variability was examined at 22 protein loci in 70 populations from the natural range of the species in Europe. Like other conifers, Norway spruce exhibits a relatively large amount of genetic variability and little differentiation among populations. Sixteen polymorphic loci (73%) segregate for a total of 51 alleles, and average heterozygosity per population is 0.115. Approximately 5% of the total genetic diversity is explained by differences between populations (GST = 0.052), and Nei's standard genetic distance is less than 0.04 in all cases.
2019 LOCALIZATION AND NAVIGATION OF MOBILE ROBOTS IN AN ENVIRONMENT WITH VARIABLE

S . U d o v e n k o Doctor of Technical Sciences, Professor, Head of Department Department of Informatics and Computer Technique Simon Kuznets Kharkiv National University of Economics Nauky аve. , 9-A, Kharkiv, Ukraine, 61166 Е-mail: serhiy.udovenko@hneu.net A . S o r o k i n Assistant Department of Electronic Computers Kharkiv National University of Radio Electronics Nauky ave., 14, Kharkiv, Ukraine, 61166 E-mail: anton.sorokin@nure.ua Запропоновано метод локалізації та навігації мобіль­ ного робота в середовищі зі змінними властивостями за умов обмежених можливостей для дистанційного керування, що передбачає можливість перемикання режиму керування роботом в стан автономної навіга­ ції. Метод базується на комбінованому застосуванні нечіткої моделі і RL­алгоритму, який дозволяє покра­ щувати набір нечітких правил, використовуючи сигна­ ли підкріплення Запропоновано удосконалення методу локалізації мобільних об’єктів з використанням тех­ нології iBeacon та NFC у просторі з відомими картами приміщень, що дозволяє скоротити кількість необхід­ них для локалізації передавачів. В роботі модифіковано алгоритм визначення марш­ руту руху мобільних об’єктів з використанням мето­ ду Jump Point Search (пошук шляху по стрибковим точкам). Суть модифі кації полягає у використанні в алгоритмі манхеттенської відстані між координа­ тами точок маршруту. Це дозволяє зменшити вплив окремих викидів на результати обчислень в порівнянні з базовим алгоритмом. Отримані результати можуть бути використані в системах керування мобільним роботом в середовищі зі змінними властивостями за умов обмежених мож­ ливостей для дистанційного керування. Результати тестування запропонованих методів та відповідних обчислювальних процедур підтверджують їх працез­ датність та перспективи практичного застосування. Застосування наведеного підходу дозволяє врахову­ вати конфігурації перешкод та корегувати страте­ гію навігації для поліпшення якості системи (у 95 % тестових експериментів мобільний робот досягав мети в середовищі з різними типами перешкод) Ключові слова: мобільний об’єкт, локалізація, авто­ номна навігація, нечіткий регулятор, керування з під­ кріпленим на вчанням UDC 004.852 DOI: 10.15587/1729-4061.2019. 164337
Multispectral imaging for highly accurate analysis of tumour‐infiltrating lymphocytes in primary melanoma

The quality and quantity of the infiltration of immune cells into tumour tissues have substantial impacts on patients’ clinical outcomes, and are associated with response to immunotherapy. Therefore, the precise analysis of tumour‐infiltrating lymphocytes (TILs) is becoming an important additional pathological biomarker. Analysis of TILs is usually performed semiquantitatively by pathologists on haematoxylin and eosin‐stained or immunostained tissue sections. However, automated quantification outperforms semiquantitative approaches, and is becoming the standard. Owing to the presence of melanin pigment, this approach is seriously hampered in melanoma, because the spectrum of melanin lies close to that of commonly used immunohistochemical stains. Aim of this study is to overcome the technical issues due to the presence of melanin for an automated and accurate quantification of TILs in melanoma.
Absolute Electron Emission Calibration: Round Eobin Tests of Au and Graphite

This study presents a round robin comparison of absolute electron yields of conducting and insulating materials performed in four international laboratories. Measurements are reported for two standard elemental conducting samples with reproducible sample preparation for Au and highly oriented pyrolytic graphite (HOPG). The primary objectives of the study were to determine the consistency and uncertainties of these absolute yields measurements, and to investigate the effects of the similarities and differences of the diverse facilities. In this initial round robin study, HOPG total electron yield results were found to be more reproducible than those for Au. Surface contamination significantly affected the total electron yield, even for relatively inert conductive samples like Au and HOPG.
Numerical Simulations of Field Values, Wave Impedance, and Received Power Inside a Nonideal Reverberation Chamber

The behavior of the ensemble averaged wave impedance computed by the rectangular field components and the impedance computed by the total field is numerically studied for a nonideal reverberation chamber. Evident departures from the medium intrinsic impedance are observed for the rectangular components when the ratio of the means and the mean of the ratios are exchanged. The power received by the antenna placed in the chamber is compared to that computed by the total field components, the rectangular field components using the wave impedance and the intrinsic impedance.
Assessing the Open Source Development Processes Using OMM

The assessment of development practices in Free Libre Open Source Software (FLOSS) projects can contribute to the improvement of the development process by identifying poor practices and providing a list of necessary practices. Available assessment methods (e.g., Capability Maturity Model Integration (CMMI)) do not address sufficiently FLOSS-specific aspects (e.g., geographically distributed development, importance of the contributions, reputation of the project, etc.). We present a FLOSS-focused, CMMI-like assessment/improvement model: the QualiPSo Open Source Maturity Model (OMM). OMM focuses on the development process. This makes it different from existing assessment models that are focused on the assessment of the product. We have assessed six FLOSS projects using OMM. Three projects were started and led by a software company, and three are developed by three different FLOSS communities. We identified poorly addressed development activities as the number of commit/bug reports, the external contributions, and the risk management. The results showed that FLOSS projects led by companies adopt standard project management approaches as product planning, design definition, and testing, that are less often addressed by community led FLOSS projects. The OMM is valuable for both the FLOSS community, by identifying critical development activities necessary to be improved, and for potential users that can better decide which product to adopt.
Power loss analysis of five-level inverters for grid tie photovoltaic system

By means of simulation-based study a loss analysis is performed on the five-level inverters for grid tie photovoltaic application. The essential objective of this analysis is the quantification of the possible improvement on the efficiency of the inverter by reducing the switching frequency applied in the conventional two-level inverter. Besides the benefit of five-level providing a higher power quality and lowering the switching loss, the drawback of high conduction loss involving many devices in series is evidenced in this paper. The simulation results show that the five-level inverter topologies achieve over 98% efficiency for switching frequencies ranging from 1 kHz to 8 kHz. However, the conduction loss of the inverter is significantly higher (over 10 times) than the switching loss.
A Genome‐Wide Study of Lupus

Abstract: Systemic lupus erythematosus (SLE) is a complex autoimmune disease in which genetics is one of the underlying risk factors. Complicating the analysis of SLE is the fact that the phenotype is heterogeneous, with variations in clinical features, and subgroups are associated with a variety of different autoantibodies. Many association studies of candidate genes as well as linkage studies have generated significant results, highlighting the multigenetic component of the disease. Those findings need to be replicated by independent laboratories and many other genes still remain to be identified. Here, we present our findings on the first genome‐wide association study performed in 105 Caucasian patients and controls using the Affymetrix NspI array. The SLE patients studied here were all characterized by the presence of autoantibodies against the U1–6 small nuclear ribonucleoprotein antigen spliceosomal complex. Testing each SNP individually for association with disease, we identified 7 markers with an uncorrected P‐value < 0.0001. Of those, three were in reported regions of linkage, namely 20p12, 2q37, and 4p15. To increase the power of our study, we included 60 controls corresponding to the parents from the publicly available CEPH families. The analysis of the 165 cases and controls leads to 28 SNPs being associated with an uncorrected P‐value < 0.0001.
Comprehensive assessment of patent ductus arteriosus by echocardiography before transcatheter closure.

BACKGROUND Anatomic type and angiographic measurements of patent ductus arteriosus (PDA) are used to determine the suitability of transcatheter closure (TCC). The purpose of this study is to evaluate whether these PDA features can be obtained by 2-dimensional echocardiography (2DE). METHODS We retrospectively compared PDA measurements and type from 36 patients submitted to TCC between November 1995 and October 2000. RESULTS The patient age ranged between 2 months to 10.5 years (median = 1.2 years). A significant correlation was found between measurements of PDA minimal diameter (R(2) = 0.88) and diameter at aortic ostium (R(2) = 0.72); whereas a poor correlation existed between measurements of the ampulla length. The 2DE and angiographic PDA classification were concordant in 31 of 36 (86%) patients. CONCLUSION Our data support the use of 2DE measurements of PDA minimal diameter and PDA diameter at the aortic end to assess suitability for TCC. In the majority of cases, PDA type can be diagnosed by 2DE.
Why Do Women Have Back Pain More Than Men?: A Representative Prevalence Study in the Federal Republic of Germany

ObjectivesIn comparison with men, women have a healthier lifestyle, are more rarely overweight, have less stressful occupations, or are not employed outside the home. The “gender pain bias” is the fact that women nevertheless have a higher prevalence of back pain. This paper looks at the possible underlying reasons for this as yet unexplained gender difference, using Stokols' socioecological health model as a basis. MethodsThe first National Health Survey for the Federal Republic of Germany was carried out from October 1997 to March 1999. It comprised a representative total sample of 5315 persons between the ages of 20 and 64. The participants took part in a medical examination and answered a self-report form. χ2 test and logistic regression analyses were used to investigate correlations between self-reported low back pain and gender-specific biopsychobehavioral and sociophysical environmental factors. ResultsSeven-day back pain prevalence in the Federal Republic of Germany is 32% for men and 40% for women. Prevalences are significantly higher for overweight subjects, persons with a marked somatization tendency or a low level of social support, physically inactive individuals, smokers, elderly subjects, the nonemployed, “blue collar workers” and lower socioeconomic groups. From a multivariate perspective, however, none of these factors reduces (and hence sufficiently explains) the gender difference. Factoring in the gender-specific somatization tendency reduces the odds ratios of women versus men from 1.42 to 1.23. DiscussionIn view of the gender difference in pain prevalence, which remains stable despite a multivariate perspective, there is clearly a need for more research into the reasons underlying the gender difference. We believe that future studies should look at rarely investigated constructs such as “sex role expectancies,” “anxiety,” “ethnicity,” and “family history” and take anatomic differences in muscle strength into account.
Toward Social Awareness in the Smart Grid

Advances in power electronics, communications and control technologies employed by Electric Utilities, have been gradually shifting the way the grid is being operated for many years. These, together with small scale renewable energy and micro-generation capabilities are now forcing the philosophy of grid operation to be rethought from the ground up. The future is likely to be a network of power prosumers (producer-consumers) who must be managed by a central coordinating body. Often overlooked, however, is the fact that increased data can give us not only additional information about the system but also about customers. This paper posits the idea of building more social sensitivity into the the operation of the grid to enhance demand side management, emergency management and building Rawlsian principles into prosumer interactions with the utility. It also gives a conceptual overview of the infrastructure topologies required to enable this shift, but does not concern itself with auxiliary matters such as cyber security.
EMPSACO: AN IMPROVED HYBRID OPTIMIZATION ALGORITHM BASED ON PARTICLE SWARM, ANT COLONY AND ELITIST MUTATION ALGORITHMS

This research presents an efficient and reliable swarm intelligence-based approach, ant colony optimization and elitist-mutated particle swarm optimization. Methods of particle swarm optimization (PSO) and ant colony optimization (ACO) and elitist mutation particle swarm optimization (EMPSO) are co-operative, population-based global search swarm intelligence metaheuristics. PSO is inspired by social behavior of bird flocking or fish schooling, while ACO imitates foraging behavior of real life ants and Elitist mutation taken from genetic mutation from genetic algorithm techniques. In this study, we explore a simple approach to improve the performance of the PSO method for optimization of multimodal continuous functions. The proposed EMPSACO algorithm is tested on several test functions from the usual literature and compared with PSO, PSACO and GA (Genetic Algorithm). Results showed that the effectiveness and efficiency of the proposed EMPSACO method had suitable accuracy to optimize multimodal functions.