Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding gene regulatory mechanisms of mouse immune cells using a convolutional neural network

Cell differentiation is controlled via complex interactions of genomic regulatory sites such as promoters and enhancers that lead to precise cell typespecific patterns of gene expression through a process that is not yet well understood. Local chromatin accessibility at these sites is a requirement of regulatory activity, and is therefore an important component of the gene regulation machinery. To understand how DNA sequence drives local chromatin accessibility within the context of immune cell differentiation, we examined a dataset of open chromatin regions (OCRs) derived with the ATAC-seq assay from 81 closely related mouse immune cell types. We trained a model that predicts local chromatin accessibility in each cell type based on DNA sequence alone, then analyzed the model to extract informative sequence features. We selected and optimized a convolutional neural network (CNN), which we named AI-TAC, that takes as input a 250bp DNA sequence of a potential OCR and predicts the relative chromatin activity at that OCR across the 81 different immune cell types in our dataset. Test dataset results showed that for many OCRs, AI-TAC is able to predict chromatin state with a high degree of accuracy, even differentiating between closely related cell types. Using CNN interpretability methods we were able to identify sequence motifs that are used by the model to make its predictions, many of which match closely to known transcription factor (TF) binding sites. The cell type specific influence assigned to each motif by AI-TAC in many instances recapitulates prior biological knowledge about the role of these TFs in immune cell differentiation, lending credibility to our model and interpretation methods. Finally, we attempt to discern if the model detected any combinatorial activity between TFs that is predictive of chromatin accessibility. In summary, we showed that a CNN can be trained to discern the chromatin accessibility among even highly similar cell types, and that biologically relevant features can be extracted from the model using deep learning interpretation methods.
Dwa oblicza wolnych rodników tlenowych The two faces of reactive oxygen species

Summary Oxidative stress has been implicated in playing a crucial role in aging and in the pathogeneses of a number of diseases, including neurodegenerative disorders such as Alzheimer’s disease. Oxidative stress occurs due to an imbalance in prooxidant and antioxidant levels. Reactive oxygen species (ROS) are highly reactive and may modify and inactivate proteins, lipids, DNA, and RNA and induce cellular dysfunctions. To prevent free radical-induced cellular damage, the organism has developed a defense mechanism, the antioxidative system. This system includes antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSHPx), and glutathione reductase (GSSGR) and low-molecular antioxidants such as glutathion and plasma proteins. Glutathion plays a key role in maintaining the physiological balance between prooxidants and antioxidants. Plasma proteins can inhibit ROS generation and lipid peroxidation by chelating free transition metals. The major exogenous antioxidants are vitamins E, C, and A.
Extension Complexity via Lifting LP Hierarchy Lower Bounds

Extension complexity measures the minimum size of all possible LP formulations that characterize a given polytope. But such lower bounds are generally not very easy to establish. On the other hand, LP hierarchies are restricted kinds of LP formulation, which is well-structured and thus relatively easier to analyze and prove size lower bound for them. In the past decade there’s a line of research that lift s existing hierarchy lower bound to general LP size lower bound. This has resulted in the breakthrough result of [CLRS13], which showed that approximating maximum constraint satisfaction problems requires quasi-polynomial size LPs. Their result is later improved to sub-exponential by [KMR17]. Based on their results, people are able to prove extension complexity lower bounds for a much richer set of problems. In this note we’ll expalain the result of [CLRS13] and some subsequent ones, in particular, an extension complexity lower bound for approximating vertex-cover [BFPS15]. We’ll also briefly discuss a very related line of research — SDP extension complexity, which studies the minimum size of SDP formulations. One of the most important paper in the recent years proves a quasi-polynomial SDP size lower bound for approximate max-3sat and sub-exponential SDP size lower bound for the cut, TSP, and stable set polytopes[LRS15]. Remarkably, its overall strategy almost parallels [CLRS13], only lifting from SDP hierarchy lower bounds.
Keratinase of a streptomycete.

Keratinase produced from Streptomyces Sp.A11 decomposed human hair, chicken feather, wool, silk and pure keratin extracted from human epidermis. Purification of the enzyme by DEAE-cellulose column chromatography resulted in 7.5-fold increase in activity relative to the activity of the culture filtrate. The enzyme was inducible, extracellular, homogeneous with a molecular weight of 49,000. The enzyme activity was inhibited by reduced glutathione, phenylmethyl sulphonyl fluoride and 2-mercaptoethanol.
Interactive comment on “Development of the global atmospheric general circulation-chemistry model BCC-GEOS-Chem v1.0: model description and evaluation” by Xiao Lu et al

This paper describes a framework and evaluation of a novel model framework which incorporates the GEOS-Chem 1-D atmospheric chemistry component into a the Beijing Climate Center’s Atmospheric GCM (BCC-AGCM). With this combination successfully established, the authors evaluate the model in comparison with a suite of observations, including for tropospheric ozone, OH concentrations, and methane chemical lifetimes. They also compare satellite observations of various important atmospheric measurements, including NO2, CO, SO2, CH2O, and AOD. The work is a significant step forward in the development of Earth System Models in China and is clearly relevant to readers of GMD, and should be accepted pending the authors addressing a few relatively minor points relating to the reproducibility and presentation quality of their
Thermophysical Properties of Nanomodified Liquids

This paper attempts to determine thermophysical properties such as density, heat capacity and thermal conductivity for four types of nanoparticle suspension in water by using theoretical models. Three concentrations of 0.01, 0.05 and 0.1 wt. % nanoparticles were used at temperatures 35, 40 and 45 °C. It also attempts to present the properties of (CNT Taunit M) and the method of its preparation. It was observed that thermal conductivity and density increased, and contrariwise, specific heat decreased with an increase in volume concentration at various temperatures.
Aspects of Spirituality in Eco-Lodges’ Landscape in Iran (from the Perspective of Tourists)

It is truly undeniable that tourism is a system leading to epistemology and resulting in spiritual growth and excellence. The mission of the journey lies in its spiritual achievements and eco-lodges provide the potential context for mutual interconnections and gaining meaning and excellence. Therefore, lacking emphasis on spiritual potentials of eco-lodges in the accommodation sector is the main concern of this research. The present study aims to identify the factors influencing the landscape development of eco-lodges from the viewpoint of tourists to explain and analyze the realization of the spiritual landscape of eco-lodges via the perception of the eco-lodges’ landscape. The main concern of this qualitative research is seeking what a tourist sees, what he understands, how the type of accommodation would lead him from objectivity to subjectivity and ultimately, how the perception of the spiritual landscape from tourist’s view is. Answering research questions through the qualitative International Journal of Tourism and Spirituality, 4(1), Summer and Autumn, 2019 58 method with an interpretive approach and inductive strategy has been conducted by a semi-structured interview tool. Besides, the research data is gathered via two phases of coding the general concepts and classification of concepts based on the frequency. Lastly, the findings have been analyzed and interpreted through a conceptual framework. Based on research results, staying in eco-lodge causes leading resident tourist from objectivity to subjectivity and this is derived from perception of spiritual landscape. The components of the eco-lodges’ landscape adapting with three parameters of spirituality in tourism, lead tourists to the perception of the spiritual landscape as well as the realization of the mutual understanding of nature and man in the journey and the achievement of the meaning and spirit through accommodation in eco-lodges.
In Transistor Circuits 1 . Mainly on fundamental noise concepts

An enormous amount of literature exists on the theory of random noise, the theory and practice of low-noise amplifier design, and measuring techniques involving noise. However, for most engineers and physicists not specializing on noise topics as such, the need is to extract from this mass of know­ ledge a certain minimum amount of basic theoretical and practical information, suffici­ ent to enable the normal types of noise problem which arise in the course of elec­ tronic work to be understood and dealt with in an intelligent manner. The aim in this article is to provide this minimum basic information in, it is hoped, an easy-to-assimilate form, and to quote, for the benefit of those desiring to delve a little more deeply, a few references which have been found particularly worthy of attention.
Relation between body composition , fat distribution , and lung function in elderly men 1 – 3

Background: Body composition changes with age, with increases in fat mass and visceral fat and declines in skeletal muscle mass; lung function also declines with age. Age-related changes in body composition and fat distribution may be associated with the pulmonary impairment observed in the elderly. Objective: Our goal was to evaluate the relations between body composition, fat distribution, and lung function in elderly men. Design: We studied 97 men aged 67–78 y with body mass indexes (BMIs; in kg/m2) ranging from 19.8 to 37.1. Body composition was evaluated by using dual-energy X-ray absorptiometry and fat distribution was evaluated by using waist and hip circumferences, waist-to-hip ratio, and sagittal abdominal diameter (SAD). Spirometry was done in all subjects and the distance walked by each subject during a 6-min walking test was evaluated as was leg strength. Results: A significant negative correlation was found between adiposity, fat distribution indexes, forced vital capacity (FVC), and forced expiratory volume in 1 s (FEV1). A positive correlation was found between fat-free mass and FVC. After adjustment for age, height, and weight, SAD still correlated negatively with FVC and FEV1 (r = 0.367 and 0.348, respectively; P < 0.01), whereas percentage body fat and fat mass correlated negatively and fat-free mass correlated positively with FVC (r = 0.313, 0.323, and 0.299, respectively; all P < 0.01). After the sample was subdivided by tertile of fat-free mass adjusted for age and BMI, FVC and FEV1 were significantly lower in the lowest fat-free mass tertile (P < 0.01). Stepwise multiple regression analysis performed with use of lung function variables as the dependent variables and age, height, fat mass, fat-free mass, waist circumference, and SAD as the independent variables showed that 3 variables entered the regression for predicting FVC: height, which entered the regression first; SAD, which entered second; and fat-free mass, which entered third. Only 2 variables entered the regression for predicting FEV1: height, which entered the regression first, and SAD, which entered second. Conclusion: Our cross-sectional data show a significant association between body composition, fat distribution, and lung function in elderly men. Am J Clin Nutr 2001;73:827–31.
Cross-modal representation alignment of molecular structure and perturbation-induced transcriptional profiles

Modeling the relationship between chemical structure and molecular activity is a key goal in drug development. Many benchmark tasks have been proposed for molecular property prediction, but these tasks are generally aimed at specific, isolated biomedical properties. In this work, we propose a new cross-modal small molecule retrieval task, designed to force a model to learn to associate the structure of a small molecule with the transcriptional change it induces. We develop this task formally as multi-view alignment problem, and present a coordinated deep learning approach that jointly optimizes representations of both chemical structure and perturbational gene expression profiles. We benchmark our results against oracle models and principled baselines, and find that cell line variability markedly influences performance in this domain. Our work establishes the feasibility of this new task, elucidates the limitations of current data and systems, and may serve to catalyze future research in small molecule representation learning.
A Survey of Barley PIP Aquaporin Ionic Conductance Reveals Ca2+-Sensitive HvPIP2;8 Na+ and K+ Conductance

Some plasma membrane intrinsic protein (PIP) aquaporins can facilitate ion transport. Here we report that one of the 12 barley PIPs (PIP1 and PIP2) tested, HvPIP2;8, facilitated cation transport when expressed in Xenopus laevis oocytes. HvPIP2;8-associated ion currents were detected with Na+ and K+, but not Cs+, Rb+, or Li+, and was inhibited by Ba2+, Ca2+, and Cd2+ and to a lesser extent Mg2+, which also interacted with Ca2+. Currents were reduced in the presence of K+, Cs+, Rb+, or Li+ relative to Na+ alone. Five HvPIP1 isoforms co-expressed with HvPIP2;8 inhibited the ion conductance relative to HvPIP2;8 alone but HvPIP1;3 and HvPIP1;4 with HvPIP2;8 maintained the ion conductance at a lower level. HvPIP2;8 water permeability was similar to that of a C-terminal phosphorylation mimic mutant HvPIP2;8 S285D, but HvPIP2;8 S285D showed a negative linear correlation between water permeability and ion conductance that was modified by a kinase inhibitor treatment. HvPIP2;8 transcript abundance increased in barley shoot tissues following salt treatments in a salt-tolerant cultivar Haruna-Nijo, but not in salt-sensitive I743. There is potential for HvPIP2;8 to be involved in barley salt-stress responses, and HvPIP2;8 could facilitate both water and Na+/K+ transport activity, depending on the phosphorylation status.
OP-ANNO190273 510..519

Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France; King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; Section of Cancer Surveillance, International Agency for Research on Cancer, Lyon, France; Division of Clinical Epidemiology and Aging Research, Division of Preventive Oncology and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg; National Center for Tumor Diseases (NCT), Heidelberg, Germany; Institute of Genetic Medicine, Newcastle University, Newcastle, UK; Center for Public Health Genomics, University of Virginia, Charlottesville; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, USA; School of Public Health, Imperial College London, London, UK; Harvard T.H. Chan School of Public Health, Boston; Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, USA; Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK; Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, Australia; SIRIC CARPEM, APHP European Georges Pompidou Hospital Paris, Universite Paris Descartes, Paris, France; Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle; Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina, Chapel Hill; Memorial Sloan Kettering Cancer Center, New York, USA; Section of Genetics, International Agency for Research on Cancer, Lyon, France
A N E FFICIENT A NALYTICS I N C REDIT C ARD F RAUD D ETECTION U SING R ESOLUTION C LASSIFICATION (R C ) T ECHNIQUE

: Data mining is the process of extracting patterns from data and discovering knowledge from large amounts of data stored either in databases or warehouses. Data mining is becoming an increasingly important tool to transform these data into information. Data analytics is a procedure of examining, removing, altering and displaying information with the objective of finding helpful data, proposing conclusions and supporting basic guidance. Classification is a data mining (machine learning) technique used to predict group membership for data instances.Credit cards are a significant component of everyday life. An extraordinary highly improved society payments is the credit(smart) card payments, particularly for ordering the product through E-commerce which probably produce the result of naturally improving fake operations which shows the fast evolution in electronic commerce, the usage of credit cards for online purchase has risen dramatically, causing a great explosive in smart(credit) card offence. Implementing effective abuse identification systems has expand into essential for overall card providing banks to decrease their loss in cost. In true life, fake transaction(business) are interspersed with genuine transaction and Matching patterns which leads to recognize them uncorrectly. Thus there’s a significant thing requirement to combine both Methods of identification of error and violence. Many modern techniques occupying the data (information) mining. The credit (smart) card abuse was reduced via to using the RC algorithm. Classifier for building linear supplying regression models. LogB with RC functions as base learners is employed for fitting the supplying models. The optimum range of LogB continues (maintaining) to execute is cross-validated, that results in automatic attribute choice. The optimal amount of iterations to be performed by LogB is cross-validated, leading to the automatically select the attributes. Through this, the credit card fraud detected on comparing with various previous techniques.
RELATIONSHIP BETWEEN LEVEL OF SERUM ADIPONECTIN AND FRAILTY IN ELDERLY PATIENTS WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE

Elderly are especially prone to the adverse health effects of chronic obstructive pulmonary disease (COPD). COPD is a typical aging disease which is found to be about 12% in the age group more than 64 years old. Frailty is an important geriatics syndrome, while adiponectin is an important adipokine that regulate homeostasis of energy. Adiponectin is affected by age, especially in males. Adiponectin levels increases as subcutaneous fat cells in older men decreases. Increased adiponectin can lead to muscle wasting which will further reduce body weight and body mass index (BMI), which indirectly also increases the degree of frailty. Until now the relationship between adiponectin with frailty degree in advanced COPD is still unknown.The aims of this study was to investigate the relationship between plasma adiponectin level and frailty in COPD elders. This was an observational analytic cross-sectional study. All anthropometric parameters, including weight, height, and body mass index (BMI), were measured. Adiponectin was measured by ELISA methods obtained from venous blood samples. Aged more than or equal to 60 years old, the patients underwent spirometry to determine the degree of airflow limitation and the degree of frailty defined by the Fried criteria. Statistic analysis used Rank Spearman. Thirty-eight male COPD patients became the subject of the study. The average age was 70-74 years, with a total of 13 robust, 12 prefrails and 13 frail patients. Level of adiponectin (mean and SD) in robust, prefrail, and frail were 6.84+ 2.66 , 6.58 + 4.27, and 11.62 + 4.90 respectively, p=0.015. Further analysis showed that level of adiponectin rose progresively with an increasing number of components of frailty. The degree of obstruction mostly with mild (42.1%), and no subjects with very severe. There were an increase in serum adiponectin levels in all subjects. In conclusion, level of adiponectin serum correlates positively with the degree of frailty.
What is the source of L 1 attrition ?

The recent hypothesis that L1 attrition affects the ability to process interface structures but not knowledge representations (Sorace, 2011) is tested by investigating the effects of recent L1 re-exposure on antecedent preferences for Spanish pronominal subjects, using offline judgements and online eye-tracking measures. Participants included a group of native Spanish speakers experiencing L1 attrition (‘attriters’), a second group of attriters exposed exclusively to Spanish before they were tested (‘re-exposed’), and a control group of Spanish monolinguals. The judgement data shows no significant differences between the groups. Moreover, the monolingual and re-exposed groups are not significantly different from each other in the eye-tracking data. The results of this novel manipulation indicate that attrition effects decrease due to L1 re-exposure, and that bilinguals are sensitive to input changes. Taken together, the findings suggest that attrition affects online sensitivity with interface structures rather than causing a permanent change in speakers’ L1 knowledge representations.
Lagrangian Flow Network: a new tool to evaluate connectivity and understand the structural complexity of marine populations

Assessing the spatial structure and dynamics of marine populations at the various scales characterizing the oceanic systems is still a major challenge for ecologists. We present a new methodological framework called Lagrangian Flow Network (LFN) which allows a systematic characterization of multi-scale dispersal and connectivity of early life history stages of marine organisms. The network is constructed by subdividing the basin into an ensemble of sub-regions which are interconnected through the transport of propagules by ocean currents. The present version allows the identification of hydrodynamical provinces and the computation of connectivity proxies measuring retention and exchange of larvae. Due to our spatial discretization and subsequent network representation, as well as our Lagrangian approach, further methodological improvements are handily accessible. It permits a better characterization of population connectivity at multiple scales and it informs its ecological and managerial interpretations toward a sound management and protection of marine ecosystems.