Miracle-dz/UniFAR-FTUs huggingface dataset:
The sensitivity of Cockayne's syndrome cells to DNA-damaging agents is not due to defective transcription-coupled repair of active genes

Two of the hallmarks of Cockayne's syndrome (CS) are the hypersensitivity of cells to UV light and the lack of recovery of the ability to synthesize RNA following exposure of cells to UV light, in spite of the normal repair capacity at the overall genome level. The prolonged repressed RNA synthesis has been attributed to a defect in transcription-coupled repair, resulting in slow removal of DNA lesions from the transcribed strand of active genes. This model predicts that the sensitivity of CS cells to another DNA-damaging agent, i.e., the UV-mimetic agent N-acetoxy-2-acetylaminofluorene (NA-AAF), should also be associated with a lack of resumption of RNA synthesis and defective transcription-coupled repair of NA-AAF-induced DNA adducts. We tested this by measuring the rate of excision of DNA adducts in the adenosine deaminase gene of primary normal human fibroblasts and two CS (complementation group A and B) fibroblast strains. High-performance liquid chromatography analysis of DNA adducts revealed that N-(deoxyguanosin-8-yl)-2-aminofluorene (dG-C8-AF) was the main adduct induced by NA-AAF in both normal and CS cells. No differences were found between normal and CS cells with respect to induction of this lesion either at the level of the genome overall or at the gene level. Moreover, repair of dG-C8-AF in the active adenosine deaminase gene occurred at similar rates and without strand specificity in normal and CS cells, indicating that transcription-coupled repair does not contribute significantly to repair of dG-C8-AF in active genes. Yet CS cells are threefold more sensitive to NA-AAF than are normal cells and are unable to recover the ability to synthesize RNA. Our data rule out defective transcription-coupled repair as the cause of the increased sensitivity of CS cells to DNA-damaging agents and suggest that the cellular sensitivity and the prolonged repressed RNA synthesis are primarily due to a transcription defect. We hypothesize that upon treatment of cells with either UV or NA-AAF, the basal transcription factor TFIIH becomes involved in nucleotide excision repair and that the CS gene products are involved in the conversion of TFIIH back to the transcription function. In this view, the CS proteins act as repair-transcription uncoupling factors. If the uncoupling process is defective, RNA synthesis will stay repressed, causing cellular sensitivity. Since transcription is essential for transcription-coupled repair, the CS defect will affect those lesions whose repair is predominantly transcription coupled, i.e., UV-induced cyclobutane pyrimidine dimers.
Five-year follow-up of wide-diameter implants placed in fresh molar extraction sockets in the mandible: immediate versus delayed loading.

PURPOSE The aim of this study was to compare the long-term success rates of wide-diameter implants in the mandibular molar region placed immediately after extraction and loaded either immediately or after a 3-month healing period. MATERIALS AND METHODS In 71 patients, 120 implants were positioned immediately after tooth extraction; 60 implants (immediate loading group) were loaded immediately and 60 were loaded after 3 months (delayed loading group). Radiographic examinations were made at baseline and at 1, 2, 3, 4, and 5 years after implant placement. RESULTS After 5 years, a survival rate of 96.67% was reported for all implants (failure rate, 3.33%). Four implants were lost, two from the immediate loading group and two from the delayed loading group. There were no patient dropouts in either group. CONCLUSIONS Wide-diameter implants placed in fresh extraction sockets and loaded immediately or after a delay showed no significant clinical or radiographic differences after 5 years.
Validity of the SenseWear Armband to assess energy expenditure in graded walking.

BACKGROUND Accurate assessments of physical activity and energy expenditure (EE) are needed to advance research on positive and negative graded walking. PURPOSE To evaluate the validity of 2 SenseWear Armband monitors (Pro3 and the recently released Mini) during graded walking. METHODS Twenty healthy adults wore both monitors during randomized walking activities on a motorized treadmill at 7 grades (0%, ±5%, ±15%, and ±25%). Estimates of total EE from the monitors were computed using different algorithms and compared with values derived from indirect calorimetry methodology using a 2-way mixed model ANOVA (Device × Condition), correlation analyses and Bland-Altman plots. RESULTS There was no significant difference in EE between the 2 armbands in any of the conditions examined. Significant main effects for device and condition, as well as a consistent bias, were observed during positive and negative graded walking with a greater over- and under-estimation at higher slope. CONCLUSIONS Both the armbands produced similar EE values and seem to be not accurate in estimation of EE during activities involving uphill and downhill walking. Additional work is needed to understand factors contributing to this discrepancy and to improve the ability of these monitors to accurately measure EE during graded walking.
Surgical Intervention of Steroid-Induced Ocular Hypertension from Ozurdex

Purpose To present a case study on the management of ocular hypertension induced by repeated Ozurdex implants. Case Report A 51-year-old white man presented to the Tallahassee Veterans Affairs Outpatient Clinic as requested by the retinal specialist for an intraocular pressure (IOP) check. Two months before this visit, the patient was given an Ozurdex implant in each eye for reoccurring diabetic macular edema. Subsequent follow-up examinations documented the intervals between repeated Ozurdex implants and the increase in IOP, with progression to surgical intervention to control eye pressures. Conclusions Results from previous studies and this case report indicate that maximum IOP occurs at approximately 8 weeks after injection of an Ozurdex implant. Although most patients can be managed by IOP-lowering medications, this case is unique because it is an example of repeated implants at approximately 4-month intervals that led to surgical intervention to control IOP. Evidence-based knowledge of Ozurdex as reviewed in this article will lead to better patient postoperative management.
A Study and Comparison of the Effect of Profitability and Operating Cash Flow on Trademarks Value in Different Industries

This article aims to study the effect of profitability and Operating Cash Flow (OCF) on trademarks value in different industries and compare them. Data were analyzed in a sample size which consisted of 76 firms from 2008 to 2013 using data fusion and Ordinary Least Squares (OLS). The article consists of two hypotheses which study the relationship between two independent variables and trade value as dependent variable. The results show that profitability and OCF are found to have a significant relationship with trade value in firms under consideration.
Multivariate Analyses of Burkholderia Species in Soil: Effect of Crop and Land Use History

ABSTRACT The assessment of Burkholderia diversity in agricultural areas is important considering the potential use of this genus for agronomic and environmental applications. Therefore, the aim of this work was to ascertain how plant species and land use management drive the diversity of the genus Burkholderia. In a greenhouse experiment, different crops, i.e., maize, oat, barley, and grass, were planted in pots containing soils with different land use histories, i.e., maize monoculture, crop rotation, and permanent grassland, for three consecutive growth cycles. The diversity of Burkholderia spp. in the rhizosphere soil was assessed by genus-specific PCR-denaturing gradient gel electrophoresis (DGGE) and analyzed by canonical correspondence analysis (CCA). CCA ordination plots showed that previous land use was the main factor affecting the composition of the Burkholderia community. Although most variation in the Burkholderia community structure was observed between the permanent grassland and agricultural areas, differences between the crop rotation and maize monoculture groups were also observed. Plant species affected Burkholderia community structure to a lesser extent than did land use history. Similarities were observed between Burkholderia populations associated with maize and grass, on the one hand, and between those associated with barley and oat, on the other hand. Additionally, CCA ordination plots demonstrated that these two groups (maize/grass versus barley/oat) had a negative correlation. The identification of bands from the DGGE patterns demonstrated that the species correlated with the environmental variables were mainly affiliated with Burkholderia species that are commonly isolated from soil, in particular Burkholderia glathei, B. caledonica, B. hospita, and B. caribiensis.
Bacteremia among children admitted to a rural hospital in Kenya.

BACKGROUND There are few epidemiologic data on invasive bacterial infections among children in sub-Saharan Africa. We studied every acute pediatric admission to a rural district hospital in Kenya to examine the prevalence, incidence, types, and outcome of community-acquired bacteremia. METHODS Between August 1998 and July 2002, we cultured blood on admission from 19,339 inpatients and calculated the incidence of bacteremia on the basis of the population served by the hospital. RESULTS Of a total of 1783 infants who were under 60 days old, 228 had bacteremia (12.8 percent), as did 866 of 14,787 children who were 60 or more days of age (5.9 percent). Among infants who were under 60 days old, Escherichia coli and group B streptococci predominated among a broad range of isolates (14 percent and 11 percent, respectively). Among infants who were 60 or more days of age, Streptococcus pneumoniae, nontyphoidal salmonella species, Haemophilus influenzae, and E. coli accounted for more than 70 percent of isolates. The minimal annual incidence of community-acquired bacteremia was estimated at 1457 cases per 100,000 children among infants under a year old, 1080 among children under 2 years, and 505 among children under 5 years. Of all in-hospital deaths, 26 percent were in children with community-acquired bacteremia. Of 308 deaths in children with bacteremia, 103 (33.4 percent) occurred on the day of admission and 217 (70.5 percent) within two days. CONCLUSIONS Community-acquired bacteremia is a major cause of death among children at a rural sub-Saharan district hospital, a finding that highlights the need for prevention and for overcoming the political and financial barriers to widespread use of existing vaccines for bacterial diseases.
Correlation between mosquito larval density and their habitat physicochemical characteristics in Mazandaran Province, northern Iran

Characteristics of mosquito larval habitats are important in determining whether they can survive and successfully complete their developmental stages. Therefore, data on the ecological factors affecting mosquito density and abundance especially the physicochemical properties of water of their breeding sites, can possibly be helpful in implementing larval management programs. Mosquito larvae were collected using a standard 350 ml dipper from fixed habitats including: artificial pool, river edge, creek and etc, in 30 villages of 16 counties from May-December 2014. Water samples were collected during larval collection and temperature (°C), acidity (pH), turbidity (NTU), electrical conductivity (μS/cm), alkalinity (mg/l CaCO3), total hardness (mg/l), nitrate (mg/l), chloride (mg/l), phosphate (mg/l) and sulphate (mg/l) were measured using standard methods. Spearman correlation coefficient, Kruskal-Wallis test of nonparametric analysis, Chi-square (χ2) analysis, regression analysis and C8 interspecific correlation coefficient were used for data analysis. A total of 7,566 mosquito larvae belonging to 15 species representing three genera were collected from fixed larval breeding places. Culex pipiens was the dominant species except in four villages where An. maculipennis s.l. and Cx. torrentium were predominant. There was a significant positive correlation between the density of Cx. pipiens and electrical conductivity, alkalinity, total hardness and chloride, whereas no significant negative correlation was observed between physicochemical factors and larval density. The highest interspecific association of up to 0.596 was observed between An. maculipennis s.l/An. pseudopictus followed by up to 0.435 between An. maculipennis s.l/An. hyrcanus and An. hyrcanus/An. pseudopictus. The correlations observed between physicochemical factors and larval density, can possibly confirm the effect of these parameters on the breeding activities of mosquitoes, and may be indicative of the presence of certain mosquito fauna in a given region.
Pharmacokinetics of florfenicol after intravenous administration in Escherichia coli lipopolysaccharide-induced endotoxaemic sheep.

Experiments in different animal species have shown that febrile conditions, induced by Escherichia coli lipopolysaccharide (LPS), may alter the pharmacokinetic properties of drugs. The objective was to study the effects of a LPS-induced acute-phase response (APR) model on plasma pharmacokinetics of florfenicol (FFC) after its intravenous administration in sheep. Six adult clinically healthy Suffolk Down sheep, 8 months old and 35.5 ± 2.2 kg in body weight (bw), were distributed through a crossover factorial 2 × 2 design, with 4 weeks of washout. Pairs of sheep similar in body weight were assigned to experimental groups: Group 1 (LPS) was treated with three intravenous doses of 1 μg/kg bw of E. coli LPS before FFC treatment. Group 2 (control) was treated with an equivalent volume of saline solution (SS) at similar intervals as LPS. At 24 h after the first injection of LPS or SS, an intravenous bolus of 20 mg/kg bw of FFC was administered. Blood samples (5 mL) were collected before drug administration and at different times between 0.05 and 48.0 h after treatment. FFC plasma concentrations were determined by liquid chromatography. A noncompartmental pharmacokinetic model was used for data analysis, and data were compared using a Mann-Whitney U-test. The mean values of AUC0-∞ in the endotoxaemic sheep (105.9 ± 14.3 μg·h/mL) were significantly higher (P < 0.05) than values observed in healthy sheep (78.4 ± 5.2 μg·h/mL). The total mean plasma clearance (CLT ) decreased from 257.7 ± 16.9 mL·h/kg in the control group to 198.2 ± 24.1 mL·h/kg in LPS-treated sheep. A significant increase (P < 0.05) in the terminal half-life was observed in the endotoxaemic sheep (16.9 ± 3.8 h) compared to the values observed in healthy sheep (10.4 ± 3.2 h). In conclusion, the APR induced by the intravenous administration of E. coli LPS in sheep produces higher plasma concentrations of FFC due to a decrease in the total body clearance of the drug.
o‐Nitrotyrosine and p‐iodophenylalanine as spectroscopic probes for structural characterization of SH3 complexes

High‐throughput screening of protein–protein and protein–peptide interactions is of high interest both for biotechnological and pharmacological applications. Here, we propose the use of the noncoded amino acids o‐nitrotyrosine and p‐iodophenylalanine as spectroscopic probes in combination with circular dichroism and fluorescence quenching techniques (i.e., collisional quenching and resonance energy transfer) as a means to determine the peptide orientation in complexes with SH3 domains. Proline‐rich peptides bind SH3 modules in two alternative orientations, according to their sequence motifs, classified as class I and class II. The method was tested on an SH3 domain from a yeast myosin that is known to recognize specifically class I peptides. We exploited the fluorescence quenching effects induced by o‐nitrotyrosine and p‐iodophenylalanine on the fluorescence signal of a highly conserved Trp residue, which is the signature of SH3 domains and sits directly in the binding pocket. In particular, we studied how the introduction of the two probes at different positions of the peptide sequence (i.e., N‐terminally or C‐terminally) influences the spectroscopic properties of the complex. This approach provides clear‐cut evidence of the orientation of the binding peptide in the SH3 pocket. The chemical strategy outlined here can be easily extended to other protein modules, known to bind linear sequence motifs in a highly directional manner.
Posterior chamber toric phakic IOL implantation for the management of pediatric anisometropic amblyopia.

PURPOSE To report the outcomes of toric posterior chamber phakic intraocular lens (PIOL) implantation in children for the treatment of amblyopia due to anisometropia with astigmatism. METHODS Six eyes of 6 amblyopic patients aged 5 to 15 years underwent toric PIOL (Visian Toric ICL; STAAR Surgical Company, Monrovia, CA) implantation for refractory anisometropic amblyopia. Preoperative and postoperative clinical evaluation included slit-lamp microscopy, visual acuity, anterior/posterior segment examination, and cycloplegic refraction. RESULTS After a mean follow-up of 23 months (range: 15 to 34 months), mean spherical equivalent cycloplegic refraction improved from -10.21 ± 4.62 diopters (D) (range -7.5 to -19.5 D) preoperatively to -0.42 ± 0.39 D (range: -0.625 to +0.125 D) postoperatively. Corrected distance visual acuity ranged from 20/40 to 20/200 preoperatively and 20/20 to 20/60 postoperatively. Five of the 6 eyes gained more than 3 lines of corrected distance visual acuity with a maximum gain of 8 lines in one eye. One eye showed an improvement of more than 2 lines (change in preoperative visual acuity of 20/100 to 20/60 postoperatively). No patients lost any lines of visual acuity. All eyes remained quiet. All PIOLs remained well centered throughout the follow-up period. CONCLUSION Toric PIOL implantation may be a viable therapeutic modality in children with clinically significant anisometropic ametropia and astigmatism with secondary amblyopia who have been refractory to medical treatment including spectacles or contact lenses. Longer follow-up visits with larger sample populations will evaluate more effectively the long-term efficacy and late-onset of complications.
Towards Dense Object Tracking in a 2D Honeybee Hive

From human crowds to cells in tissue, the detection and efficient tracking of multiple objects in dense configurations is an important and unsolved problem. In the past, limitations of image analysis have restricted studies of dense groups to tracking a single or subset of marked individuals, or to coarse-grained group-level dynamics, all of which yield incomplete information. Here, we combine convolutional neural networks (CNNs) with the model environment of a honeybee hive to automatically recognize all individuals in a dense group from raw image data. We create new, adapted individual labeling and use the segmentation architecture U-Net with a loss function dependent on both object identity and orientation. We additionally exploit temporal regularities of the video recording in a recurrent manner and achieve near human-level performance while reducing the network size by 94% compared to the original U-Net architecture. Given our novel application of CNNs, we generate extensive problem-specific image data in which labeled examples are produced through a custom interface with Amazon Mechanical Turk. This dataset contains over 375,000 labeled bee instances across 720 video frames at 2FPS, representing an extensive resource for the development and testing of tracking methods. We correctly detect 96% of individuals with a location error of ~ 7% of a typical body dimension, and orientation error of 12Â°, approximating the variability of human raters. Our results provide an important step towards efficient image-based dense object tracking by allowing for the accurate determination of object location and orientation across time-series image data efficiently within one network architecture.
Determining Quality Teachers: Mathematical Content Knowledge, Perceptions of Teaching Self-Efficacy, and Attitudes toward Mathematics among a Teach for America Cohort.

The purpose of this study was to understand the relationships between mathematical content knowledge, perceptions of teaching self-efficacy, and attitudes toward mathematics in one cohort of Teach for America teachers who took the New York State Content Special Test in mathematics at the start of their program, and a mathematics attitude instrument taken before and after their first year teaching while taking graduate courses in a teacher education program. Additionally, teachers completed a self-efficacy instrument in their second year of teaching and graduate coursework. The major finding revealed that mathematical content knowledge was related to attitudes toward mathematics, and attitudes toward mathematics were related to perceptions of self-efficacy. It was found that teachers with mathematics related majors had higher mathematical content knowledge than did business majors, but similar levels of self-efficacy. Liberal arts majors had similar content knowledge and levels of self-efficacy as did mathematics related majors.
EDITORIAL COMMENTS

1. Francois Cocquemas 1. is The FMRC Research Scholar at Vanderbilt University in Nashville, TN and a PhD candidate at EDHEC Business School in Nice, France. (francois.cocquemas{at}owen.vanderbilt.edu) 2. Robert E. Whaley 1. is the Valere Blair Potter Professor of Management and
Single-session alcohol-retention sclerotherapy for simple renal cysts: comparison of 2- and 4-hr retention techniques.

OBJECTIVE The objectives of our study were to evaluate the feasibility of ethanol sclerotherapy in treating simple renal cysts with prolonged ethanol retention and to compare the therapeutic results of 2- and 4-hr retention techniques. MATERIALS AND METHODS We retrospectively reviewed 36 renal cysts in 33 patients treated by ethanol sclerotherapy with a single-session single-injection technique during the past 6 years. After complete aspiration of the cystic fluid, 95% ethanol was injected into the cyst and was retained for 4 hr in 14 cysts (group 1) and for 2 hr in 22 cysts (group 2). The average maximal diameter and aspirated volume of the cysts were 8.3 cm and 223 mL in group 1 patients and 7.9 cm and 167 mL in group 2, respectively. The ablated cysts were followed up regularly by sonography, CT, or both at 3- to 6-month intervals for at least 1 year. The nonparametric Mann-Whitney U test was used to compare differences in characteristics, treatment results, and laboratory data of the subjects in the two groups. The level of statistical significance was set at a p value of less than 0.05. RESULTS Technically, all the patients tolerated the procedures. One patient had gross hematuria 10 days after the procedure. She underwent surgical deroofing treatment and was excluded in the later statistical analysis. After sclerotherapy, 14 cysts disappeared completely and 16 cysts showed marked regression with residual maximal diameter of less than 3 cm. The overall volume reduction rate was 97.6% in all 35 cysts. The mean residual longest diameters and average volume reduction rates of the treated cysts were 1.9 cm and 97.9% in group 1 patients and 1.1 cm and 97.3% in group 2 patients, respectively, which showed no statistical significance of volume reduction rate with a p value 0.149. CONCLUSION The single-session prolonged ethanol-retention technique is safe and efficacious for the treatment of renal cysts. There is no statistical difference in therapeutic efficacy between 2- and 4-hr ethanol-retention techniques.