Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Characterisation of Malawian Pneumococci Prior to the Roll-Out of the PCV13 Vaccine Using a High-Throughput Whole Genome Sequencing Approach

Background Malawi commenced the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) into the routine infant immunisation schedule in November 2011. Here we have tested the utility of high throughput whole genome sequencing to provide a high-resolution view of pre-vaccine pneumococcal epidemiology and population evolutionary trends to predict potential future change in population structure post introduction. Methods One hundred and twenty seven (127) archived pneumococcal isolates from randomly selected adults and children presenting to the Queen Elizabeth Central Hospital, Blantyre, Malawi underwent whole genome sequencing. Results The pneumococcal population was dominated by serotype 1 (20.5% of invasive isolates) prior to vaccine introduction. PCV13 is likely to protect against 62.9% of all circulating invasive pneumococci (78.3% in under-5-year-olds). Several Pneumococcal Molecular Epidemiology Network (PMEN) clones are now in circulation in Malawi which were previously undetected but the pandemic multidrug resistant PMEN1 lineage was not identified. Genome analysis identified a number of novel sequence types and serotype switching. Conclusions High throughput genome sequencing is now feasible and has the capacity to simultaneously elucidate serotype, sequence type and as well as detailed genetic information. It enables population level characterization, providing a detailed picture of population structure and genome evolution relevant to disease control. Post-vaccine introduction surveillance supported by genome sequencing is essential to providing a comprehensive picture of the impact of PCV13 on pneumococcal population structure and informing future public health interventions.
Classical critical behavior of spin models with long-range interactions

We present the results of extensive Monte Carlo simulations of Ising models with algebraically decaying ferromagnetic interactions in the regime where classical critical behavior is expected for these systems. We corroborate the values for the exponents predicted by renormalization theory for systems in one, two, and three dimensions and accurately observe the predicted logarithmic corrections at the upper critical dimension. We give both theoretical and numerical evidence that above the upper critical dimension the decay of the critical spin-spin correlation function in finite systems consists of two different regimes. For one-dimensional systems our estimates for the critical couplings are more than two orders of magnitude more accurate than existing estimates. In two and three dimensions we are unaware of any other results for the critical couplings.
Diurnal‐seasonal and weather‐related variations of land surface temperature observed from geostationary satellites

The time series of clear‐sky Land Surface Temperatures (LST) for one year, 2001, obtained from pyrgeometric observations at five selected US surface radiation (SURFRAD) stations and independently retrieved for the locations of these stations from Infrared Imager hourly observations of two geostationary satellites, GOES‐8 and GOES‐10, are presented as a sum of time‐dependent expected value (diurnal and seasonal cycles), and weather‐related anomalies. The availability of three independent observations is used to assess random and systematic errors in LST data. Temporal variation of the expected value is approximated as a superposition of the first two annual and diurnal Fourier harmonics. This component of temporal variations of LST absorbs all systematic errors; which themselves are often a subject of diurnal and seasonal variations. The results revealed that the weather‐related temporal variation of LST is much smaller than the temporal variations of the expected value, but much larger than the random errors of observation. Scale of temporal autocorrelation of weather‐related component of clear‐sky LST variations is about 3 days.
Revisiting the washout period in the incident user study design: why 6-12 months may not be sufficient.

AIMS The purpose of this study was to describe how washout period duration affects the size and accuracy of retrospective incident user cohorts. MATERIALS & METHODS MarketScan commercial claims data from 2007 to 2010 were used and included adults with an antihyperlipidemic, antidiabetic or antidepressant claim in 2010. Incident user cohorts using 3-, 6-, 12-, 24- and 36-month washouts were created and changes in sample size and incident user misclassification were described. RESULTS & CONCLUSION The 6- and 12-month washouts excluded 75 and 85% of the samples, respectively. Half of subjects in the 6-month washout cohorts were actually prevalent users, and the 12-month washout period resulted in 30% misclassified. Using common washout periods of 6-12 months may insufficiently address prevalent user bias in large commercial claims databases.
Smoking and the Long-Term Incidence of Cataract: The Blue Mountains Eye Study

Purpose: To assess the association between smoking and the long-term incidence of cataract and cataract surgery. Methods: In a population-based cohort of Australians aged 49 years and over, 3654 participants were seen at baseline (1992–94) and 2406 were seen after 5- and/or 10-years and had photographs taken to assess incident cataract. Smoking status was recorded at interview. History, physical examination and fasting blood samples provided data on possible risk factors. Cataract incidence was calculated using the Kaplan-Meier survival approach. Discrete linear logistic models were used to assess risk of incident cataract. Results: After controlling for age, sex and other factors, ever smokers had an increased risk of developing nuclear cataract compared to never smokers (relative risk (RR) 1.41; 95% confidence interval (CI) 1.09–1.83; RR 1.37, CI 1.04–1.81 for past smoking and RR 1.57, CI 1.06–2.31 for current smoking). The effect of smoking was strongest in ever smokers reporting 36 + pack-years of smoking compared to never smokers (RR 1.46; CI, 1.02–2.08). Current smokers also developed nuclear cataract slightly younger than non-smokers (mean age 65.2 versus 67.5 years, p = 0.049). No statistically significant associations were found between smoking status and the incidence of cortical or posterior subcapsular cataract, or cataract surgery. Conclusions: These epidemiological data confirm smoking as a modest risk factor for the development of nuclear cataract.
Fixation of cochlear implants: an evidence-based review of literature.

HYPOTHESIS There are numerous cochlear implant fixation techniques to prevent soft tissue complications related to device migration. The literature does not provide sufficient evidence to determine the most suitable fixation method. BACKGROUND Cochlear implants (CI) are becoming a routine treatment for patients with severe to profound deafness. Steadily growing numbers of implant centres and surgeons worldwide are inevitably leading to higher rates of complications, including device migration. It is currently unknown whether this can be prevented by proper implant fixation during surgery. The low prevalence of this complication makes it challenging to interpret publications regarding CI fixation techniques. METHODS An exhaustive literature review reveals a variety of different fixation techniques. Most authors advocate the creation of a bony well for the CI receiver/stimulator (R/S); however, an increasing number of surgeons no longer secure implants at all. Here we give an overview of all published fixation methods, with special attention to the evidence-based quality and descriptions of the advantages and drawbacks of each. CONCLUSIONS Literature review reveals an absence of level I evidence-based publications addressing device migration. Existing publications report on too few cases to draw a conclusion on whether surgical fixation prevents implant migration. To have statistical power, studies of alternative or new fixation methods should include high numbers of implantations in each study arm and the studies should be longitudinal and prospective. In default of other evidence, it seems fair to define good practice as the creation of at least a bony well and/or (bony) sutures.
AutoScale: Dynamic, Robust Capacity Management for Multi-Tier Data Centers

Energy costs for data centers continue to rise, already exceeding $15 billion yearly. Sadly much of this power is wasted. Servers are only busy 10--30% of the time on average, but they are often left on, while idle, utilizing 60% or more of peak power when in the idle state. We introduce a dynamic capacity management policy, AutoScale, that greatly reduces the number of servers needed in data centers driven by unpredictable, time-varying load, while meeting response time SLAs. AutoScale scales the data center capacity, adding or removing servers as needed. AutoScale has two key features: (i) it autonomically maintains just the right amount of spare capacity to handle bursts in the request rate; and (ii) it is robust not just to changes in the request rate of real-world traces, but also request size and server efficiency. We evaluate our dynamic capacity management approach via implementation on a 38-server multi-tier data center, serving a web site of the type seen in Facebook or Amazon, with a key-value store workload. We demonstrate that AutoScale vastly improves upon existing dynamic capacity management policies with respect to meeting SLAs and robustness.
Differences in clinical presentation and pregnancy outcomes in antepartum preeclampsia and new-onset postpartum preeclampsia: Are these the same disorder?

Objective New-onset postpartum preeclampsia is a poorly defined condition that accounts for a significant percentage of eclampsia cases. It is unclear whether new-onset postpartum preeclampsia is a different disorder from or belongs to the same spectrum of classic antepartum preeclampsia. The objective of this study was to compare the clinical presentation and pregnancy outcomes of antepartum preeclampsia and new-onset postpartum preeclampsia. Methods A retrospective study including 92 patients with antepartum preeclampsia and 92 patients with new-onset postpartum preeclampsia was performed. Clinical presentation and pregnancy outcomes were compared. Chi-square test was used to analyze categorical variables, and independent t-test and Mann-Whitney U-test for numerical variables. P-values of <0.05 were used to indicate statistical signifi cance. Results Patients with antepartum preeclampsia and new-onset postpartum preeclampsia differ significantly in profile, symptoms at presentation, laboratory markers and pregnancy outcomes. Conclusion New-onset postpartum preeclampsia has a distinct patient profile and clinical presentation than antepartum preeclampsia, suggesting they may represent different disorders. Characterization of a patient profile with increased risk of developing this condition will help clinicians to identify patients at risk and provide early and targeted interventions to decrease the morbidity associated with this condition.
Non‐thermal transient sources from rotating black holes

Rotating black holes can power the most extreme non-thermal transient sources. They have a long-duration viscous time-scale of spin-down, and produce non-thermal emissions along their spin-axis, powered by a relativistic capillary effect. We report on the discovery of exponential decay in Burst and Triensient Source Experiment (BATSE) light curves of long gamma-ray bursts (GRBs) by matched filtering, consistent with a viscous time-scale, and identify ultra-high energy cosmic rays (UHECRs) about the Greisen–Zatsepin–Kuzmin (GZK) threshold with linear acceleration of ion contaminants along the black hole spin-axis, consistent with black hole masses and lifetimes of Fanaroff–Riley type II (FR II) active galactic nuclei (AGN). We explain the absence of UHECRs from BL Lac objects due to UHECR emissions preferably at appreciable angles away from the black hole spin-axis. Black hole spin may be the key to unification of GRBs and their host environments, and to AGN and their host galaxies. Our model points to long-duration bursts in radio from long GRBs without supernovae and gravitational waves from all long GRBs.
Liposomal butamben gel formulations: toxicity assays and topical anesthesia in an animal model

Abstract The aim of this study was to evaluate the in vitro cytotoxicity and the in vivo analgesic effect and local toxicity of the local anesthetic butamben (BTB) encapsulated in conventional or elastic liposomes incorporated in gel formulations. The results showed that both gel formulations of liposomal BTB reduced the cytotoxicity (p < 0.001; one-way ANOVA/Tukey’s test) and increased the topical analgesic effect (p < 0.05; one-way ANOVA/Tukey’s test) of butamben, compared to plain BTB gel. The gel formulations presented good rheological properties, and stability assays detected no differences in physicochemical stability up to 30 d after preparation. Moreover, histological assessment revealed no morphological changes in rat skin after application of any of the gel formulations tested.
Twin Support Vector Machine for Multiple Instance Learning Based on Bag Dissimilarities

In multiple instance learning (MIL) framework, an object is represented by a set of instances referred to as bag. A positive class label is assigned to a bag if it contains at least one positive instance; otherwise a bag is labeled with negative class label. Therefore, the task of MIL is to learn a classifier at bag level rather than at instance level. Traditional supervised learning approaches cannot be applied directly in such kind of situation. In this study, we represent each bag by a vector of its dissimilarities to the other existing bags in the training dataset and propose a multiple instance learning based Twin Support Vector Machine (MIL-TWSVM) classifier. We have used different ways to represent the dissimilarity between two bags and performed a comparative analysis of them. The experimental results on ten benchmark MIL datasets demonstrate that the proposed MIL-TWSVM classifier is computationally inexpensive and competitive with state-of-the-art approaches. The significance of the experimental results has been tested by using Friedman statistic and Nemenyi post hoc tests.
Human Thymine DNA Glycosylase Binds to Apurinic Sites in DNA but Is Displaced by Human Apurinic Endonuclease 1*

In vitro, following the removal of thymine from a G·T mismatch, thymine DNA glycosylase binds tightly to the apurinic site it has formed. It can also bind to an apurinic site opposite S 6-methylthioguanine (SMeG) or opposite any of the remaining natural DNA bases. It will therefore bind to apurinic sites formed by spontaneous depurination, chemical attack, or other glycosylases. In the absence of magnesium, the rate of dissociation of the glycosylase from such complexes is so slow (k off 1.8 − 3.6 × 10−5 s−1; i.e. half-life between 5 and 10 h) that each molecule of glycosylase removes essentially only one molecule of thymine. In the presence of magnesium, the dissociation rates of the complexes with C·AP andSMeG·AP are increased more than 20-fold, allowing each thymine DNA glycosylase to remove more than one uracil or thymine from C·U and SMeG·T mismatches in DNA. In contrast, magnesium does not increase the dissociation of thymine DNA glycosylase from G·AP sites sufficiently to allow it to remove more than one thymine from G·T mismatches. The bound thymine DNA glycosylase prevents human apurinic endonuclease 1 (HAP1) cutting the apurinic site, so unless the glycosylase was displaced, the repair of apurinic sites would be very slow. However, HAP1 significantly increases the rate of dissociation of thymine DNA glycosylase from apurinic sites, presumably through direct interaction with the bound glycosylase. This effect is concentration-dependent and at the probable normal concentration of HAP1 in cells the dissociation would be fast. This interaction couples the first step in base excision repair, the glycosylase, to the second step, the apurinic endonuclease. The other proteins involved in base excision repair, polymerase β, XRCC1, and DNA ligase III, do not affect the dissociation of thymine DNA glycosylase from the apurinic site.
Identification of Human P2X1 Receptor-interacting Proteins Reveals a Role of the Cytoskeleton in Receptor Regulation*

P2X1 receptors are ATP-gated ion channels expressed by smooth muscle and blood cells. Carboxyl-terminally His-FLAG-tagged human P2X1 receptors were stably expressed in HEK293 cells and co-purified with cytoskeletal proteins including actin. Disruption of the actin cytoskeleton with cytochalasin D inhibited P2X1 receptor currents with no effect on the time course of the response or surface expression of the receptor. Stabilization of the cytoskeleton with jasplakinolide had no effect on P2X1 receptor currents but decreased receptor mobility. P2X2 receptor currents were unaffected by cytochalasin, and P2X1/2 receptor chimeras were used to identify the molecular basis of actin sensitivity. These studies showed that the intracellular amino terminus accounts for the inhibitory effects of cytoskeletal disruption similar to that shown for lipid raft/cholesterol sensitivity. Stabilization of the cytoskeleton with jasplakinolide abolished the inhibitory effects of cholesterol depletion on P2X1 receptor currents, suggesting that lipid rafts may regulate the receptor through stabilization of the cytoskeleton. These studies show that the cytoskeleton plays an important role in P2X1 receptor regulation.
Legal Literacy and Users' Awareness of Privacy, Data Protection and Copyright Legislation in the Web 2.0 Era

Web 2.0 offers an easy way for individuals to share any kind of con- tent. The users' new role of being a content producer is associated with the re- sponsibility to observe the relevant law. In this article, relevant regulations of the German and Austrian law are presented. In an attempt to understand the fac- tors that influence users' lawful behavior, the presented research examines the effects of legal literacy, awareness and lawful attitude on lawful and unlawful actions. The empirical study shows results from a survey of 1,134 students from three different faculties. Regression and mediation analyses were used to ana- lyze the effects. The results indicate that legal literacy has a negative direct in- fluence on lawful behavior, while lawful attitude shows a positive effect among Austrian students. Furthermore, legal awareness has a stronger effect on lawful attitude than legal literacy.
Radiofrequency volumetric tissue reduction of the palate in subjects with sleep-disordered breathing.

STUDY OBJECTIVES To evaluate pain, swallowing, speech, edematous response, tissue shrinkage, sleep, snoring, and safety (energy limits and adverse effects) following radiofrequency (RF) treatment to the palate in 22 subjects with sleep-disordered breathing. DESIGN This investigation is a prospective nonrandomized study. Polysomnography, radiographic imaging, and infrared thermography, along with questionnaires and visual analog scales, were used to evaluate the effects of RF treatment to the palate. SETTING Treatments were delivered on an outpatient basis at Stanford University Medical Center. PATIENTS Twenty-two healthy patients (18 men), with a mean age of 45.3+/-9.1 years, were enrolled. All were snorers seeking treatment and met predetermined criteria: a respiratory disturbance index < or = 15, oxygen saturation > or = 85%, and a complaint of daytime sleepiness. INTERVENTION RF was delivered to the submucosa of the palate with a custom-fabricated electrode for a mean duration of 141+/-30 s with a mean of 3.6+/-1.2 treatments per patient. Reduction of their snoring scores determined the end point of the study. RESULTS Neither speech nor swallowing was adversely affected. Pain was of short duration (0 to 48 h) and was controlled with acetaminophen. There were no infections. Although there was documented edema at 24 to 48 h, there were no clinical airway compromises. Polysomnographic data showed improvement in esophageal pressure measurements of the mean nadir and the 95th percentile nadir (p=0.031, p=0.001) respectively, as well as the mean sleep efficiency index (p=0.002). Radiographic imaging showed a mean shrinkage of 5.5+/-3.7 mm (p< or =0.0001). Subjective snoring scores fell by a mean of 77% (8.3+/-1.8 to 1.9+/-1.7, p=0.0001) accompanied by improved mean Epworth sleepiness scores (8.5+/-4.4 to 5.2+/-3.3, p=0.0001). CONCLUSION The results of this investigation allowed the formulation of safety parameters for RF in this defined population with mild sleep-disordered breathing. There was a documented tissue reduction and improvement in symptoms in all subjects. However, given the small sample size and short-term follow-up, these results should be confirmed by further investigation.
Maximum Entropy, Word-Frequency, Chinese Characters, and Multiple Meanings

The word-frequency distribution of a text written by an author is well accounted for by a maximum entropy distribution, the RGF (random group formation)-prediction. The RGF-distribution is completely determined by the a priori values of the total number of words in the text (M), the number of distinct words (N) and the number of repetitions of the most common word (kmax). It is here shown that this maximum entropy prediction also describes a text written in Chinese characters. In particular it is shown that although the same Chinese text written in words and Chinese characters have quite differently shaped distributions, they are nevertheless both well predicted by their respective three a priori characteristic values. It is pointed out that this is analogous to the change in the shape of the distribution when translating a given text to another language. Another consequence of the RGF-prediction is that taking a part of a long text will change the input parameters (M, N, kmax) and consequently also the shape of the frequency distribution. This is explicitly confirmed for texts written in Chinese characters. Since the RGF-prediction has no system-specific information beyond the three a priori values (M, N, kmax), any specific language characteristic has to be sought in systematic deviations from the RGF-prediction and the measured frequencies. One such systematic deviation is identified and, through a statistical information theoretical argument and an extended RGF-model, it is proposed that this deviation is caused by multiple meanings of Chinese characters. The effect is stronger for Chinese characters than for Chinese words. The relation between Zipf’s law, the Simon-model for texts and the present results are discussed.