Miracle-dz/UniFAR-FTUs huggingface dataset:
APOBEC3 Deaminases Induce Hypermutation in Human Papillomavirus 16 DNA upon Beta Interferon Stimulation

ABSTRACT Apolipoprotein B mRNA-editing catalytic polypeptide 3 (APOBEC3) proteins are interferon (IFN)-inducible antiviral factors that counteract various viruses such as hepatitis B virus (HBV) and human immunodeficiency virus type 1 (HIV-1) by inducing cytidine (C)-to-uracil (U) mutations in viral DNA and inhibiting reverse transcription. However, whether APOBEC3 proteins (A3s) can hypermutate human papillomavirus (HPV) viral DNA and exhibit antiviral activity in human keratinocyte remains unknown. Here we examined the involvement of A3s in the HPV life cycle using cervical keratinocyte W12 cells, which are derived from low-grade lesions and retain episomal HPV16 genomes in their nuclei. We focused on the viral E2 gene as a potential target for A3-mediated hypermutation because this gene is frequently found as a boundary sequence in integrated viral DNA. Treatment of W12 cells with beta interferon (IFN-β) increased expression levels of A3s such as A3A, A3F, and A3G and induced C-to-U conversions in the E2 gene in a manner depending on inhibition of uracil DNA glycosylase. Exogenous expression of A3A and A3G also induced E2 hypermutation in W12 cells. IFN-β-induced hypermutation was blocked by transfection of small interfering RNAs against A3G (and modestly by those against A3A). However, the HPV16 episome level was not affected by overexpression of A3A and A3G in W12 cells. This study demonstrates that endogenous A3s upregulated by IFN-β induce E2 hypermutation of HPV16 in cervical keratinocytes, and a pathogenic consequence of E2 hypermutation is discussed.
Application of the Marketing Concept and Performance of Supermarkets in Kisumu City, Kenya

This paper sought to examine the relationship between the application marketing concept and performance of retail supermarkets in Kisumu City, Kenya. The study adopted descriptive survey design to explore the above relationship. Stratified simple random sampling technique was used to select a sample of 162 employees out of a population of 410 employees. A self administered structure and semi structure Questionnaires were used to obtain primary data from the field. The Regression results showed that 39.8% or (R 2 =0.398, p<0.05) of variation in retail supermarkets’ financial performance was explained by the application of the Marketing Concept and 52.5% (R 2 =0.525, p<0.05) of non-financial performance.The study provided an exposition of the Marketing Concept application by supermarkets by concluding that it exerted a significant influence on both non-financial performance and financial performance measures. To the academia, the output will contribute to enriching the knowledge base particularly in the field of Marketing Concepts and its performance consequences in the context of emerging and developing economies.
Operant Conditioning of H-Reflex Can Correct a Locomotor Abnormality after Spinal Cord Injury in Rats

This study asked whether operant conditioning of the H-reflex can modify locomotion in spinal cord-injured rats. Midthoracic transection of the right lateral column of the spinal cord produced a persistent asymmetry in the muscle activity underlying treadmill locomotion. The rats were then either exposed or not exposed to an H-reflex up-conditioning protocol that greatly increased right soleus motoneuron response to primary afferent input, and locomotion was reevaluated. H-reflex up-conditioning increased the right soleus burst and corrected the locomotor asymmetry. In contrast, the locomotor asymmetry persisted in the control rats. These results suggest that appropriately selected reflex conditioning protocols might improve function in people with partial spinal cord injuries. Such protocols might be especially useful when significant regeneration becomes possible and precise methods for reeducating the regenerated spinal cord neurons and synapses are needed for restoring effective function.
Clustering Related Tuples in Databases

Presentation des resultats empiriques obtenus avec l'utilisation d'une technique heuristique de reduction de graphes. Cette technique est utilisee pour le placement des donnees dans les supports de stockage. Les resultats sont encourageants et pourront etre tres utiles dans la conception de futures bases de donnees. Les deux algorithmes proposes sont compares
Fungal spore concentrations in indoor and outdoor air in university libraries, and their variations in response to changes in meteorological variables

The fungal spore concentration (FSC) in the air poses a risk for human health. This work studied the FSC in university libraries and how it is affected by environmental factors. A total of 347 samples were obtained using a Microbio MB2® Aerosol Sampler. The wind speed (WS), cross wind (CW), temperature (T), relative humidity (HR), barometric pressure (BP) and dew point (DP) were recorded using a Kestrel® 4500 weather station. The median indoor/outdoor FSC was 360/1230 CFU m−3. FSC correlated inversely with BP, HR and DP; and positively with WS and CW; whereas T showed negative or positive correlation with FSC, depending on the region or sampling time. Eleven fungal genera were found and the dominant isolates were identified as Aspergillus niger, Aspergillus tamarii and Aspergillus oryzae. All fungi identified are known to be allergenic. It was concluded that environmental variables can influence the air FSC in different ways.
Semiparametric Inference for Surrogate Endpoints with Bivariate Censored Data

Summary Considerable attention has been recently paid to the use of surrogate endpoints in clinical research. We deal with the situation where the two endpoints are both right censored. While proportional hazards analyses are typically used for this setting, their use leads to several complications. In this article, we propose the use of the accelerated failure time model for analysis of surrogate endpoints. Based on the model, we then describe estimation and inference procedures for several measures of surrogacy. A complication is that potentially both the independent and dependent variable are subject to censoring. We adapt the Theil–Sen estimator to this problem, develop the associated asymptotic results, and propose a novel resampling‐based technique for calculating the variances of the proposed estimators. The finite‐sample properties of the estimation methodology are assessed using simulation studies, and the proposed procedures are applied to data from an acute myelogenous leukemia clinical trial.
Sweat Rate and Electrolyte Composition in Young Women of Varying Body Mass Indices during Moderate Exercise

Sweat is a hypotonic fluid excreted by sweat glands to cool the body. There are conflicting reports on whether or not body composition has an effect on thermoregulatory responses especially during exercise. This study was aimed at determining and comparing sweat rate and electrolyte composition in underweight (BMI 2), normal weight (18.5 kg/m2 > BMI 2), overweight (25kg/m2 2) and obese women (BMI > 30 kg/m2) during moderate exercise. Forty women (19 - 25 years) were used during this study after assessing their health status. They were stratified for BMI with each group having a total of ten women. It was ensured that all the women used in the study were euhydrated before commencing the research. Before sweat collection, the treadmill was calibrated according to the Bruce Treadmill Protocol. Sweat samples were obtained with a sweat suction apparatus from a 120 cm2 circular area marked on the skin of the face and neck, after a 15 minute fast walk on a treadmill at an inclination of 15° and at a speed of 4.2 km/h at 27°C room temperature. The time at which sweating commenced in the subjects was recorded. Sweat rate (L/hour) was calculated using the formula: sweat rate (L/hr) = (pre-exercise body weight - Post-exercise body weight)/exercise duration. Each sweat sample was collected and analysed immediately. The results showed that obese women had a significantly (P < 0.05) higher sweat rate and underweight women had a significantly (P < 0.05) lower sweat rate than all the other groups. Furthermore, subjects with a high body surface area showed significantly higher sweat rates compared to subjects with lower body surface area. Sweat electrolyte composition did not change in all BMI groups. In conclusion, obese subjects are more likely to develop fluid imbalances than underweight and normal weight subjects during moderate exercise. Also, underweight women might be at a thermoregulatory disadvantage because of their reduced body fat and body surface area.
Macrophage inflammatory proteins 1 and 2: members of a novel superfamily of cytokines

A number of studies of inflammation and of cell growth and transformation have recently converged by defining two related families of cytokines. The first, represented by macrophage inflammatory protein 1, is composed of several gene products that have been identified in activated T cells, macrophages, and fibroblasts. The biological activities of this family are still being characterized but so far include effects on neutrophils, monocytes, and hematopoietic cells. The second, represented by macrophage inflammatory protein 2, includes platelet products such as platelet factor 4 and β‐thromboglobulin as well as several other recently described gene products that have effects on a number of cell types including neutrophils, fibroblasts, hematopoietic cells, and melanoma cells. The two families are structurally related and may have evolved from a common ancestral gene that duplicated and then diverged. Their differential control and expression in a wide variety of cell types suggests that they may have multiple functions in regulating inflammation and cell growth. —Wolpe, S. D. ; Cerami, A. Macrophage inflammatory proteins 1 and 2: members of a novel superfamily of cytokines. FASEB J. 3: 2565‐2573; 1989.
Lexical Definitions of Some Performative Verbs

Abstract The author upholds Anna Wierzbicka’s opinion that unless strict scientific definitions of performatives are reached, no successful classification of these verbs can be made. The article compares definitions of the verb elect and four performative verbs (appoint, declare, excommunicate and pronounce) as presented in four English dictionaries, as well as in the form of Wierzbicka’s explicatives and the author’s formulations reached by means of the collocational method. This method seeks to gain a realistic insight into the semantic structure of lexemes because most metalinguistic elements are drawn from facts offered by the language itself. The definitions of the performative verbs, like of any other verb, can be marshalled by combining and incorporating semantic definitions of the collocating grammar words and constructions. The latter task is done by extracting the common content of the grammar words and constructions in the relevant meanings as appearing in collocations of their own. The same procedure is carried out for the noun collocates occurring in the subject and object slots of the verbs in question. The performative force within this small lexical field manifests gradation, depending on the presence of a person in authority.
E FFECT OF S AUDI DIALECT P REPROCESSING ON A RABIC S ENTIMENT A NALYSIS

Over the recent years there was a rapid increase of social networking services such as Facebook and Twitter and social media websites such as YouTube. These sites and services allowed people from all over the world to express and share their opinions, likes, and dislikes, about a certain issue or a product freely and openly. Therefore, a new field known as sentiment analysis (SA) / opinion mining (OM) emerged with the goal of extracting people’s sentiment from written texts. This emerging field has attracted a large research interest, but most of the existing work focuses on English text. With the availability of huge volume of Arabic opinionated posts on different social media forums, comes an increased demand for Arabic sentiment analysis tools and resources. These social media posts are usually written using dialectal Arabic (DA) and include a lot of slang. Even though, there was some work done to build modern standard Arabic (MSA) sentiment lexicons, there has been a limitation in building a dialectal Arabic lexicon especially for Saudi dialect. The main goal of this paper is studying the effect of preprocessing on Arabic sentiment analysis using Rapidminer. The collected dataset for this project will be online collected from Twitter using Twitter API.
Ethidium DNA agarose gel electrophoresis: How it started

We started ethidium DNA agarose gel electrophoresis when our ultracentrifuge broke down and we needed an alternative method to check the quality of our mitochondrial DNA preparations. Agarose proved convenient for sizing DNA; ethidium in gel and buffer allowed visualization of DNA bands immediately after the run and improved the separation of the closed and open duplex forms of mitochondrial DNA circles. At smaller gel pore size mitochondrial DNA circles were excluded from the gel, whereas long linear DNAs were not. We concluded that the linear DNAs 'crawl like snakes head on through the gel'. This paper reviews some of the early experiments preceding the introduction of ethidium agarose gel electrophoresis. IUBMB Life, 57: 745‐747, 2005
Part I: Impact of Field-Induced Quantum Confinement on the Subthreshold Swing Behavior of Line TFETs

Trap-assisted tunneling (TAT) is a major hurdle in achieving a sub-60-mV/decade subthreshold swing (SS) in tunnel field-effect transistors (TFETs). This paper presents an insight into the TAT process in the presence of field-induced quantum confinement (FIQC) in line TFETs. We show that the SS degradation in line TFETs is mainly caused by TAT through traps located in the bulk of the semiconductor nearby the gate dielectric. For an Si n-type TFET, the energy quantization in the conduction band is found to suppress the TAT through the interface-region traps by several orders of magnitude and delay the TAT through bulk traps nearby the gate dielectric with several hundreds of millivolts. The trap levels closer to the conduction band were found to be the most efficient for TAT in this n-TFET. The FIQC onset voltage shift in TAT through bulk taps is found to be smaller than the band-to-band tunneling (BTBT) shift, enhancing the effective SS degradation in TFETs. We therefore show that it is equally important to include the FIQC effect when calculating TAT as when calculating BTBT generation rates.
Role of rpoS in Escherichia coli O157:H7 Strain H32 Biofilm Development and Survival

ABSTRACT The protein RpoS is responsible for mediating cell survival during the stationary phase by conferring cell resistance to various stressors and has been linked to biofilm formation. In this study, the role of the rpoS gene in Escherichia coli O157:H7 biofilm formation and survival in water was investigated. Confocal scanning laser microscopy of biofilms established on coverslips revealed a nutrient-dependent role of rpoS in biofilm formation, where the biofilm biomass volume of the rpoS mutant was 2.4- to 7.5-fold the size of its rpoS + wild-type counterpart in minimal growth medium. The enhanced biofilm formation of the rpoS mutant did not, however, translate to increased survival in sterile double-distilled water (ddH2O), filter-sterilized lake water, or unfiltered lake water. The rpoS mutant had an overall reduction of 3.10 and 5.30 log10 in sterile ddH2O and filter-sterilized lake water, respectively, while only minor reductions of 0.53 and 0.61 log10 in viable counts were observed for the wild-type form in the two media over a 13-day period, respectively. However, the survival rates of the detached biofilm-derived rpoS + and rpoS mutant cells were comparable. Under the competitive stress conditions of unfiltered lake water, the advantage conferred by the presence of rpoS was lost, and both the wild-type and knockout forms displayed similar declines in viable counts. These results suggest that rpoS does have an influence on both biofilm formation and survival of E. coli O157:H7 and that the advantage conferred by rpoS is contingent on the environmental conditions.
Spontaneous Rejection of Poorly Immunogenic P1.HTR Tumors by Stat6-Deficient Mice1

Experimental evidence suggests that a type 1 T cell response may result in optimal tumor rejection in vivo. This phenotype is determined in part by cytokines that influence T cell differentiation. In transplantable tumor models such as P1.HTR, tumors grow progressively despite expression of defined tumor Ags. We hypothesized that this failure to reject may be due to poor generation of a type 1 phenotype, through a dominant influence of the type 2-promoting cytokines IL-4 and/or IL-13. This hypothesis was tested by implanting P1.HTR tumors into mice deficient in Stat6. In contrast to progressive growth of P1.HTR tumors in wild-type mice, and aggressive growth even of IL-12-transfected P1.HTR in Stat1−/− mice, P1.HTR was spontaneously rejected by Stat6−/− mice. Rejection was accompanied by augmented tumor-specific IFN-γ production and CTL activity. These results suggest that pharmacologic inhibition of Stat6 signaling could potentiate anti-tumor immunity in vivo.
Monolithic Integrated InP Transmitters Using Switching of Prefixed Optical Phases

Recent progresses on monolithic InP integration are presented for achieving high-performance transmitters for cost-sensitive metropolitan networks. We demonstrate the generation of advanced modulation format using two types of integrated transmitters with prefixed optical phases. Complex modulation formats are generated with constellations exploiting the whole complex plane such as BPSK, quadrature phase-shift keying, N-QIM, and 2ASK-2PSK modulation. We achieve data rate up to 224 Gb/s using 2ASK-2PSK modulation with polarization division multiplexing. Finally, we assess its suitability for metropolitan networks with a large number of cascaded nodes.
Predicting Fault-proneness of Object-Oriented System Developed with Agile Process using Learned Bayesian Network

In the prediction of fault-proneness in object-oriented (OO) systems, it is essential to have a good prediction method and a set of informative predictive factors. Although logistic regression (LR) and naïve Bayes (NB) have been used successfully for prediction of fault-proneness, they have some shortcomings. In this paper, we proposed the Bayesian network (BN) with data mining techniques as a predictive model. Based on the Chidamber and Kemerer’s (C-K) metric suite and the cyclomatic complexity metrics, we examine the difference in the performance of LR, NB and BN models for the fault-proneness prediction at the class level in continual releases (five versions) of Rhino, an open-source implementation of JavaScript written in Java. From the viewpoint of modern software development, Rhino uses a highly iterative or agile development methodology. Our study demonstrates that the proposed BN can achieve a better prediction than LR and NB for the agile software.
Evaluation of Power-Aware Routing for Sensor Networks with Forwarder Nodes

Wireless sensor networks are envisioned to consist of many small devices that can sense the environment and communicate the data as required. The most critical requirement for widespread sensor networks is power efficiency since battery replacement is not viable. Many protocols attempt to minimize the power consumption by using complex algorithms. However, it is difficult to perform these complex methods since an individual sensor node in sensor networks does not have high computational capacity. On the other hand, many sensor nodes should transfer the data packet to the sink node that collects the required data. Therefore, the operations of the sensor nodes over the route are terminated; it is difficult to deliver the data packet to the sink node even if some sensor nodes are active. In this paper, we propose a simple power-aware routing protocol for sensor networks. Our proposed protocol is based on the ad hoc on-demand distance vector (AODV) protocol, which is one of the reactive routing protocols. In addition, we introduce forwarder nodes in the sensor networks in order to extend the lifetime of the entire sensor network. From the simulation results, we evaluate the performance of the protocols and clarify the effect of forwarder nodes on the sensor networks. Keywords— Sensor networks, Power aware routing, Forwarder nodes, Life time
Time resolution of the plastic scintillator strips with matrix photomultiplier readout for J-PET tomograph

Recent tests of a single module of the Jagiellonian Positron Emission Tomography system (J-PET) consisting of 30 cm long plastic scintillator strips have proven its applicability for the detection of annihilation quanta (0.511 MeV) with a coincidence resolving time (CRT) of 0.266 ns. The achieved resolution is almost by a factor of two better with respect to the current TOF-PET detectors and it can still be improved since, as it is shown in this article, the intrinsic limit of time resolution for the determination of time of the interaction of 0.511 MeV gamma quanta in plastic scintillators is much lower. As the major point of the article, a method allowing to record timestamps of several photons, at two ends of the scintillator strip, by means of matrix of silicon photomultipliers (SiPM) is introduced. As a result of simulations, conducted with the number of SiPM varying from 4 to 42, it is shown that the improvement of timing resolution saturates with the growing number of photomultipliers, and that the 2×5 ? > configuration at two ends allowing to read twenty timestamps, constitutes an optimal solution. The conducted simulations accounted for the emission time distribution, photon transport and absorption inside the scintillator, as well as quantum efficiency and transit time spread of photosensors, and were checked based on the experimental results. Application of the 2×5 ? > matrix of SiPM allows for achieving the coincidence resolving time in positron emission tomography of ≈ ? >0.170 ns for 15 cm axial field-of-view (AFOV) and ≈ ? >0.365 ns for 100 cm AFOV. The results open perspectives for construction of a cost-effective TOF-PET scanner with significantly better TOF resolution and larger AFOV with respect to the current TOF-PET modalities.
Giant Cell Tumor of Bone: A Model for the in Vitro Human Osteoclast Characterization

The in vitro growth pattern of cells obtained from bioptic material of ten patients with giant cell tumor of bone (GCT) was investigated. Cytochemical reactions and monoclonal antibodies raised against macrophage markers were tested on the two histologically identifiable GCT cell populations. Only monoclonal antibody EBM/11 stained both mononuclear and giant cells. EBM/11 positivity and resistance of acid phosphatase to high doses of tartrate strongly suggest that both mononuclear and giant cells belong to the same lineage.
Designing a Master of Public Health Degree Within a Department of Pharmacy Practice

The demand for public health services is being outpaced by a shrinking public health workforce. This creates a unique opportunity for pharmacists to become more engaged in public health activities, particularly in rural underserved areas. To meet the need for additional public health professionals, we designed a master of public health (MPH) program in a rural state under the leadership of a department of pharmacy practice. In addition to a core set of courses, the MPH program has public health specialty tracks (disease state management, emergency management, health promotion practice, infectious disease management, food safety, gerontology, and medical management and administration) that could be completed as a certificate program or used towards an MPH degree. The program allows students to complete the graduate degree with a minimum of prerequisite coursework. The MPH degree provides an opportunity for pharmacists and other health care professionals to gain an understanding of the interprofessional approach to solving public health problems and will enhance their role in public health and within their health care team.