Miracle-dz/UniFAR-FTUs huggingface dataset:
Challenges in the Multivariate Analysis of Mass Cytometry Data: The Effect of Randomization

Cytometry by time‐of‐flight (CyTOF) has emerged as a high‐throughput single cell technology able to provide large samples of protein readouts. Already, there exists a large pool of advanced high‐dimensional analysis algorithms that explore the observed heterogeneous distributions making intriguing biological inferences. A fact largely overlooked by these methods, however, is the effect of the established data preprocessing pipeline to the distributions of the measured quantities. In this article, we focus on randomization, a transformation used for improving data visualization, which can negatively affect multivariate data analysis methods such as dimensionality reduction, clustering, and network reconstruction algorithms. Our results indicate that randomization should be used only for visualization purposes, but not in conjunction with high‐dimensional analytical tools. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
Chart-making of the Earth''s main magnetic field

[1] Methods of magnetic prospecting have long history. Investigations of geomagnetism started when magnetic iron ore (rock rich of magnetite) was found. It is believed that a few hundreds years B. C. the Chinese were the first ones to use properties of magnetic iron ore to point out the directions. However, a thought that the Earth itself acts as a magnet appeared considerably later. First information on the use of magnetic compass in Europe relates to the end of XII century. Ideas on geomagnetic field, its direction and effects were put onto scientific grounds after the book “About magnet, magnetic bodies and about big magnet – the Earth” had been published. Systematic quantitative investigations on the direction of the magnetic field of the Earth commenced in London over the lifetime of Gilbert. In Sweden as early as 1640, observations of local anomalies of the geomagnetic field direction were used for the prospecting of the iron ore. Sphere of application of magnetic methods covers different areas of geomagnetism, magnetism of rocks, paleomagnetism, magnetic prospecting, navigation on the basis of magnetometry, effects of magnetic field variation on human health, including crews of air-crafts, etc. Variety of applications of magnetic methods is so broad that it is practically impossible to consider all aspects in one paper. Apart from that, by now the most effective results of research of geomagnetism are connected with getting data on such imagination taking hypotheses as continental drift, sea floor spreading and plates tectonics, movement of geographical and magnetic poles, etc. Intensity of geomagnetic field is measured from satellites, air-crafts/planes, ships, as well as in observatories, and then classified, formed and recorded every 5 years since 1945. Nonsystematic measurements have been carried out considerably earlier. However, until now there is no sufficient visual interpretation of data on geomagnetic field with the purpose of its reliable analysis and study for the further fundamental and applied research. This work offers cartographic method of interpretation of geomagnetic field measurements, creation of geographic maps of the magnetic field of the Earth, and creation of geoinformation system.
ORGANISATIONAL STRESS AND EMPLOYEES' INTENTION TO QUIT AMONGST ADMINISTRATIVE PERSONNEL AT THE UNIVERSITY OF FORT HARE, EASTERN CAPE, SOUTH AFRICA

This research study investigated the effect of organisational stress and the employees’ intention to quit among administrative personnel at the University of Fort Hare. The main objectives of this study were determining the effects of organisational stress on employees’ intention to quit, and providing results that would lead to a deeper understanding of the nature and extent of the relationship between organisational stress and intention to quit. A survey method was adopted for this study. A questionnaire comprising of three sections: biographical information, ERI questionnaire for stress, turnover intention scale, was administered to non-academic support personnel of the University of Fort Hare in all three campuses namely Alice, Bhisho, and East London. Simple random sampling was used to select the participants. The literature reviewed displayed a great need for managers to understand organisational stress and its causes, and how to manage and cope with stress so as to avoid losing employees, especially highly competent employees. The study yielded results that show that there is a relationship between organisational stress and employees’ intention to quit.
The relative biological effectiveness of proton irradiation in dependence of DNA damage repair.

Clinical parameters and empirical evidence are the primary determinants for current treatment planning in radiation oncology. Personalized medicine in radiation oncology is only at the very beginning to take the genetic background of a tumor entity into consideration to define an individual treatment regimen, the total dose or the combination with a specific anticancer agent. Likewise, stratification of patients towards proton radiotherapy is linked to its physical advantageous energy deposition at the tumor site with minimal healthy tissue being co-irradiated distal to the target volume. Hence, the fact that photon and proton irradiation also induce different qualities of DNA damages, which require differential DNA damage repair mechanisms has been completely neglected so far. These subtle differences could be efficiently exploited in a personalized treatment approach and could be integrated into personalized treatment planning. A differential requirement of the two major DNA double strand break repair pathways, homologous recombination and non-homologous end joining, was recently identified in response to proton and photon irradiation, respectively, and subsequently influence the mode of ionizing radiation-induced cell death and susceptibility of tumor cells with defects in DNA repair machineries to either quality of ionizing radiation.This review focuses on the differential DNA-damage responses and subsequent biological processes induced by photon and proton irradiation in dependence of the genetic background and discusses their impact on the unicellular level and in the tumor microenvironment and their implications for combined treatment modalities.
Commercial software tools for intelligentautonomous systems

This article identifies some of the commercial software tools that can potentially be examined, or relied upon for their techniques, within new EPSRC projects entitled "Reconfigurable Autonomy" and "Distributed Sensing and Control. " awarded and to be undertaken between Liverpool, Southampton and Surrey Universities in the next 4 years. Although such projects strive to produce new techniques of various kinds, the software reviewed here could also influence, shape and help to integrate the algorithmic outcome of all 16 projects awarded within the EPSRC Autonomous and Intelligent Systems programme early 2012. To avoid mis-representation of technololgies provided by the software producer companies listed, most of this review is based on using quotes from original product descriptions.
Determination of HER 2 / NEU gene amplification and protein overexpression in bladder transitional cell carcinoma

HER2/neu 185 kDa is a transmembrane receptor tyrosine kinase being a part of epidermal growth factor receptor family. Especially overexpression was shown in breast cancer and treatment procedures targeting this protein are in clinical use. The aim of this study is to show the overexpression of HER2/neu in bladder TCC patients by using immunohistochemical methods. 46 TCC and 15 healthy bladder tissues as a control group were used in the study. Deparafinized tumor specimens were marked by using monoclonal antihuman HER2 protein antibody and the protein was shown by using peroxidase secondary antibody. Non-staining or membrane staining less than 10% were classified as 0, while membrane staining partly more than 10% were 1, poor complete membrane staining or moderate staining more than 10% were 2 and complete membrane strongly staining were classified as 3. Classification 2 and 3 were evaluated as over staining of HER2/neu. Overexpression of HER2/Neu protein were shown in 12/46 (24.5%) of TCC specimens. Overexpression of HER2/neu were detected in 2 (12.5%) of Grade 1, 1 (16.6%) of Grade 2 and 12 (50%) of Grade 3 patients. Overexpression of HER2/Neu protein were positive in 5 (17.8%) of 28 superficial (Ta-T1) tumor specimens and 7 (38.8%) of 18 invasive (T2-T3) tumor specimens. Overexpression of HER2/neu in Grade III tumors were statistically significant when compared with Grade I and Grade II (p=0.012). Overexpression of HER2/neu detected in bladder TCC will be used in clinical setting as a treatment option targeting this protein as in the breast cancer in the future.
Sensory- and Motor-Related Responses of Layer 1 Neurons in the Mouse Visual Cortex

Cortical layer 1 (L1) contains a sparse and molecularly distinct population of inhibitory interneurons. Their location makes them ideally suited for affecting computations involving long-range corticocortical and subcortical inputs, yet their response properties remain largely unexplored. Here we attempt to characterize some of the functional properties of these neurons in the primary visual cortex of awake mice. We find that the strongest driver of L1 neuron activity is locomotion, with at least half of L1 neurons displaying locomotion-related activity. Visual responses are present in a similar fraction of neurons, but these responses are weaker and frequently suppressive. We also find that ∼43% of L1 neurons respond to noise stimuli and at least 14% respond to whisker touch, with these two populations being statistically independent. Finally, we find that 45% of L1 neurons have generally weak responses correlated with whisking activity. Overall, the spatial distributions of modality-specific responses were more or less random. Our work helps to establish the basic sensory- and motor-related responses of L1 interneurons, revealing several previously unreported characteristics. SIGNIFICANCE STATEMENT Cortical processing even in primary sensory areas is strongly influenced by nonlocal corticocortical and neuromodulatory inputs. Many of these inputs are known to converge onto layer 1 where they target not only distal dendrites of pyramidal neurons but also a sparse population of inhibitory neurons. Previous studies have suggested that layer 1 neurons may play a crucial role in mediating the effects of these long-range projections, but the different types of inputs have mostly been studied in isolation. Here, we take a closer look at the response properties of layer 1 neurons in mouse visual cortex, examining both their visual properties, likely caused by direct thalamocortical inputs, and other sensory and motor properties, likely reflecting corticocortical and neuromodulatory inputs.
Evaluation of the effects of bredemolic acid on selected markers of glucose homeostasis in diet-induced prediabetic rats

Abstract Context Pentacyclic triterpenes (such as maslinic acid) are natural anti-diabetic agents that ameliorate glucose metabolism in diet-induced prediabetes. However, the effects of bredemolic acid (BA), maslinic acid isomer, is yet unknown in prediabetic (PD) conditions. Objectives To investigate the effects of BA on some glucose homeostasis parameters in high-fat high-carbohydrate (HFHC) diet-induced PD rats. Methods Thirty-six (36) male rats (150–180 g) were divided into two groups, the normal diet (ND) non-prediabetic, NPD (n = 6) and the HFHC diet PD groups (n = 30). The PD animals were further sub-divided into five groups (n = 6) where they were treated with BA for 12 weeks while monitoring changes in blood glucose, caloric intake, and body weight. Results Diet-induced prediabetes resulted in increased body weight, caloric intake, glycated haemoglobin, and glucose tolerance. BA treatment ameliorated glucose tolerance, lowered plasma insulin and increased expression of glucose transporter 4 (GLUT 4) in rats. Conclusions BA administration restored glucose homeostasis in diet-induced prediabetes regardless of diet intervention.
Numerical investigation of the compressible flow past an aerofoil

Numerical investigation of the compressible flow past an 18% thick circular-arc aerofoil was carried out using detached-eddy simulation for a free-stream Mach number M∞ = 0.76 and a Reynolds number Re = 1.1 × 107. Results have been validated carefully against experimental data. Various fundamental mechanisms dictating the intricate flow phenomena, including moving shock wave behaviours, turbulent boundary layer characteristics, kinematics of coherent structures and dynamical processes in flow evolution, have been studied systematically. A feedback model is developed to predict the self-sustained shock wave motions repeated alternately along the upper and lower surfaces of the aerofoil, which is a key issue associated with the complex flow phenomena. Based on the moving shock wave characteristics, three typical flow regimes are classified as attached boundary layer, moving shock wave/turbulent boundary layer interaction and intermittent boundary layer separation. The turbulent statistical quantities have been analysed in detail, and different behaviours are found in the three flow regimes. Some quantities, e.g. pressure-dilatation correlation and dilatational dissipation, have exhibited that the compressibility effect is enhanced because of the shock wave/boundary layer interaction. Further, the kinematics of coherent vortical structures and the dynamical processes in flow evolution are analysed. The speed of downstream-propagating pressure waves in the separated boundary layer is consistent with the convection speed of the coherent vortical structures. The multi-layer structures of the separated shear layer and the moving shock wave are reasonably captured using the instantaneous Lamb vector divergence and curl, and the underlying dynamical processes are clarified. In addition, the proper orthogonal decomposition analysis of the fluctuating pressure field illustrates that the dominated modes are associated with the moving shock waves and the separated shear layers in the trailing-edge region. The results obtained in this study provide physical insight into the understanding of the mechanisms relevant to this complex flow.
Backstepping Direct Power Control for Power Quality Enhancement of Grid-connected Photovoltaic System Implemented with PIL Co-simulation Technique

Received: 1 November 2018 Accepted: 16 February 2019 This paper proposes a combined nonlinear backstepping approach with direct power control technique for improving power quality of a three-phase grid-connected solar energy conversion system. The presented system basically extracts maximum power from solar photovoltaic array, converts it into AC power via a voltage source converter, and supplies it to the grid and connected loads. The proposed system offers not only the function of grid connected PV system but also it acts as a shunt active power filter (PV-SAPF). The system intends to eliminate the poor power quality issues and provides current conditioning while operating in coherence under nonlinear load variations. In order to validate the proposed double function system, processor-in-the-loop (PIL) tests are carried out for steady state and dynamic regimes under a nonlinear load operating condition.
Successful Word Recognition by 10‐Month‐Olds Given Continuous Speech Both at Initial Exposure and Test

Most words that infants hear occur within fluent speech. To compile a vocabulary, infants therefore need to segment words from speech contexts. This study is the first to investigate whether infants (here: 10-month-olds) can recognize words when both initial exposure and test presentation are in continuous speech. Electrophysiological evidence attests that this indeed occurs: An increased extended negativity (word recognition effect) appears for familiarized target words relative to control words. This response proved constant at the individual level: Only infants who showed this negativity at test had shown such a response, within six repetitions after first occurrence, during familiarization.
Application of Dust Mitigation Strategies to Single-Axis-Tracking Photovoltaic Modules in the Semi-Arid Areas of South Africa

This paper provides field generated data for single-axis-tracker (SAT) photo voltaic (PV) modules subjected to the semi-arid Northern Cape environment of South Africa. The research objectives are the investigation of the effects of dust soiling on PV module performance and the application of experimental dust mitigation methods. This includes the use of a hydrophobic anti-soiling coating and also the execution of a self-cleaning manoeuvre by the SAT systems. Two SAT systems were deployed to serve as experimental platform, from which data was obtained for a three month period (97 days). Raw data validation is established with comprehensive weather monitoring (ambient temperature, wind speed, wind direction, rainfall, pressure, and humidity), irradiance and PV module back sheet temperatures recorded, in accordance with the IEC61724 standard. An intelligent device was used to extract Current-Voltage (I-V) curves from individual PV modules. Maximum PV module power output is derived from the measured I-V curves, validated with a single-diode curve fitting routine. The comparative study between the different PV modules is done with a performance ratio (PR), defined as the temperature and irradiance corrected performance factor of a PV module. Contrary to the initial hypothesis, results indicated that the hydrophobic coating actually promoted dust soiling. The applied self-cleaning capability of the SAT system did not yield any conclusive results as a dust mitigation method. Finally, interesting in-field observations are discussed.
Influence of the time of housing on the quality of pig meat

In the experiment, 367 hybrid meat pigs were tested. Transport of all observed pigs took 1 hour to get to a slaughterhouse. The housing period of the observed groups in the slaughterhouse took 1, 2, 4, 12, 13, 14, 16, 17, and 41 hours. The pH value was measured in the musculus longissimus dorsi (MLD) as well as in musculus semimembranosus in the thigh meat (MSM) 45 minutes after slaughter. The highest average pH MLD value (6.36) was recorded in the group of pigs that were housed in the slaughterhouse for the shortest period of time. The average pH MLD value in pigs with the shortest period of housing was statistically arguably higher (P<0.01) in comparison with the groups that were housed in the slaughterhouse from 4 - 17 hours. The group of pigs with the shortest housing period of time had also achieved the highest average value (6.45±0.27) of the pH MSM indicator. Compared to that group, a provably lower average of pH MSM values were recorded in groups with the length of housing 13, 14, and 17 hours (P<0.01). It has resulted from the experiment that after a short - lasting transport it is desirable, in terms of pork quality, to slaughter the animals as soon as possible after their arrival to the slaughterhouse. An animal that is slaughtered after a 12- hour housing might mean a threat for the increased occurence of the PSE meat due to the consequence of stress caused during the stay in the slaughterhouse.
SIRT1-Mediated Protective Effect of Aralia elata (Miq.) Seem against High-Glucose-Induced Senescence in Human Umbilical Vein Endothelial Cells

Aralia elata (Miq.) Seem (AS) is widely been for treating many diseases, enhancing energy, and boosting immunity; however, its protective effects against high-glucose (HG)-triggered endothelial dysfunction and the potential underlying mechanisms have not been investigated. In this study, we determined the effect of AS on senescence in human umbilical vein endothelial cells (HUVECs) and elucidated the mechanisms underlying its anti-aging effects. The senescence model of endothelial cells (ECs) was established by culturing HUVECs in media containing HG (30 mM). We found that the proportion of senescent (senescence-associated β-galactosidase+) cells in the HG group was significantly higher than that in the control group; however, this increase was suppressed by AS treatment. Moreover, cell cycle analysis revealed that AS (20 μg/mL) significantly recovered HG-induced cell cycle arrest in ECs, and Western blot revealed that AS prevented HG-induced decreases in silent information regulator 1 (SIRT1) level and endothelial nitric oxide synthase (eNOS) phosphorylation. These results show that AS delayed HG-induced senescence in ECs by modulation of the SIRT1/5′ AMP-activated protein kinase and AKT/eNOS pathways.
Immersed boundary method for the compressible Navier-Stokes equations using high order summation-by-parts difference operators

A ghost-point immersed boundary method is devised for the compressible Navier–Stokes equations by employing high order summation-by-parts (SBP) difference operators. The immersed boundaries are treated as sharp interfaces by enforcing the solid wall boundary conditions via flow variables at ghost points using bilinearly interpolated flow variables at mirror points. The approach is verified and validated for compressible flow past a circular cylinder at moderate Reynolds numbers.
Predicting outcome after multiple trauma : which scoring system ?

Trauma is an important health problem and a leading cause of death particularly in younger adults and adolescents; it may be seen as a neglected disease of modern society. Reported mortality rates for severely injured patients remain substantial, ranging from 7 to 45%. The observed variation in mortality and longterm morbidity between different centres and countries could reflect differences in the quality of management, or different injury severity and/or individual patient characteristics in the study populations. In such instances it is vital that study populations be comparable regarding the prognostic variables used. This aim can be achieved by using an instrument, a scoring system, which considers these variables. However, we should note that the differences could reflect inaccuracies, or errors, inherent in the scoring system used to synthesise or quantify such information. A satisfactory scoring system is essential to answer such questions as ‘how it is that the survival rate of 58% in your trauma centre is actually better than the survival rate of 97% in some other hospital where the patients are much less seriously injured’. It is therefore of pivotal importance that a scoring system should measure what it is supposed to measure. Injury, Int. J. Care Injured (2004) 35, 347—358