Miracle-dz/UniFAR-FTUs huggingface dataset:
Heat shock represses rRNA synthesis by inactivation of TIF-IA and lncRNA-dependent changes in nucleosome positioning

Attenuation of ribosome biogenesis in suboptimal growth environments is crucial for cellular homeostasis and genetic integrity. Here, we show that shutdown of rRNA synthesis in response to elevated temperature is brought about by mechanisms that target both the RNA polymerase I (Pol I) transcription machinery and the epigenetic signature of the rDNA promoter. Upon heat shock, the basal transcription factor TIF-IA is inactivated by inhibition of CK2-dependent phosphorylations at Ser170/172. Attenuation of pre-rRNA synthesis in response to heat stress is accompanied by upregulation of PAPAS, a long non-coding RNA (lncRNA) that is transcribed in antisense orientation to pre-rRNA. PAPAS interacts with CHD4, the adenosine triphosphatase subunit of NuRD, leading to deacetylation of histones and movement of the promoter-bound nucleosome into a position that is refractory to transcription initiation. The results exemplify how stress-induced inactivation of TIF-IA and lncRNA-dependent changes of chromatin structure ensure repression of rRNA synthesis in response to thermo-stress.
Gait training for chronic ankle instability improves neuromechanics during walking

A novel gait‐training device has been shown to improve gait patterns while patients with chronic ankle instability (CAI) are using the device and our current objective was to analyze the effect of structured gait training with the device on plantar pressure and surface electromyography (sEMG) following repeated gait training sessions. Sixteen CAI patients participated. Plantar pressure and sEMG were collected simultaneously during walking pre‐ and post‐gait training. Plantar pressure (pressure time integral, peak pressure, time to peak pressure, contact area, contact time, and center of pressure trajectory) of the entire foot and nine specific regions of the foot were recorded concurrently with sEMG root mean square amplitudes from the anterior tibialis, peroneus longus, medial gastrocnemius, and gluteus medius. Five gait training sessions were performed with each session lasting approximately 15 min. Pre‐ and post‐gait training self‐reported function, plantar pressure, and sEMG were compared using paired t‐tests with a priori level of significance of p ≤ 0.05. Gait training improved self‐reported function (FAAM‐Sport scale: Pre = 75.1 ± 7.1%, Post = 85.7 ± 12.2%, p < 0.001) and caused a medial shift in the COP from 10% of stance through toe‐off (p < 0.05 for all analyses). The medial shift in COP was driven by concurrent increases in peroneus longus muscle activity from 21% to 60% and 81% to 90% of stance (p < 0.05 for all analyses). There was a corresponding reduction in gluteus medius muscle activity during 71–100% of stance (p < 0.05 for all analyses). Overall, gait training with a device that targets the peroneus longus and gluteus medius throughout the gait cycle improved gait patterns in CAI patients. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:515–524, 2018.
The Effect of Voice Cuing on Releasing Speech From Informational Masking Disappears in Older Adults

Objective: To investigate whether older adults can use voice information to unmask speech. Design: Under a voice-priming condition, before a target-speech sentence was presented with a noise or speech masker, one or two voice-priming sentences were recited with the same voice reciting the target sentence. Eighteen younger adults and 12 older adults with clinically normal hearing were instructed to loudly repeat the target sentence. Results: Presenting the voice-priming sentence(s) improved target-speech identification only when the masker was speech in younger adults but not older adults. Conclusion: For older adults, the inability to use voice information to reduce informational masking contributes to their speech-recognition difficulties in “cocktail-party” environments.
SYNTHESIS AND CHARACTERIZATION OF GOLD NANOPARTICLES

Scattering (DLS), was used to characterize AuNPs in terms of size and stability. Particle size was expressed as mean hydrodynamic diameter ± standard deviation. Results. The four methodologies yielded NPs characterized by different dimensions. NPs obtained using citrate showed a mean diameter of 16.59±1.79 nm. After thirty days of storage at room temperature, the mean particle size slightly increased (19.30±1.63 nm) and a new particle population (38.60±1.41 nm), accounting for 2.65% of the total, was observed. The use of gelatine as stabilizing agent did not change the NP mean size and stability in comparison with the first method. However, when gelatine was added before starting the reaction, reduction to Au 0 lasted 20 days. AuNPs obtained using Pluronic P84 showed three populations (18.66±9.06 nm, 91.96%; 127.53±1.71 nm, 7.63%; 210.4±4.7 nm, 0.77%) while glycerol yielded just two populations; the first one (91.7%) of 17.76±1.75 nm and the second (8.3%) of 122.03±0.98 nm. After ten days, AuNP prepared with the last 2 methods described showed no or minimal particle size variation. Conclusion. AuNPs prepared using the different methodologies are characterized by different particle size and are stable upon storage at room temperature for at least 10 days. The different methods, avoiding the use of organic solvents, can be considered as green synthesis.
A Novel Magnetic Coupling Mechanism for Dynamic Wireless Charging System for Electric Vehicles

In this paper, a magnetic coupling mechanism composed of an "n-type" multipolar power supply rail and triple-coil receiver for electric vehicle dynamic wireless charging is introduced. This coupling mechanism is effective to reduce the volume of the magnetic core through the structure of the "n-type" framework. The triple coil receiver is composed of a dual coil and a quadrature coil which compensates the zero of receiving power of dual coil that can ensure the power transferring stability. The characteristics of the proposed mechanism was verified through simulation and calculation in this paper.
Green, formaldehyde-free, foams for thermal insulation

New, green and cheap rigid foams presenting outstanding performances for thermal insulation are described. Such ultra- lightweight cellular materials are mainly based on renewable chemicals: tannin and furfuryl alcohol, are very easy to produce and have thermal conductivity as low as 38 mW/m/K. Compared to previously reported tannin-based foams, these new materials are much "greener" and present improved resistance to compression and to water. Especially the formaldehyde, formerly used as cross-linking agent of tannins but known as a volatile and harmful chemical, could be successfully removed from the formulation. The as-obtained, 2 nd generation, tannin-based foams are totally stable and have an expected interest for thermal insulation of buildings. Copyright © 2011 VBRI press.
Essential role for ligand-dependent feedback antagonism of vertebrate hedgehog signaling by PTCH1, PTCH2 and HHIP1 during neural patterning

Hedgehog (HH) signaling is essential for vertebrate and invertebrate embryogenesis. In Drosophila, feedback upregulation of the HH receptor Patched (PTC; PTCH in vertebrates), is required to restrict HH signaling during development. By contrast, PTCH1 upregulation is dispensable for early HH-dependent patterning in mice. Unique to vertebrates are two additional HH-binding antagonists that are induced by HH signaling, HHIP1 and the PTCH1 homologue PTCH2. Although HHIP1 functions semi-redundantly with PTCH1 to restrict HH signaling in the developing nervous system, a role for PTCH2 remains unresolved. Data presented here define a novel role for PTCH2 as a ciliary localized HH pathway antagonist. While PTCH2 is dispensable for normal ventral neural patterning, combined removal of PTCH2- and PTCH1-feedback antagonism produces a significant expansion of HH-dependent ventral neural progenitors. Strikingly, complete loss of PTCH2-, HHIP1- and PTCH1-feedback inhibition results in ectopic specification of ventral cell fates throughout the neural tube, reflecting constitutive HH pathway activation. Overall, these data reveal an essential role for ligand-dependent feedback inhibition of vertebrate HH signaling governed collectively by PTCH1, PTCH2 and HHIP1.
JetStream: enabling high performance event streaming across cloud data-centers

The easily-accessible computation power offered by cloud infrastructures coupled with the revolution of Big Data are expanding the scale and speed at which data analysis is performed. In their quest for finding the Value in the 3 Vs of Big Data, applications process larger data sets, within and across clouds. Enabling fast data transfers across geographically distributed sites becomes particularly important for applications which manage continuous streams of events in real time. Scientific applications (e.g. the Ocean Observatory Initiative or the ATLAS experiment) as well as commercial ones (e.g. Microsoft's Bing and Office 365 large-scale services) operate on tens of data-centers around the globe and follow similar patterns: they aggregate monitoring data, assess the QoS or run global data mining queries based on inter site event stream processing. In this paper, we propose a set of strategies for efficient transfers of events between cloud data-centers and we introduce JetStream: a prototype implementing these strategies as a high performance batch-based streaming middleware. JetStream is able to self-adapt to the streaming conditions by modeling and monitoring a set of context parameters. It further aggregates the available bandwidth by enabling multi-route streaming across cloud sites. The prototype was validated on tens of nodes from US and Europe data-centers of the Windows Azure cloud using synthetic benchmarks and with application code from the context of the Alice experiment at CERN. The results show an increase in transfer rate of 250 times over individual event streaming. Besides, introducing an adaptive transfer strategy brings an additional 25% gain. Finally, the transfer rate can further be tripled thanks to the use of multi-route streaming.
The effect of different doses of aerobic exercise training on endothelial function in postmenopausal women with elevated blood pressure: results from the DREW study

Objectives The aim of this study was to examine the effect of three different doses of aerobic exercise training (corresponding to approximately 50%, 100% and 150% of the National Institutes of Health consensus guidelines) on endothelial function in sedentary obese postmenopausal women with elevated blood pressure. Aerobic exercise training improves endothelial function in individuals with cardiovascular risk; however, it is unknown whether these adaptations occur in a dose-dependent manner. Methods Obese postmenopausal women (n=155) with elevated blood pressure (systolic blood pressure between 120 and 159.0 mm Hg) were randomly assigned to one of four groups: 4, 8 or 12 kilocalories per kilogram of energy expenditure per week (kcal/kg/week) or a non-exercise control group for 6 months. Endothelial function was assessed via flow-mediated dilation (FMD) at baseline and post-intervention. Results After exercise training, there was a similar improvement (1.02–1.5%) in FMD in all three exercise groups (p<0.05) compared with control (–0.5%). Change in FMD after exercise training was significantly correlated with FMD at baseline (r= –0.35, p<0.001). Post hoc analyses found a significant improvement in FMD in exercisers (all exercise groups combined) with endothelial dysfunction (FMD < 5.5%) at baseline (1.8%, 95% CI: 1.17 to 2.38; p<0.001) compared with exercisers with normal endothelial function (FMD ≥ 5.5%) (–1.2%; 95% CI: –1.17 to 0.69; p=0.60). Conclusions Aerobic exercise training was associated with improved FMD in postmenopausal women with elevated blood pressure. In addition, exercise training may be more efficacious in improving endothelial function in postmenopausal women with endothelial dysfunction than individuals with normal endothelial function at baseline.
SYMAES: A Fully Symbolic Polynomial System Generator for AES-128 ⋆

SYMAES is a software tool that generates a system of polynomials in GF(2), corresponding to the round transformation and key schedule of the block cipher AES-128 [1]. Most of the existing polynomial system generators for AES are typically used under the assumption that the plaintext and ciphertext bits are known, and therefore are treated as constants. Although some of the generators, such as the AES (SR) Polynomial System Generator [2,3], can also be used when this assumption is not made, the instructions to do this are not always very natural. SYMAES is specifically designed to address the case in which (some of) the plaintext and ciphertext bits are unknown and are therefore treated as symbolic variables. Such a scenario is realistic and arises during the algebraic cryptanalysis of AES-based constructions, where only parts of the plaintext and/or ciphertext are known. An example of such a construction is the stream cipher LEX [4], a small-scale version of which has been analysed using SYMAES [5]. The inputs to SYMAES are the bits of the plaintext and the bits of the original key, represented as symbolic variables in GF(2). The output is a system of equations describing the output bits of one round of AES as a function of the input bits and the key. SYMAES also generates symbolic equations for the AES key schedule. Then, the bits of the round keys are expressed as polynomials in the bits of the original key. As a final note we would like to stress that SYMAES should not be seen as a competitor to existing AES polynomial system generators, but rather as an addition to them. SYMAES achieves in a more natural way what can also be achieved using SR [3]. Similarly to SR, SYMAES is also written in Python and is used within the open source computer algebra Sage [6]. This makes possible a future integration of the SYMAES code into SR. This submission is accompanied by an appendix containing the SYMAES source code and usage instructions.
Tissue microarray analysis of methylthioadenosine phosphorylase protein expression in melanocytic skin tumors.

BACKGROUND Using tissue microarrays, we investigated whether methylthioadenosine phosphorylase (MTAP) protein expression is associated with clinicopathologic variables in benign and malignant melanocytic skin tumors. OBSERVATIONS Cytoplasmic MTAP expression was detected in 227 (72.1%) of 315 informative cases. Expression was significantly reduced in primary malignant melanomas and in melanoma metastases compared with benign nevi (P<.001 for both). No difference was noted in MTAP expression between primary malignant melanomas and melanoma metastases. In primary malignant melanomas, a Ki67-labeling index less than 5% was associated with MTAP expression (P = .04), suggesting that loss of MTAP expression is associated with proliferation. No other variables had significant associations with MTAP expression. Lymph node metastases demonstrated significantly higher MTAP expression compared with skin metastases (P = .01). In the overall cohort, MTAP expression was not associated with prognosis. Among 26 patients with MTAP-positive melanomas and tumor recurrence, 18 patients who received interferon therapy had a significant benefit compared with 8 patients who did not receive interferon therapy (P = .009). This was not seen in the patients with MTAP-negative tumors. Conclusion Methylthioadenosine phosphorylase protein expression may be a predictive marker of interferon therapy resistance in patients with melanoma and disease progression.
The Effect of Botulinum Toxin A on Ischemia-Reperfusion Injury in a Rat Model

Introduction While studies using various materials to overcome ischemia-reperfusion (IR) injury are becoming increasingly common, studies on the effects of botulinum toxin A (BoTA) on IR injury in musculocutaneous flaps are still limited. The purpose of this study was to examine our hypotheses that BoTA provide protection of musculocutaneous flap from ischemia-reperfusion injury. Method Five days after pretreatment injection (BoTA versus normal saline), a right superior musculocutaneous flap (6 × 1.5 cm in size) was made. Ischemia was created by a tourniquet strictly wrapping the pedicle containing skin and muscle for 8 h. After ischemia, the tourniquet was cut, and the musculocutaneous flap was reperfused. Results The overall survival percentage of flap after 8 h of pedicle clamping followed by reperfusion was 87.32 ± 3.67% in the control group versus 95.64 ± 3.25% in the BoTA group (p < 0.001). The BoTA group had higher expression of CD34, HIF-1α, VEGF, and NF-kB comparing to control group in qRT-PCR analysis. Conclusions In this study, we found that local BoTA preconditioning yielded significant protection against IR injury in a rat musculocutaneous flap model.
Light propagation in a turbid medium with insonified microbubbles

Abstract. Surfactant stabilized microbubbles are widely used clinical contrast agents for ultrasound imaging. In this work, the light propagation through a turbid medium in the presence of microbubbles has been investigated. Through a series of experiments, it has been found that the optical attenuation is increased when the microbubbles in a turbid medium are insonified by ultrasound. Such microbubble enhanced optical attenuation is a function of both applied ultrasound pressure and microbubble concentration. To understand the mechanisms involved, a Monte Carlo (MC) model has been developed. Under ultrasound exposure, the sizes of microbubbles vary in space and time, and their dynamics are modeled by the Rayleigh-Plesset equation. By using Mie theory, the spatially and temporally varying optical scattering and scattering efficiency of microbubbles are determined based on the bubble sizes and internal refractive indices. The MC model is shown to effectively describe a medium with rapidly changing optical scattering, and the results are validated against both computational results using an N-layered diffusion equation model and experimental results using a clinical microbubble contrast agent (SonoVue®).
Early and long-term cognitive outcome after conventional cardiac valve surgery.

Objectives Adverse cognitive outcome is well recognized after coronary artery bypass grafting (CABG) while little is known about the extent and duration of decline after cardiac valve surgery. We investigated changes in cognitive function following conventional cardiac valve surgery over up to 4 years. Methods Among 36 patients (65.2 ± 9.2 years, 36% women) who received valve surgery, we assessed serial cognitive function with a battery of 11 standardized tests across 3-4 years. Cognitive function was analysed to identify: (1) cognitive decline (i.e. within-patient changes in test scores) and (2) cognitive deficit (i.e. drop of score ≥1 SD in ≥3 tests). Diffusion-weighted magnetic resonance imaging (DW-MRI) was applied pre- and post-procedure to detect ischaemic brain injury. Data were compared to a historical cohort of 39 patients undergoing CABG. Results After both valve surgery and CABG, a significant decline at discharge was detected in 7 of 11 cognitive tests. The rate of patients with a cognitive deficit after valve surgery vs CABG was 39% vs 56% at discharge, 14% vs 23% at 3 months, and 16% vs 26% at 3-4 years (not significant, [n.s.]). After valve surgery, DW-MRI identified 19 (53%) patients with evidence of 50 new focal ischaemic lesions (CABG: 20 [51%] patients with 42 lesions, n.s.). Cumulative cerebral ischaemic load per patient was not significantly different between the valve surgery group and CABG group (503 ± 485 mm 3 vs 415 ± 234 mm 3 ). After correction for multiple potential risk factors in both groups, reduced verbal memory at discharge could be identified as a predictor of long-term cognitive impairment in CABG patients only ( P = 0.04). For both the valve surgery and CABG group, no association between cognitive impairment and new ischaemic cerebral lesions was found. Conclusions The course of cognitive performance after valve surgery and CABG was similar with early postoperative decline followed by subsequent recovery. Although silent small brain infarcts were present in about half of all patients, they did not impact cognitive performance neither at early nor during long-term follow-up.
Fitness costs of infection with Serratia symbiotica are associated with greater susceptibility to insecticides in the pea aphid Acyrthosiphon pisum.

BACKGROUND Aphids are agricultural pests that damage crops by direct feeding and by vectoring important plant viruses. Bacterial symbionts can influence aphid biology, e.g. by providing essential nutrients or facilitating adaptations to biotic and abiotic stress. RESULTS We investigated the pea aphid (Acyrthosiphon pisum Harris) and its commonly associated secondary bacterial symbiont Serratia symbiotica to study the effect of this symbiont on host fitness and susceptibility to the insecticides imidacloprid, chlorpyrifos methyl, methomyl, cyantraniliprole and spirotetramat. There is emerging evidence that members of the genus Serratia can degrade and/or detoxify diverse insecticides. Therefore, we hypothesized that S. symbiotica may promote resistance to these artificial stress agents in aphids. Our results showed that Serratia-infected aphids were more susceptible to most of the tested insecticides than non-infected aphids. This probably reflects the severe fitness costs associated with S. symbiotica, which negatively affects development, reproduction and body weight. CONCLUSION Our study demonstrates that S. symbiotica plays an important role in the ability of aphid hosts to tolerate insecticides. These results provide insight into the potential changes in tolerance to insecticides in the field because there is a continuous and dynamic process of symbiont acquisition and loss that may directly affect host biology. © 2018 Society of Chemical Industry.
Development of a risk prediction model for lung cancer: The Japan Public Health Center‐based Prospective Study

Although the impact of tobacco consumption on the occurrence of lung cancer is well‐established, risk estimation could be improved by risk prediction models that consider various smoking habits, such as quantity, duration, and time since quitting. We constructed a risk prediction model using a population of 59 161 individuals from the Japan Public Health Center (JPHC) Study Cohort II. A parametric survival model was used to assess the impact of age, gender, and smoking‐related factors (cumulative smoking intensity measured in pack‐years, age at initiation, and time since cessation). Ten‐year cumulative probability of lung cancer occurrence estimates were calculated with consideration of the competing risk of death from other causes. Finally, the model was externally validated using 47 501 individuals from JPHC Study Cohort I. A total of 1210 cases of lung cancer occurred during 986 408 person‐years of follow‐up. We found a dose‐dependent effect of tobacco consumption with hazard ratios for current smokers ranging from 3.78 (2.00‐7.16) for cumulative consumption ≤15 pack‐years to 15.80 (9.67‐25.79) for >75 pack‐years. Risk decreased with time since cessation. Ten‐year cumulative probability of lung cancer occurrence estimates ranged from 0.04% to 11.14% in men and 0.07% to 6.55% in women. The model showed good predictive performance regarding discrimination (cross‐validated c‐index = 0.793) and calibration (cross‐validated χ2 = 6.60; P‐value = .58). The model still showed good discrimination in the external validation population (c‐index = 0.772). In conclusion, we developed a prediction model to estimate the probability of developing lung cancer based on age, gender, and tobacco consumption. This model appears useful in encouraging high‐risk individuals to quit smoking and undergo increased surveillance.