Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutations that affect activity of the Rhizobium meliloti trpE(G) promoter in Rhizobium meliloti and Escherichia coli

The cloned Rhizobium meliloti trpE(G) gene is not expressed in Escherichia coli. Oligonucleotide-directed mutagenesis was used to introduce base substitution mutations in the promoter region of this gene. Three separate mutations that increased homology of the putative -10 region of this promoter with the E. coli -10 promoter consensus sequence by 1 bp converted this promoter to an active promoter in E. coli. A deletion extending to position -43 from the 5' side had a minor effect on transcription in R. meliloti. However, transcription was nearly eliminated when a deletion extended to position -33, indicating that the crucial domain of the R. meliloti trpE(G) promoter begins in the region downstream of position -43. The R. meliloti trpE(G) promoter has two regions that show homology with the E. coli -35 and -10 promoter consensus sequences. Mutations in these putative -35 and -10 regions, but not in the spacer region, affected promoter strength in R. meliloti. By comparing four known R. meliloti promoter sequences, we identified a highly conserved trimer near position -35 (5'-TTG-3') but no noticeably conserved sequence near position -10.
Adolescent alcohol use: risks and consequences.

AIMS The aim of the study was to summarize results of recent epidemiological research on adolescent alcohol use and its consequences, to outline the risk factors for drinking in adolescents and to consider effective treatment and preventative interventions. METHODS A literature review of relevant studies on adolescent alcohol use. RESULTS Alcohol use and other risk-taking behaviours such as smoking, substance use and risky sexual behaviour emerge in adolescence and tend to cluster together. Heavy alcohol consumption in late adolescence appears to persist into adulthood and is associated with alcohol problems, including dependence, premature death and diminished work capacity. Early identification of adolescent risk factors may be helpful in preventing and/or attenuating risk. CONCLUSION There is a need for high-quality long-term prospective cohort studies to investigate the long-term consequences of adolescent drinking and further work is needed to identify the most effective intervention strategies.
Full Genome-Based Classification of Rotaviruses Reveals a Common Origin between Human Wa-Like and Porcine Rotavirus Strains and Human DS-1-Like and Bovine Rotavirus Strains

ABSTRACT Group A rotavirus classification is currently based on the molecular properties of the two outer layer proteins, VP7 and VP4, and the middle layer protein, VP6. As reassortment of all the 11 rotavirus gene segments plays a key role in generating rotavirus diversity in nature, a classification system that is based on all the rotavirus gene segments is desirable for determining which genes influence rotavirus host range restriction, replication, and virulence, as well as for studying rotavirus epidemiology and evolution. Toward establishing such a classification system, gene sequences encoding VP1 to VP3, VP6, and NSP1 to NSP5 were determined for human and animal rotavirus strains belonging to different G and P genotypes in addition to those available in databases, and they were used to define phylogenetic relationships among all rotavirus genes. Based on these phylogenetic analyses, appropriate identity cutoff values were determined for each gene. For the VP4 gene, a nucleotide identity cutoff value of 80% completely correlated with the 27 established P genotypes. For the VP7 gene, a nucleotide identity cutoff value of 80% largely coincided with the established G genotypes but identified four additional distinct genotypes comprised of murine or avian rotavirus strains. Phylogenetic analyses of the VP1 to VP3, VP6, and NSP1 to NSP5 genes showed the existence of 4, 5, 6, 11, 14, 5, 7, 11, and 6 genotypes, respectively, based on nucleotide identity cutoff values of 83%, 84%, 81%, 85%, 79%, 85%, 85%, 85%, and 91%, respectively. In accordance with these data, a revised nomenclature of rotavirus strains is proposed. The novel classification system allows the identification of (i) distinct genotypes, which probably followed separate evolutionary paths; (ii) interspecies transmissions and a plethora of reassortment events; and (iii) certain gene constellations that revealed (a) a common origin between human Wa-like rotavirus strains and porcine rotavirus strains and (b) a common origin between human DS-1-like rotavirus strains and bovine rotaviruses. These close evolutionary links between human and animal rotaviruses emphasize the need for close simultaneous monitoring of rotaviruses in animals and humans.
A Comparison of Teacher and Student Attitudes Concerning Use and Effectiveness of Web-based Course Management Software

The purpose of this study was to assess the perceived effectiveness of the CourseInfo instructional technology package implemented at a regional Midwestern university. An online survey was administered, with 971 students and 44 faculty responding. Results indicate attitudes of both faculty and students were positive – both believed that the web, and specifically Blackboard's CourseInfo, were beneficial educational tools. They felt confident in their ability to utilize both CourseInfo and the Web and considered themselves computer literate. Faculty, significantly more than students, believed both teacher-student and studentstudent communication was facilitated. Students, much more than faculty felt that CourseInfo had improved student learning.
The Effect of Lubricating Oil on Temperature of Chainsaw Cutting System

Nacrtak Portable chainsaw is a basic operational instrument in forestry. To ensure long-lasting performance of a chainsaw, it is necessary to perform the necessary maintenance of its cutting system. The basis of this maintenance lies in the lubrication of the chain, which protects it from excessive wearing and deterioration. Various lubricating oils are used for lubricating the chain. Biodegradable oils are promoted nowadays, with their main advantage being shorter decomposition time in the environment, and the same lubricating properties as conventional lubricants. This paper is aimed to evaluate and compare the ability to lubricate and cool the cutting system of a portable chainsaw filled with biodegradable oil and oils commonly used for its operation. Conditions of measurements were specified to simulate the actual operating conditions. During the evaluation no major differences between these oils were observed.
Mobile Money – A Potential Threat to Banks?

Money, the medium of exchange has seen significant transformation over centuries. In the last few hundred years, money has been regulated by banks. Such regulation of the flow of money in itself has become a money making venture becoming the main stay of several kinds of institutions including banking institutions. The paper focuses on the emerging trend of the use of mobile devices to facilitate the payment of goods and services. This is essentially, using a mobile phone to perform some of the duties of traditional banks. This fast paced substitution of the mobile phone with traditional banking is sometimes viewed as a threat to the existence of banks in Ghana. The paper finds, through the use of empirical data and interviews, that although, banks may lose minimally in the short term, mobile money is actually more complementary and will only fast track the achievement of the goal of a cashless economy.
Complete mitochondrial genome of the Tioman Island rock gecko, Cnemaspis limi (Sauria, Gekkota, Gekkonidae)

Abstract We sequenced the complete mitochondrial genome of the Tioman Island rock gecko, Cnemaspis limi, which is known as an endemic species to Malaysia. The complete mitogenome is 16,680 bp in size, consisting of 37 genes coding for 13 proteins, 22 transfer RNAs, two ribosomal RNAs and one control region. The A + T content of the overall base composition of H-strand is 53.09% (T: 23.20%, C: 32.48%, A: 29.89% and G: 14.43%). The major non-coding region (control region) is 1254 bp in length with the A + T content of 55.09% and four replicates of a 76-bp repeat within this region.
Iron Mobilization in Mineral Dust : Can Anthropogenic SO 2 Emissions Affect Ocean Productivity ?

In order for Fe contained in aeolian dust to act as a micronutrient for oceanic phytoplankton it must be first mobilized or dissolved. We propose that significant Femobilization can occur in mineral dust from East Asia as a result of the incorporation of SO2 from pollutant emissions into the advecting dust plumes and the subsequent acidification of the dust by heterogeneous SO2 oxidation. To test this acid-mobilization hypothesis, we consider a dust plume that originated from the gobi deserts and advected over the Yellow Sea in March of 2001. Data collected during the TRACE-P field campaign confirm that this plume contained high concentrations of both dust and SO2. Measurements within the plume of significant concentrations of gaseous HNO3 suggest that the dust particles were highly acidified (i.e., pH< 2). At these pH’s, approximately 1– 2% of the Fe contained in a deliquescent mineral dust particle would be mobilized within the nominal 3–5 day lifetime of the particle. These results suggest that there may be a link between the rate of C-fixation in so-called High-Nitrate-Low-Chlorophyll regions of the ocean and the rate of SO2 emissions from East Asia.
miR-155 Is Associated with the Leukemogenic Potential of the Class IV Granulocyte Colony-Stimulating Factor Receptor in CD34+ Progenitor Cells

Granulocyte colony-stimulating factor (G-CSF) is a major regulator of granulopoiesis on engagement with the G-CSF receptor (G-CSFR). The truncated, alternatively spliced, class IV G-CSFR (G-CSFRIV) has been associated with defective differentiation and relapse risk in pediatric acute myeloid leukemia (AML) patients. However, the detailed biological properties of G-CSFRIV in human CD34+ hematopoietic stem and progenitor cells (HSPCs) and the potential leukemogenic mechanism of this receptor remain poorly understood. In the present study, we observed that G-CSFRIV-overexpressing (G-CSFRIV+) HSPCs demonstrated an enhanced proliferative and survival capacity on G-CSF stimulation. Cell cycle analyses showed a higher frequency of G-CSFRIV+ cells in the S and G2/M phase. Also, apoptosis rates were significantly lower in G-CSFRIV+ HSPCs. These findings were shown to be associated with a sustained Stat5 activation and elevated miR-155 expression. In addition, G-CSF showed to further induce G-CSFRIV and miR-155 expression of peripheral blood mononuclear cells isolated from AML patients. A Stat5 pharmacological inhibitor or ribonucleic acid (RNA) interference-mediated silencing of the expression of miR-155 abrogated the aberrant proliferative capacity of the G-CSFRIV+ HSPCs. Hence, the dysregulation of Stat5/miR-155 pathway in the G-CSFRIV+ HSPCs supports their leukemogenic potential. Specific miRNA silencing or the inhibition of Stat5-associated pathways might contribute to preventing the risk of leukemogenesis in G-CSFRIV+ HSPCs. This study may promote the development of a personalized effective antileukemia therapy, in particular for the patients exhibiting higher expression levels of G-CSFRIV, and further highlights the necessity of pre-screening the patients for G-CSFR isoforms expression patterns before G-CSF administration.
Monitoring Population Trends of Eleutherodactylus Frogs

Abstract Like many Neotropical frogs, a number in the genus Eleutherodactylus have declined or gone extinct in the past two decades. However, the extent of Eleutherodactylus population declines is unknown. Our objective was to identify a good method for monitoring the density of Eleutherodactylus populations to assess the extent of declines. We did this in two ways. First, we compared two methods of directly estimating density, closed population capture-recapture analysis and distance sampling, and one method of indirectly estimating density, visual encounter surveys, for multiple Eleutherodactylus species at three sites in Ecuador. We then conducted a power analysis to estimate the power of our current sampling design to detect declines. Distance sampling estimates of density were biased low compared to capture-recapture estimates. When we corrected this bias, distance sampling estimates became imprecise. Estimates of density from visual encounter surveys were also imprecise. In contrast, capture-recapture estimates were fairly precise and most likely unbiased. Moreover, capture-recapture analysis had the most power to detect declines, although even with capture-recapture analysis, power was low with only five years of sampling. We conclude that capture-recapture analysis is a good method for monitoring Eleutherodactylus density over time, but the sampling area and/or the number of sampling occasions should be increased from the area and number of occasions used here in order to increase sample sizes and therefore power.
Measurement of specimen‐induced aberrations of biological samples using phase stepping interferometry

Confocal or multiphoton microscopes, which deliver optical sections and three‐dimensional (3D) images of thick specimens, are widely used in biology. These techniques, however, are sensitive to aberrations that may originate from the refractive index structure of the specimen itself. The aberrations cause reduced signal intensity and the 3D resolution of the instrument is compromised. It has been suggested to correct for aberrations in confocal microscopes using adaptive optics. In order to define the design specifications for such adaptive optics systems, one has to know the amount of aberrations present for typical applications such as with biological samples. We have built a phase stepping interferometer microscope that directly measures the aberration of the wavefront. The modal content of the wavefront is extracted by employing Zernike mode decomposition. Results for typical biological specimens are presented. It was found for all samples investigated that higher order Zernike modes give only a small contribution to the overall aberration. Therefore, these higher order modes can be neglected in future adaptive optics sensing and correction schemes implemented into confocal or multiphoton microscopes, leading to more efficient designs.
Is red blood cell rheology preserved during routine blood bank storage?

BACKGROUND: Red blood cell (RBC) units stored for more than 2 weeks at 4°C are currently considered of impaired quality. This opinion has primarily been based on altered RBC rheologic properties (i.e., enhanced aggregability, reduced deformability, and elevated endothelial cell interaction), during prolonged storage of nonleukoreduced RBC units. In this study, the rheologic properties and cell variables of leukoreduced RBC units, during routine blood bank storage in saline‐adenine‐glucose‐mannitol, were investigated.
V-BLAST Adaptive Detector Based On Affine Projection Algorithm

Bell Laboratories space-time (BLATS) wireless systems are multiple antenna communication schemes that can achieve very high spectral efficiencies in scattering environment with no increase in bandwidth or transmitted power. In this paper we propose an adaptive algorithm for detection in V-BLAST systems based on affine projection algorithm. The proposed technique can improve convergence speed compared to least mean-squares (LMS) with much reduced computational cost compared to recursive least squares (RLS). We present comparison of computational complexities of LMS, RLS, and APA-based detection algorithms. Simulation results illustrate the performance of the proposed algorithm
A novel method to analyze logs generated by wireless telecommunication systems

Traditional analysis for logs generated by wireless telecommunication systems requires a priori knowledge to explore the common patterns and structures. To overcome this difficulty, this paper presents a new method to analyze logs. We first implement natural language processing (NLP) techniques and machine learning (ML) models to process logs and directly vectorize logs. Then we train a classification model to determine the states of logs. Experiments are carried out to confirm the effectiveness of our method.
Comparison of Pulsed-Field Gel Electrophoresis and Amplified Fragment Length Polymorphism Techniques for Investigating Outbreaks of Enteritis Due to Campylobacters

ABSTRACT Campylobacters are the most commonly reported cause of acute bacterial enteritis in the United Kingdom and United States, with poultry, milk, and water implicated as sources or vehicles of infection. The majority of campylobacter infections are sporadic, although outbreaks may occur, and these provide an opportunity to evaluate genotypic fingerprinting techniques. In this study, pulsed-field gel electrophoresis (PFGE) was compared with single-enzyme-amplified fragment length polymorphism (SAFLP). The results for the three separate episodes indicated that SAFLP and PFGE both clustered the strains from the first incident as 100% homologous. The strains from the second and third incidents clustered as distinct from both the first incident and from each other. PFGE is well recognized as a discriminatory fingerprinting technique for campylobacters; however, SAFLP has proven to be equally discriminatory, but far less labor intensive and with the added advantages of less “hands-on” time and inexpensive equipment, it is an excellent alternative to PFGE for investigation of outbreaks.
Anthropometric Profile and Body Composition of Irish Adolescent Rugby Union Players Aged 16–18

Abstract Delahunt, E, Byrne, RB, Doolin, RK, McInerney, RG, Ruddock, CTJ, and Green, BS. Anthropometric profile and body composition of Irish adolescent rugby union players aged 16–18. J Strength Cond Res 27(12): 3252–3258, 2013—The literature suggests that one of the key determinants of success at rugby union international competitions is the anthropometric profile of players. The Irish Rugby Football Union (IRFU) long-term player development (LTPD) model is a framework designed to guide the development of the tactical, physical, and psychological domains of sporting participation. In Ireland, the Train-to-Train stage of the IRFU model is a critical stage, whereby the next developmental progression would include the transition of players into professional academies. To date, no previously published studies have examined the anthropometric profile of Irish Schools' rugby union players at the Train-to-Train stage of the IRFU model. The anthropometric profile of 136 male adolescent rugby union players at the Train-to-Train stage of the IRFU model was assessed using total-body dual-energy x-ray absorptiometry. Significant differences in height, body mass, body fat percentage, fat mass, lean mass, and fat-free mass were observed between players assigned to the forward and back units, and for specific position categorizations within each unit. Direct logistic regression revealed that body mass was a statistically significant (p < 0.01) predictor of unit position classification, with an odds ratio of 2.35, indicating that the players with a higher body mass were twice as likely to be classified as forwards. The results of this study indicate that at the Train-to-Train stage of the IRFU model, forward and back units have distinctly different anthropometric profiles. Furthermore, anthropometric differentiation also exists within specific position categorizations within each of these playing units. Thus, anthropometric profiling should be carried out on a systematic and periodic basis, because this will allow for the evaluation of the effectiveness of the implementation strategies of the IRFU model on a national basis.
Applications of bioluminescence imaging to the study of infectious diseases

Bioluminescence imaging (BLI) has emerged as a powerful new method to analyse infectious diseases in animal models. BLI offers real‐time monitoring of spatial and temporal progression of infection in the same animal, as opposed to euthanizing a cohort of animals and quantifying colony or plaque forming units at multiple time points. Pathogens or mice are engineered to express genetically encoded luciferase enzymes from bacteria, insects, or the sea pansy. The seminal study showing the feasibility of detecting microbially generated luminescence within a living mouse was published by Contag and colleagues in 1995, using Salmonella typhimurium transformed with the lux operon from Photorhabdus luminescens. Following this, they and others performed many studies of infection by bioluminescent Gram‐negative and Gram‐positive bacteria. Viruses can also be engineered to encode luciferase. Our laboratory has used bioluminescent reporter viruses to follow HSV and vaccinia pathogenesis; others have used an alphavirus or novirhabdovirus. Recently, even eukaryotic parasites Plasmodium, Leishmania and Toxoplasma have been transformed with luciferase and yielded unique insights into their in vivo behaviour. We expect that both the range of organisms and the molecular events able to be studied by BLI will continue to expand, yielding important insights into mechanisms of pathogenesis.
Topography-Guided vs Wavefront-Optimized Surface Ablation for Myopia Using the WaveLight Platform: A Contralateral Eye Study.

PURPOSE to compare treatments with wavefront-optimized and topography-guided ablations. METHODS this prospective, randomized, contralateral study comprised 40 eyes (20 patients) with low to moderate myopia with or without astigmatism that underwent topography-guided photorefractive keratectomy (PRK) (ALLEGRO Topolyzer, Alcon Laboratories Inc) in one eye and wavefront-optimized PRK (ALLEGRETTO WAVE software version 2.020 default treatment, Alcon Laboratories Inc) in the fellow eye. Visual acuity, refractive error, contrast sensitivity, and Orbscan (Bausch & Lomb) 3- and 5-mm corneal irregularities were measured preoperatively and 3 and 6 months postoperatively. The results were compared between the two eyes. RESULTS in both groups, preoperative corrected distance visual acuity (CDVA) (0.03±0.09 logMAR for topography-guided and 0.01 ± 0.06 logMAR for wavefront-optimized [P=.1]), 3-month postoperative uncorrected distance visual acuity (UDVA) (-0.0 1± 0.03 logMAR for topography-guided and -0.01 ± 0.03 logMAR for wavefront-optimized [P=.4]), and 6-month postoperative UDVA (0.01 ± 0.03 logMAR for topography-guided and 0.0 ± 0.01 logMAR for wavefront-optimized [P=.3]) were the same. All wavefront-optimized and 18 (90%) topography-guided eyes had UDVA of 20/20 or better. No significant differences were noted between groups in pre- and postoperative spherical and cylindrical refractive errors or corneal irregularity and contrast sensitivity measurements. Six months postoperatively, contrast sensitivity values at 3, 6, 12, and 18 cycles/degree were 5.7 ± 0.7, 6.0 ± 1.5, 6.1 ± 1.3, and 5.5 ± 1.5, respectively, in the topography-guided group, and 6.2 ± 0.6, 6.4 ±1.2, 6.4 ± 1.1, and 5.8 ± 1.3, respectively, in the wavefront-optimized group (P=.3, P=.5, P=.4, and P=.6, respectively). CONCLUSIONS using the WaveLight excimer laser platform for PRK, CDVA and contrast sensitivity outcomes were statistically similar between the wavefront-optimized and topography-guided ablations in eyes with low to moderate myopia with and without astigmatism.