Miracle-dz/UniFAR-FTUs huggingface dataset:
Analytical modeling of Transmission Control Protocol NewReno using Generalized Stochastic Petri Nets

This paper presents a novel analytical model of Transmission Control Protocol (TCP) using a generalized stochastic Petri net (GSPN). Extensive simulation work has been done for the performance evaluation of TCP NewReno protocol. In view of the limitations of the simulation technique, we present an analytical approach using GSPN. A GSPN is a useful mathematical tool that solves continuous time Markov chains for complex systems and evaluates the stationary behavior. In this paper, we analyze the slow‐but‐steady variant of TCP NewReno. The model captures the behavioral aspects of the slow start and the congestion avoidance phase together with the fast retransmit and recovery capabilities of TCP NewReno. Performance metrics such as throughput, goodput, and task completion time of the system are obtained. The effect of variation in the model parameters on the performance is studied. The results are validated using the network simulator, and their accuracy is verified by evaluating the confidence interval. The performance of the proposed model is compared with that of TCP Reno. The performance of the proposed model is also compared with one of the previous models. The numerical illustrations and comparison of the proposed technique with simulation validates the accuracy, efficiency, and competence of the GSPN technique. While GSPN modeling for TCP is investigated in depth for the TCP NewReno and TCP Reno variant in this paper, other protocols could be also analyzed similarly. Copyright © 2013 John Wiley & Sons, Ltd.
DEXUS: identifying differential expression in RNA-Seq studies with unknown conditions

Detection of differential expression in RNA-Seq data is currently limited to studies in which two or more sample conditions are known a priori. However, these biological conditions are typically unknown in cohort, cross-sectional and nonrandomized controlled studies such as the HapMap, the ENCODE or the 1000 Genomes project. We present DEXUS for detecting differential expression in RNA-Seq data for which the sample conditions are unknown. DEXUS models read counts as a finite mixture of negative binomial distributions in which each mixture component corresponds to a condition. A transcript is considered differentially expressed if modeling of its read counts requires more than one condition. DEXUS decomposes read count variation into variation due to noise and variation due to differential expression. Evidence of differential expression is measured by the informative/noninformative (I/NI) value, which allows differentially expressed transcripts to be extracted at a desired specificity (significance level) or sensitivity (power). DEXUS performed excellently in identifying differentially expressed transcripts in data with unknown conditions. On 2400 simulated data sets, I/NI value thresholds of 0.025, 0.05 and 0.1 yielded average specificities of 92, 97 and 99% at sensitivities of 76, 61 and 38%, respectively. On real-world data sets, DEXUS was able to detect differentially expressed transcripts related to sex, species, tissue, structural variants or quantitative trait loci. The DEXUS R package is publicly available from Bioconductor and the scripts for all experiments are available at http://www.bioinf. jku.at/software/dexus/.
Is alcopop consumption in Switzerland associated with riskier drinking patterns and more alcohol-related problems?

OBJECTIVES To examine (a) whether consumers of alcopops compared to consumers of other alcoholic beverages but not alcopops have riskier drinking patterns and more alcohol-related consequences (e.g. truancy, scuffles, problems with parents) and (b) whether the amount of alcopops consumed is associated independently with risky drinking patterns and alcohol-related consequences over and above those associated with the amount of other alcoholic beverages consumed. SAMPLE As part of the ESPAD international study, a cross-sectional national representative sample of 5,444 drinkers aged 13-16 years was interviewed by means of an anonymous, self-report questionnaire administered in a classroom setting. RESULTS Earlier initiation of consumption, more frequent risky single occasion drinking (RSOD), and a higher likelihood of negative consequences for consumers than for non-consumers of alcopops were due mainly to higher overall consumption. Other alcoholic beverages had similar effects, and whether the same amount of alcohol was consumed as alcopops or as any conventional alcoholic beverage made no difference. CONCLUSIONS Alcopops in Switzerland do not seem to be linked to specific riskier drinking patterns or consequences per se. Like all alcoholic beverages, they add to the problems caused by drinking and seem to be consumed in addition to conventional alcoholic beverages without replacing them. As the alcohol industry will continue to launch new beverages, prevention targeting alcohol consumption in general might be more effective than focusing on new beverages only.
Clinical efficacy and safety of sublingual immunotherapy with tree pollen extract in children

Background: Subcutaneous immunotherapy has been the principal approach of immunotherapy in the treatment of allergic diseases. Several clinical studies with birch, alder or hazel pollen extract conducted as subcutaneous immunotherapy have been published suggesting a well‐tolerated and clinically effective treatment. Only a few clinical studies of sublingual immunotherapy (SLIT) with these allergens have been published. This study investigated the clinical efficacy, safety and dose–response relationship of SLIT in children suffering from rhinoconjunctivitis with/without asthma.
Tension-Compression Fatigue Behavior of a Silicon Carbide Calcium-Aluminosilicate Ceramic Matrix Composite

The fatigue behavior of a silicon carbide fiber reinforced glass ceramic matrix composite, SiC/CAS subjected to tension-compression cycling was investigated. Two laminate layups were studied: cross-ply, [0/90]25 and unidirectional, [0]16. At first, the fatigue limit based on one million cycles was established for a tension-tension fatigue condition. Then, compression cycling was superimposed on this measured fatigue limit. The addition of this compression loading resulted in the development of longitudinal cracks parallel to the loading direction. This increased the amount of damage and ulti mately led to total specimen failure prematurely. The larger the magnitude of the compres sion cycle, the earlier the development of longitudinal crack occurred and, consequently, the earlier failure occurred. This behavior was due to the inherently poor interfacial bond between matrix and fiber of the tested ceramic matrix composite.
Genetic instability and associated genome plasticity in Streptomyces ambofaciens: pulsed-field gel electrophoresis evidence for large DNA alterations in a limited genomic region

Using pulsed-field gel electrophoresis (PFGE) analysis, the amplifiable units of DNA (AUD) loci AUD6 and AUD90 of Streptomyces ambofaciens DSM40697 could be mapped in the wild-type genome within two adjacent AseI restriction fragments estimated to be about 75 and 850 kb. In addition, the genetic instability and formation of very large deletions were strictly correlated. Their sizes were estimated to range from 250 to more than 2,000 kb. These deletions affected the DNA region overlapping both amplifiable loci. PFGE also allowed us to localize the amplified DNA sequences and to establish their structure: amplification takes place at the AUD locus as a tandem array of the wild-type AUD sequence.
Impact of daylight saving time on road traffic collision risk: a systematic review

Background Bills have been put forward in the UK and Republic of Ireland proposing a move to Central European Time (CET). Proponents argue that such a change will have benefits for road safety, with daylight being shifted from the morning, when collision risk is lower, to the evening, when risk is higher. Studies examining the impact of daylight saving time (DST) on road traffic collision risk can help inform the debate on the potential road safety benefits of a move to CET. The objective of this systematic review was to examine the impact of DST on collision risk. Methods Major electronic databases were searched, with no restrictions as to date of publication (the last search was performed in January 2017). Access to unpublished reports was requested through an international expert group. Studies that provided a quantitative analysis of the effect of DST on road safety-related outcomes were included. The primary outcomes of interest were road traffic collisions, injuries and fatalities. Findings Twenty-four studies met the inclusion criteria. Seventeen examined the short-term impact of transitions around DST and 12 examined long-term effects. Findings from the short-term studies were inconsistent. The long-term findings suggested a positive effect of DST. However, this cannot be attributed solely to DST, as a range of road collision risk factors vary over time. Interpretation The evidence from this review cannot support or refute the assertion that a permanent shift in light from morning to evening will have a road safety benefit.
The Carboxyl Terminus of GLUT4 Contains a Serine-Leucine-Leucine Sequence That Functions as a Potent Internalization Motif in Chinese Hamster Ovary Cells*

To characterize the trafficking motifs contained in the carboxyl terminus of GLUT4, a chimera (GTCTR) was constructed in which the carboxyl-terminal 30 amino acids of GLUT4 were substituted for the amino-terminal cytoplasmic domain of the transferrin receptor (TR). The endocytic behavior of this chimera was characterized in Chinese hamster ovary cells. The GTCTR chimera had a more predominant intracellular distribution compared to the TR. Only 20% of the GTCTR chimera is on the surface at steady-state compared to 35% of the TR. The GTCTR chimera is internalized 50% more rapidly and recycled 20% more slowly than the TR. Acidification of the cytosol inhibited internalization of the GTCTR chimera, indicating that the chimera is internalized through clathrin-coated pits. Mutations of GTCTR were constructed in which a di-leucine sequence of the carboxyl domain of GLUT4 was mutated to a di-alanine sequence (GTCTR-AA) and serine residue 488, immediately preceding the di-leucine sequence, was mutated to either an alanine or aspartate residue. In each case, albeit to varying degrees, the substitutions shifted the distribution of the mutated GTCTR constructs toward the surface. The shift in the distribution of GTCTR-AA resulted from a 10-fold reduction in internalization, and the shift of serine 488 mutants resulted from a 3-fold reduction in the internalization rate compared to GTCTR. None of these mutations affected the recycling rate. These results demonstrate that the carboxyl terminus of GLUT4 contains a serine-leucine-leucine-based motif that, when expressed in non-insulin responsive cells, functions as a potent internalization motif which promotes more rapid internalization than does the native TR internalization motif.
Prognostic significance of DNA patterns and resistance‐predictive tests in non‐small cell lung carcinoma

In a cooperative study, 240 surgical specimens of patients with non‐small cell lung carcinomas (NSCLC) were investigated by means of flow cytometry, xenotransplantation to athymic mice and, an in vitro short‐term test for predicting resistance. Aneuploidy was found in 83% of the tumors, and 20% showed more than one aneuploid DNA stemline. Patients with both aneuploid tumors and tumors with more than one DNA stemline had a significantly shorter survival rate than those with only diploid or only one DNA stemline. Patients whose tumors showed a low G0/G1‐cell proportion or a high proliferation pool (S and G2/M‐cell proportion) died earlier. A relationship could not be discerned between growth of tumors in nude mice or establishment of cell lines and the prognosis for the patients. Patients with in vitro‐resistant tumors died earlier under chemotherapy than those with in vitro‐sensitive tumors. Patients treated by radiation survived longer if the tumors were resistant in vitro. Thus, DNA patterns and in vitro short‐term tests for predicting resistance represent useful tools for prognostic evaluation of patients with NSCLC.
Simplified Instability Measurement Devices for Air-Jet Textured Yarns

12. Kamal, M. M. , Zeronian, S. H. , Ellison, M. S. , and Hyer, A. H. , Selected Single Fiber Mechanical Properties of Different Gossypium barbadense Cotton Varieties, Textile Res. J. 54, 343-350 (1984). 13. Meredith, R. , in "The Mechanical Properties of Textile Fibres," R. Meredith, Ed., North-Holland Publishing Company, Amsterdam, 1956, p. 146. 14. Roff, W. J., The Determination of the Formaldehyde Yield of Cellulose Textiles Treated with Formaldehyde, Urea-formaldehyde or Melamine-formaldehyde, J. Textile Inst. 47, T309-318 ( 1956). 15. Rowland, S. P., Hydroxyl Reactivity and Availability in Cellulose, in "Modified Cellulosics," R. M. Rowell and R. A. Young, Eds., Academic Press, New York, 1978, pp. 147-167. 16. Weiss, L. C. , Grant, J. N. , and George, M. , Recovery and Strength of Chemically Modified Single Cotton Fibers, Textile Res. J. 40, 583-590 ( 1970). 17. Zeronian, S. H. , Intracrystalline Swelling of Cellulose, in "Cellulose Chemistry and Its Applications," T. P. Nevell and S. H. Zeronian, Eds., Ellis Horwood/Halsted Press, New York, 1985, pp. 159-180. 18. Zeronian, S. H. , Alger, K. W. , and Cabradilla, K. E. , Tensile Properties of Cotton Treated with Alkali Metal Hydroxides, J. Appl. Polym. Sci. 20, 1689-1693 ( 1976). 19. Zeronian, S. H. , Coole, M. L. , Alger, K. W. , and Chandler, J. M. , Studies on the Water Sorption Isotherms of Celluloses and Their Use for Determining Cellulose Crystallinities, J. Appl. Polym. Sci. Appl. Polym. Sym. 37, 1053-1069 (1983).
Giant Cell Tumor of Long Bones Outcomes of Treatment Corelating with Histopathological Grade.

INTRODUCTION Giant cell tumor (GCT) of bone is a borderline lesion of bones, meaning that in certain conditions it could be transforming in malignant tumor. This article describes the clinical outcome of patients with giant cell tumor of bone and discusses the surgical options for this lesion corelating with histopathological grade. MATERIAL AND METHODS From 2007 to 2015, 15 patients who met the histological criteria of giant cell tumor of bone were treated at our institution. Diagnosis and histopathological grade were established by biopsy and extemporaneous exam during surgery. Procedure to be selected was decided based on histopathological grade. Outcomes: In all cases the joint functional results were good except 3 cases (20%) where recurrence occurred. In one case the local recurrence was observed after 6 months, and in the other 2 cases, at 3, respectively 5 years after primary treatment. In all 3 cases the initial histopathological exam showed inactive lesions and were treated with curettage and bone grafting. CONCLUSION In our series it was an early reccurence at 6 months and 2 recidives after 2 years.The histopathological exam has significant role in the management of GCT. All inactive lesions were treated by curettage and bone grafting, and active lesions, by curettage and bone cement filling no matter of Campanacci's grading system. The management is depending mostly on histopathological exam. Low rate of recurrence can be achieved if treatment is selected according to this parameter and with a properly technique.
Effect of Equal-Channel Angular Rolling Pass on Microstructure and Properties of Magnesium Alloy Sheets

The objective of this study was to determine the effect of rolling pass on AZ31 magnesium alloy sheets, which were produced by a new concept process, so-called equal-channel angular rolling process. Processing that causes continuous shearing deformation leads to a shifting of the crystal orientation from basal plane to non-basal plane. Compared with the as-received specimens, a lower yield strength and a higher ductility of the specimens produced by equal-channel angular rolling in tensile tests at ambient temperature were presented because of the non-basal crystal orientation. Drawability was also improved greatly.
The Effects of Prenatal Alcohol and Marijuana Exposure: Disturbances in Neonatal Sleep Cycling and Arousal

ABSTRACT: Neonatal EEG and sleep findings are presented from a longitudinal study of the effects of maternal alcohol and marijuana use during pregnancy. Infant outcome has been examined relative to the trimester(s) of pregnancy during which use occurred. Disturbances in sleep cycling, motility, and arousals were noted that were both substance and trimester specific. Alcohol consumed during the first trimester of pregnancy was associated with disruptions in sleep and arousal, whereas marijuana use affected sleep and motility regardless of the trimester in which it was used. Although these findings are preliminary and based on a small sample of women exhibiting only moderate substance use during pregnancy, they do suggest that specific neurophysiological systems may be differentially affected by prenatal alcohol or marijuana exposure even in the absence of morphological abnormalities.
On the top-Lyapunov exponent of block-triangular stationary random matrices

The objective of this note is to prove a useful, nontrivial technical lemma that is needed in the statistical analysis of linear stochastic systems with random system matrices. This study is motivated by the study of the quasi-maximum-likelihood identification method of certain stochastic volatility processes, called the GARCH (Generalized Autoregressive Conditional Heteroscedasticity) processes.
Novel Clones of Streptococcus pneumoniae Causing Invasive Disease in Malaysia

Although Streptococcus pneumoniae is a leading cause of childhood disease in South East Asia, little has previously been reported regarding the epidemiology of invasive pneumococcal disease in Malaysia and very few studies have explored pneumococcal epidemiology using multilocus sequence typing (MLST). Here we describe serotype, multilocus sequence type (ST), and penicillin susceptibility of thirty pneumococcal invasive disease isolates received by the University of Malaya Medical Centre between February 2000 and January 2007 and relate this to the serotypes included in current pneumococcal conjugate vaccines. A high level of diversity was observed; fourteen serotypes and 26 sequence types (ST), (11 of which were not previously described) were detected from 30 isolates. Penicillin non-susceptible pneumococci accounted for 33% of isolates. The extent of molecular heterogeneity within carried and disease-causing Malaysian pneumococci remains unknown. Larger surveillance and epidemiological studies are now required in this region to provide robust evidence on which to base future vaccine policy.
Comparison of Diffuse Weighted Imaging and Fluid Attenuation Inversion Recovery Sequences of MRI in Brain Multiple Sclerosis Plaques Detection

Objective Suitable magnetic resonance imaging (MRI) techniques from conventional to new devices can help physicians in diagnosis and follow up of Multiple Sclerosis (MS) patients. The aim of present research was to compare effectiveness of Fluid Attenuation Inversion Recovery (FLAIR) sequence of conventional MRI and Diffuse Weighted Imaging (DWI) sequence as a new technique in detection of brain MS plaques. Materials & Methods In this analytic cross sectional study, sample size was assessed as 40 people to detect any significant difference between two sequences with a level of 0.05. DWI and FLAIR sequences of without contrast brain MRI of consecutive MS patients referred to MRI center of Shahid Sadoughi Hospital, Yazd, Iran from January to May 2012, were evaluated. Results Thirty-two females and 8 males with mean age of 35.20±9.80 yr (range = 11-66 yr) were evaluated and finally 340 plaques including 127(37.2%) in T2WI, 127(37.2%) in FLAIR, 63(18.5%) in DWI and 24(7.1%) in T1WI were detected. FLAIR sequence was more efficient than DWI in detection of brain MS plaques, oval, round, amorphous plaque shapes, frontal and occipital lobes, periventricular, intracapsular, corpus callosum, centrum semiovale, subcortical, basal ganglia plaques and diameter of detected MS plaques in DWI sequence was smaller than in FLAIR. Conclusion Old lesion can be detected by conventional MRI and new techniques might be more useful in early inflammatory phase of MS and assessment of experimental treatments.
SIRT6 rescues the age related decline in base excision repair in a PARP1-dependent manner

In principle, a decline in base excision repair (BER) efficiency with age should lead to genomic instability and ultimately contribute to the onset of the aging phenotype. Although multiple studies have indicated a negative link between aging and BER, the change of BER efficiency with age in humans has not been systematically analyzed. Here, with foreskin fibroblasts isolated from 19 donors between 20 and 64 y of age, we report a significant decline of BER efficiency with age using a newly developed GFP reactivation assay. We further observed a very strong negative correlation between age and the expression levels of SIRT6, a factor which is known to maintain genomic integrity by improving DNA double strand break (DSB) repair. Our mechanistic study suggests that, similar to the regulatory role that SIRT6 plays in DNA DSB repair, SIRT6 regulates BER in a PARP1-depdendent manner. Moreover, overexpression of SIRT6 rescues the decline of BER in aged fibroblasts. In summary, our results uncovered the regulatory mechanisms of BER by SIRT6, suggesting that SIRT6 reactivation in aging tissues may help delay the process of aging through improving BER.
Micromechanisms of crack growth in ceramics and glasses in corrosive environments

AbstractAt normal temperatures and pressures water is known to have a strong influence on the strength of ceramics and glasses. Behaving as a stress corrosion agent, water causes these materials to fail prematurely as a consequence of subcritical crack growth. A basic premise of this paper is that stress corrosion cracking of ceramics is a chemical process which involves a stress-enhanced chemical reaction between the water and the highly stressed ceramic near the crack tip. Plastic deformation is believed to play no role in this fracture process. After a brief survey of chemical reaction rate theory, the basic rate equation from this theory is modified to reflect physical and chemical processes which occur at crack tips. Modification of the rate equation is based on the assumption thatl the crack tip can be modelled as an elastic continuum, an assumption that is supported by a simple atomistic model of crack growth. When tested against experimental data collected on glass the theory was found to be consi.
Class Start Times, Sleep, and Academic Performance in College: A Path Analysis

Path analysis was used to examine the relationship between class start times, sleep, circadian preference, and academic performance in college-aged adults. Consistent with observations in middle and high school students, college students with later class start times slept longer, experienced less daytime sleepiness, and were less likely to miss class. Chronotype was an important moderator of sleep schedules and daytime functioning; those with morning preference went to bed and woke up earlier and functioned better throughout the day. The benefits of taking later classes did not extend to academic performance, however; grades were somewhat lower in students with predominantly late class schedules. Furthermore, students taking later classes were at greater risk for increased alcohol consumption, and among all the factors affecting academic performance, alcohol misuse exerted the strongest effect. Thus, these results indicate that later class start times in college, while allowing for more sleep, also increase the likelihood of alcohol misuse, ultimately impeding academic success. (Author correspondence: sonyper@stlawu.edu)