Miracle-dz/UniFAR-FTUs huggingface dataset:
MutY repair is mutagenic in mutT- strains of Escherichia coli.

We have determined the numbers and types of mutations that occur in strains of Escherichia coli defective in mutT and (or) mutY repair. High rates of C.G to A.T mutations in mutY- cells are unaffected by the status of mutT. However, mutT-/mutY+ strains have higher rates of A.T to C.G mutations than mutT-/mutY- strains. This result indicates that the high rates of A.T to C.G mutations seen in mutT- strains of E. coli are due in part to the activity of the mutY repair system. We conclude that mutY repair is mutagenic in a mutT- background.
Verifying reference intervals for coagulation tests by using stored data

Abstract Objective: The purpose of the study was to verify the reference intervals for prothrombin time (PT) and activated partial thromboplastin time (APTT), using stored data of ambulatory pre-op subjects with exclusion of certain clinics, according to age and sex. Materials and Methods: Results of test requests (13,600 PT and 14,083 APTT) of subjects aged 15–80 made from outpatient clinics of surgical departments before surgical interventions in 2008 were retrieved from the electronic medical record. Thromborel S and Actin (Dade Behring, Germany) were used on the Sysmex® CA-1500 coagulation analyzer. Extreme values were determined by using Horn's algorithm after Box-Cox transformation, and the upper and lower reference limits were determined as the 2.5th and 97.5th percentiles of the cleaned data. Results: The values outside the interval of PT data 10.5–17.0 seconds and the interval of APTT data 20.6–35.8 seconds were excluded from the analysis. There were significant differences among age subsets of PT measurements ( p < 0.0001) and of APTT measurements ( p < 0.0001). Accordingly, the data were tested for gender differences and a significant difference was found in PT ( p = 0.002). APPT results did not differ statistically between men and women. Conclusion: Although we found values different from the limits stated in the kit insert, it would be better to confirm our findings with the direct method, especially in APTT for patients under the age of 40 and over the age of 59, and also for sex differences in PT.
Introducing the non-invasive prenatal test for trisomy 21 in Belgium: a cost-consequences analysis

Background The first- and second-trimester screening for trisomy 21 (T21) are reimbursed for all pregnant women in Belgium. Using a cut-off risk of 1:300 for T21, about 5% of all pregnant women are referred for definitive prenatal diagnosis using an invasive test, at a sensitivity of (only) 72.5%. The sensitivity and specificity of the non-invasive prenatal test (NIPT) are over 99% but come at a cost of €460 (£373) per test. The objective is to estimate the consequences of introducing NIPT for the detection of T21. Methods A cost-consequences analysis was performed presenting the impact on benefits, harms and costs. Context-specific real-world information was available to set up a model reflecting the current screening situation in Belgium. This model was used to construct the second and first line NIPT screening scenarios applying information from the literature on NIPT's test accuracy. Results Introducing NIPT in the first or second line reduces harm by decreasing the number of procedure-related miscarriages after invasive testing. In contrast with NIPT in the second line, offering NIPT in the first line additionally will miss fewer cases of T21 due to less false-negative test results. The introduction of NIPT in the second line results in cost savings, which is not true for NIPT at the current price in the first line. If NIPT is offered to all pregnant women, the price should be lowered to about €150 to keep the screening cost per T21 diagnosis constant. Conclusions In Belgium, the introduction and reimbursement of NIPT as a second line triage test significantly reduces procedure-related miscarriages without increasing the short-term screening costs. Offering and reimbursing NIPT in the first line to all pregnant women is preferred in the long term, as it would, in addition, miss fewer cases of T21. However, taking into account the government's limited resources for universal reimbursement, the price of NIPT should first be lowered substantially before this can be realised.
Changes in NMDA Receptor Subunit Expression in Response to Contusive Spinal Cord Injury

Abstract : Differential assembly of N‐methyl‐D‐aspartate (NMDA) receptor subunits determines their functional characteristics. Using in situ hybridization, we found a selective increase of the subunits NR1 and NR2A mRNA at 24 h in ventral motor neurons (VMN) caudal to a standardized spinal cord contusion injury (SCI). Other neuronal cell populations and VMN rostral to the injury site appeared unaffected. Significant up‐regulation of NR2A mRNA also was seen 1 month after SCI in thoracic and lumbar VMN. The selective effects on VMN caudal to the injury site suggest that the loss of descending innervation leads to increased NMDA receptor subunit expression in these cells after SCI, which may alter their responses to glutamate. In contrast, protein levels determined by western blot analysis show decreased levels of NR2A 1 month after SCI in whole thoracic segments of spinal cord that included the injury sites. No effects of injury were seen on subunit levels in cervical or lumbar segments. Taken together with our previous study showing α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazole propionate receptor subunit down‐regulation after injury, our data suggest that glutamate receptor composition is significantly altered after SCI. These changes need to be taken into account to properly understand the function of, and potential pharmacotherapy for, the chronically injured spinal cord.
Convergent Validity of the Beck Depression Inventory-II With the Reynolds Adolescent Depression Scale in Psychiatric Inpatients

The Beck Depression Inventory-II (BDI-II; Beck, Steer, & Brown, 1996) and the Reynolds Adolescent Depression Scale (RADS; Reynolds, 1987) were administered to 56 female and 44 male psychiatric inpatients whose ages ranged from 12 to 17 years old. The Cronbach coefficient as for the BDI-II and RADS were, respectively, . 92 and . 91 and indicated comparably high levels of internal consistency. The correlation between the BDI-II and RADS total scores was . 84, p < . 001. Binormal receiver-operating-characteristic analyses indicated that both instruments were comparably effective in differentiating inpatients who were and were not diagnosed with a major depressive disorder; the areas under the ROC curves for the BDI-II and RADS were, respectively, . 78 and . 76. The results (a) indicate that the BDI-II and the RADS have similar psychometric characteristics and (b) support the convergent validity of the BDI-II for assessing self-reported depression in adolescent inpatients.
Relating and Visualising CSP, VCR and Structural Traces

As well as being a useful tool for formal reasoning, a trace can provide insight into a concurrent program's behaviour, especially for the purposes of run-time analysis and debugging. Long-running programs tend to produce large traces which can be difficult to comprehend and visualise. We examine the relationship between three types of traces (CSP, VCR and Structural), establish an ordering and describe methods for conversion between the trace types. Structural traces preserve the struc- ture of composition and reveal the repetition of individual processes, and are thus well-suited to visualisation. We introduce the Starving Philosophers to motivate the value of Structural traces for reasoning about behaviour not easily predicted from a program's specification. A remaining challenge is to integrate Structural traces into a more formal setting, such as the Unifying Theories of Programming - however, Struc- tural traces do provide a useful framework for analysing large systems.
Evaluating Sensitivity of Auto-Scaling Decisions in an Environment with Different Workload Patterns

Cost-performance trade off is one of the critical challenges in cloud computing environments. Predictive auto-scaling systems mitigate this issue by scaling in/out system automatically based on performance prediction results. The goal of this research is to investigate the impact of different prediction results on the scaling actions generated by predictive auto-scaling systems. In this study, predictive auto-scaling systems are divided into Predictor and Decision-maker components, and experiments have been conducted to measure the influence of the Predictor results on the Decision-maker output. We have used Support Vector Machine (SVM) and Neural Networks (NN) as the Predictor component and the threshold-based technique as the Decision-maker component. In addition, the influence of different workload patterns on the prediction accuracy of SVM and NN has been investigated in this paper. The experiment results show that although either of the prediction algorithms (i.e., SVM and NN) is suitable for a specific workload pattern, SVM and NN predictions lead to similar scaling actions in 97.9% of time, which suggests that focus should be on the decision-maker techniques.
Controlling Crowd Simulations using Neuro-Evolution

Crowd simulations have become increasingly popular in films over the last decade, appearing in large crowd shots of many big name block-buster films. An important requirement for crowd simulations in films is that they should be directable both at a high and low level. As agent-based techniques allow for low-level directability and more believable crowds, they are typically used in this field. However, due to the bottom-up nature of these techniques, to achieve high level directability, agent-level parameters must be adjusted until the desired crowd behavior emerges. As manually adjusting parameters is a time consuming and tedious process, this paper investigates a method for automating this, using Neuro-Evolution. To this end, the Conventional Neuro-Evolution (CNE), Covariance Matrix Adaptation Evolutionary Strategy (CMA-ES), Neuro-Evolution of Augmenting Topologies (NEAT), and Enforced Sub Populations (ESP) algorithms are compared across a variety of representative crowd simulation scenarios. Overall, it was found that CMA-ES generally performs the best across the selected simulations.
A Survey on Load Testing of Large-Scale Software Systems

Many large-scale software systems must service thousands or millions of concurrent requests. These systems must be load tested to ensure that they can function correctly under load (i.e., the rate of the incoming requests). In this paper, we survey the state of load testing research and practice. We compare and contrast current techniques that are used in the three phases of a load test: (1) designing a proper load, (2) executing a load test, and (3) analyzing the results of a load test. This survey will be useful for load testing practitioners and software engineering researchers with interest in the load testing of large-scale software systems.
Analysis of dichotomous outcome data for community intervention studies

Community intervention trials are becoming increasingly popular as a tool for evaluating the effectiveness of health education and intervention strategies. Typically, units such as households, schools, towns, counties, are randomized to receive either intervention or control, then outcomes are measured on individuals within each of the units of randomization. It is well recognized that the design and analysis of such studies must account for the clustering of subjects within the units of randomization. Furthermore, there are usually both subject level and cluster level covariates that must be considered in the modelling process. While suitable methods are available for continuous outcomes, data analysis is more complicated when dichotomous outcomes are measured on each subject. This paper will compare and contrast several of the available methods that can be applied in such settings, including random effects models, generalized estimating equations and methods based on the calculation of `design effects', as implemented in the computer package SUDAAN. For completeness, the paper will also compare these methods of analysis with more simplistic approaches based on the summary statistics. All the methods will be applied to a case study based on an adolescent anti-smoking intervention in Australia. The paper concludes with some general discussion and recommendations for routine design and analysis.
Interference alignment through user cooperation for two-cell MIMO interfering broadcast channels

This paper focuses on two-cell multiple-input multiple-output (MIMO) Gaussian interfering broadcast channels (MIMO-IFBC) with K cooperating users on the cell-boundary of each BS. It corresponds to a downlink scenario for cellular networks with two base stations (BSs), and K users equipped with Wi-Fi interfaces enabling to cooperate among users on a peer-to-peer basis. In this scenario, we propose a novel interference alignment (IA) technique exploiting user cooperation. Our proposed algorithm obtains the achievable degrees of freedom (DoF) of 2K when each BS and user have M = K + 1 transmit antennas and N = K receive antennas, respectively. Furthermore, the algorithm requires only a small amount of channel feedback information with the aid of the user cooperation channels. The simulations demonstrate that not only are the analytical results valid, but the achievable DoF of our proposed algorithm also outperforms those of conventional techniques.
Polymer statistics in a random flow with mean shear

We consider the dynamics of a polymer with finite extensibility placed in a chaotic flow with large mean shear, to explain how the polymer statistics changes with Weissenberg number, ${\it Wi}$, the product of the polymer relaxation time and the Lyapunov exponent of the flow, $\bar\lambda$. The probability distribution function (PDF) of the polymer orientation is peaked around a shear-preferred direction, having algebraic tails. The PDF of the tumbling time (separating two subsequent flips), $\tau$, has a maximum estimated as $\bar\lambda^{-1}$. This PDF shows an exponential tail for large $\tau$ and a small-$\tau$ tail determined by the simultaneous statistics of the velocity PDF. Four regimes of ${\it Wi}$ are identified for the extension statistics: one below the coil–stretched transition and three above the coil–stretched transition. Emphasis is given to explaining these regimes in terms of the polymer dynamics.
Translational and posttranslational regulation of XIAP by eIF2α and ATF4 promotes ER stress–induced cell death during the unfolded protein response

Chronic ER stress down-regulates XIAP by activating the PERK branch of the UPR. PERK attenuates Xiap translation via eIF2α phosphorylation. PERK promotes XIAP degradation via ATF4. CHOP induction and XIAP suppression act in parallel to sensitize cells to ER stress–induced apoptosis.
Potential nephroprotective effects of the Chinese herb Angelica sinensis against cisplatin tubulotoxicity

Abstract Context: Acute kidney injury (AKI) is often encountered in patients receiving cisplatin (CisPt), a chemotherapeutic drug that induces numerous toxic side effects. Techniques used to limit nephrotoxicity during CisPt treatment are not fully effective; about a third of patients experience AKI. New nephroprotective strategies, including pharmacological approaches, must be developed. Objective: The present study investigated the nephroprotective potential of Angelica sinensis (Oliv.) Diels (Apiaceae) root towards CisPt tubulotoxicity. Materials and methods: HK-2 cells were incubated with CisPt (10 µM) and/or with a methanolic extract of A. sinensis (AS). Nephroprotective capacity was evaluated by means of cellular viability (resazurin assay) and apoptosis (annexin-V/PI staining), oxidative stress generation (H2DCF-DA oxidation), Ki-67 index (immunofluorescence), cell cycle analysis (DNA staining), cell migration rate (scratch assay), extracellular matrix deposition (collagen determination), and β-catenin relocalization. Results: CisPt decreased cell viability [76% versus Ctrl], which was associated with an increased apoptosis. Simultaneous treatment with 50 µg/ml AS enhanced cell survival [84% versus Ctrl] and decreased the apoptosis rate. AS could not alleviate CisPt-induced oxidative stress; but doses of 5 and 50 µg/ml raised the Ki-67 index [135 and 244% versus Ctrl] and cell migration rates [1.2 and 1.3-fold versus Ctrl]. Finally, both doses of AS limited the amount of collagen deposition [121.6 and 119.6% for 5 and 50 µg/ml, respectively, versus 131.0% for CisPt-treated cells] and prevented the relocalization of β-catenin from the membrane to the nucleus. Conclusion: These results confirm the nephroprotective potential of A. sinensis and require further investigations aiming at identifying its active compounds.
In Vitro Toxicity of Aluminum Nanoparticles in Human Keratinocytes

Abstract : Nanotechnology promises to be the defining technology of the 21st century. At an annual investment of $1B, it provides significant contributions to manufacturing, medicine, energy conservation, and the environment. Nanoparticles are structures with at least one dimension in the 1 to 100 nanometer (nm) range. DoD and US Air Force interest in aluminum nanoparticles (AL NPs) stems from its ability to enhance combustion jet fuel, thus increasing fuel efficiency. The addition of AL NPs to JP-8 may pose a unique dermal hazard to aircraft maintenance workers. There is no published data on AL NP toxicity effects on human skin. This research used in vitro techniques to determine the cytotoxicity of AL NPs, sized 50, 80, and 120 nm, on human keratinocytes. AL NPs at concentrations 10 - 10,000 micrograms/mL and 24-hour exposure did not have a negative effect on cell viability, as assessed by membrane leakage, metabolic function, and reactive oxygen species generation. Keratinocyte expression of proinflammatory interleukins-1alpha and -8 was quantified to determine if AL NPs induced precursor cytokines for irritant contact or sensitizer response dermatitis. After 24-hour exposure to AL NPs, keratinocytes expressed significant concentrations of IL-8, 24 - 100 times greater than IL-1alpha, indicating that AL NPs may induce sensitizer response dermatitis.
Preclinical model in HCC: the SGK1 kinase inhibitor SI113 blocks tumor progression in vitro and in vivo and synergizes with radiotherapy

The SGK1 kinase is pivotal in signal transduction pathways operating in cell transformation and tumor progression. Here, we characterize in depth a novel potent and selective pyrazolo[3,4-d]pyrimidine-based SGK1 inhibitor. This compound, named SI113, active in vitro in the sub-micromolar range, inhibits SGK1-dependent signaling in cell lines in a dose- and time-dependent manner. We recently showed that SI113 slows down tumor growth and induces cell death in colon carcinoma cells, when used in monotherapy or in combination with paclitaxel. We now demonstrate for the first time that SI113 inhibits tumour growth in hepatocarcinoma models in vitro and in vivo. SI113-dependent tumor inhibition is dose- and time-dependent. In vitro and in vivo SI113-dependent SGK1 inhibition determined a dramatic increase in apotosis/necrosis, inhibited cell proliferation and altered the cell cycle profile of treated cells. Proteome-wide biochemical studies confirmed that SI113 down-regulates the abundance of proteins downstream of SGK1 with established roles in neoplastic transformation, e.g. MDM2, NDRG1 and RAN network members. Consistent with knock-down and over-expressing cellular models for SGK1, SI113 potentiated and synergized with radiotherapy in tumor killing. No short-term toxicity was observed in treated animals during in vivo SI113 administration. These data show that direct SGK1 inhibition can be effective in hepatic cancer therapy, either alone or in combination with radiotherapy.
“The 3/3 Strategy”: A Successful Multifaceted Hospital Wide Hand Hygiene Intervention Based on WHO and Continuous Quality Improvement Methodology

Background Only multifaceted hospital wide interventions have been successful in achieving sustained improvements in hand hygiene (HH) compliance. Methodology/Principal Findings Pre-post intervention study of HH performance at baseline (October 2007– December 2009) and during intervention, which included two phases. Phase 1 (2010) included multimodal WHO approach. Phase 2 (2011) added Continuous Quality Improvement (CQI) tools and was based on: a) Increase of alcohol hand rub (AHR) solution placement (from 0.57 dispensers/bed to 1.56); b) Increase in frequency of audits (three days every three weeks: “3/3 strategy”); c) Implementation of a standardized register form of HH corrective actions; d) Statistical Process Control (SPC) as time series analysis methodology through appropriate control charts. During the intervention period we performed 819 scheduled direct observation audits which provided data from 11,714 HH opportunities. The most remarkable findings were: a) significant improvements in HH compliance with respect to baseline (25% mean increase); b) sustained high level (82%) of HH compliance during intervention; c) significant increase in AHRs consumption over time; c) significant decrease in the rate of healthcare-acquired MRSA; d) small but significant improvements in HH compliance when comparing phase 2 to phase 1 [79.5% (95% CI: 78.2–80.7) vs 84.6% (95% CI:83.8–85.4), p<0.05]; e) successful use of control charts to identify significant negative and positive deviations (special causes) related to the HH compliance process over time (“positive”: 90.1% as highest HH compliance coinciding with the “World hygiene day”; and “negative”:73.7% as lowest HH compliance coinciding with a statutory lay-off proceeding). Conclusions/Significance CQI tools may be a key addition to WHO strategy to maintain a good HH performance over time. In addition, SPC has shown to be a powerful methodology to detect special causes in HH performance (positive and negative) and to help establishing adequate feedback to healthcare workers.
Parallelizing more Loops with Compiler Guided Refactoring

The performance of many parallel applications relies not on instruction-level parallelism but on loop-level parallelism. Unfortunately, automatic parallelization of loops is a fragile process, many different obstacles affect or prevent it in practice. To address this predicament we developed an interactive compilation feedback system that guides programmers in iteratively modifying their application source code. This helps leverage the compiler's ability to generate loop-parallel code. We employ our system to modify two sequential benchmarks dealing with image processing and edge detection, resulting in scalable parallelized code that runs up to 8.3 times faster on an eight-core Intel Xeon 5570 system and up to 12.5 times faster on a quad-core IBM POWER6 system. Benchmark performance varies significantly between the systems. This suggests that semi-automatic parallelization should be combined with target-specific optimizations. Furthermore, comparing the first benchmark to manually-parallelized, hand-optimized pthreads and OpenMP versions, we find that code generated using our approach typically outperforms the pthreads code (within 93-339%). It also performs competitively against the OpenMP code (within 75-111%). The second benchmark outperforms manually-parallelized and optimized OpenMP code (within 109-242%).