Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance Evaluation and Visualization of Scientific Applications Using PMlib

The computational performance of scientific applications on HPC systems is often much lower than user expectation based on the system's maximum performance specifications. To understand the basis for this performance gap, a multi-perspective evaluation is important. For instance, from the user perspective, correlating the theoretical computation coded as a source program with the actual computation workload produced by the compilers is valuable. From the system perspective, evaluating the characteristics of microarchitecture elements such as processor core and memory is of significance. An open source library called PMlib was developed to address these types of synthetic evaluations. PMlib provides an avenue for reporting the arithmetic/application workload explicitly coded in the source program, as well as the actually executed system workload. It also provides detailed utilization reports of processor-specific hardware including the categorized SIMD instruction statistics, the layered cache hit/miss rate, and the effective memory bandwidth, which are captured via hardware performance counters (HWPC). Using PMlib, users can conduct a synthetic analysis of application performance, and obtain useful feedback for further optimized execution of applications.
A system for environmental monitoring of hydroelectric reservoirs in Brazil

Environmental monitoring of aquatic systems is an important tool to support policy makers and environmental managers’ decisions. Long-term, continuous collection of environmental data is fundamental to the understanding of an aquatic system. This paper aims to present the integrated system for environmental monitoring (SIMA), a long-term temporal series system with a web-based archive for limnological and meteorological data. The following environmental parameters are measured by SIMA: chlorophyll-a ( ), water surface temperature (oC), water column temperature by a thermistor string (oC), turbidity (NTU), pH, dissolved oxygen concentration (mg L -1 ), electric conductivity (µS cm -1 ), wind speed (ms -1 ) and direction (o), relative humidity (%), shortwave radiation (Wm -2 ) and barometric pressure (hPa). The data were collected in a preprogrammed time interval (1 hour) and were transmitted by satellite in quasi-real time for any user within 2500 km of the acquisition point. So far, 11 hydroelectric reservoirs are being monitored with the SIMA buoy. Basic statistics (mean and standard deviation) and an example of the temporal series of some parameters were displayed at a database with web access. However, sensor and satellite problems occurred due to the high data acquisition frequency. Sensors problems occurred due to the environmental characteristics of each aquatic system. Water quality sensors rapidly degrade in acidic waters, rendering the collected data invalid. Data is also rendered invalid when sensors become infested with periphyton. Problems occur with the satellites’ reception of system data when satellites pass over the buoy antenna. However, the data transfer at some inland locations was not completed due to the satellite constellation position. Nevertheless, the integrated system of water quality and meteorological parameters is an important tool in understanding the aquatic system dynamic. It can also be used to create hydrodynamics models of the aquatic system to allow for the study of meteorological implications to the water body. 1 − gL μ
Dynamic evolution of schistosomiasis distribution under different control strategies: Results from surveillance covering 1991–2014 in Guichi, China

Background Since the founding of the China, the Chinese government, depending on the changing epidemiological situations over time, adopted different strategies to continue the progress towards elimination of schistosomiasis in the country. Although the changing pattern of schistosomiasis distribution in both time and space is well known and has been confirmed by numerous studies, the problem of how these patterns evolve under different control strategies is far from being understood. The purpose of this study is, therefore, to investigate the spatio-temporal change of the distribution of schistosomiasis with special reference to how these patterns evolve under different control strategies. Methodology / Principal findings Parasitological data at the village level were obtained through access to repeated cross-sectional surveys carried out during 1991–2014 in Guichi, a rural district along the Yangtze River in Anhui Province, China. A hierarchical dynamic spatio-temporal model was used to evaluate the evolving pattern of schistosomiasis prevalence, which accounted for mechanism of dynamics of the disease. Descriptive analysis indicates that schistosomiasis prevalence displayed fluctuating high-risk foci during implementation of the chemotherapy-based strategy (1991–2005), while it took on a homogenous pattern of decreasing magnitude in the following period when the integrated strategy was implemented (2006–2014). The dynamic model analysis showed that regularly global propagation of the disease was not present after the effect of proximity to river was taken into account but local pattern transition existed. Maps of predicted prevalence shows that relatively high prevalence (>4%) occasionally occurred before 2006 and prevalence presents a homogenous and decreasing trend over the study area afterwards. Conclusions Proximity to river is still an important determinant for schistosomiasis infection regardless of different types of implemented prevention and control strategies. Between the transition from the chemotherapy-based strategy to the integrated one, we noticed a decreased prevalence. However, schistosomiasis would remain an endemic challenge in these study areas. Further prevention and control countermeasures are warranted.
Energy Based Solutions of the Bidirectional Vortex with Multiple Mantles

*† In a previous article, an energy optimization technique was used to derive multiple solutions for the bidirectional vortex. These were obtained for a single mantle describing a single flow reversal scenario. However, the existence of multiple mantles sustaining compound flow turns has been reported in previous work. The current study focuses on the application of the energy based optimization technique to the bidirectional vortex with multiple mantles. We follow a similar analysis and uncover two families of solutions, namely, Type I and Type II solutions with increasing or decreasing energy levels respectively. Both types approach the Type 0 reference solution either from below or above as the energy power index is increased. The solution with multiple mantles entertains a more versatile representation of the bidirectional vortex with allowance for additional physical mechanisms that the flowfield may sustain.
Effect of Jakyakgamcho-Tang Extracts on H2O2-Induced C2C12 Myoblasts

Oxidative stress is a major contributor to muscle aging and loss of muscle tissue. Jakyakgamcho-tang (JGT) has been used in traditional Eastern medicine to treat muscle pain. Here, we compared the total phenolic and flavonoid contents in 30% ethanol and water extracts of JGT and tested the preventive effects against oxidative stress (hydrogen peroxide)-induced cell death in murine C2C12 skeletal muscle cells. The total phenolic content and total flavonoid content in 30% ethanol extracts of JGT were higher than those of water extracts of JGT. Ethanol extracts of JGT (JGT-E) had stronger antioxidant activities of 2,2′-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and 2,2′-diphenyl-1-picrylhydrazyl-scavenging activity (DPPH) than water extracts of JGT (JGT-W). JGT-E contained 19–53% (1.8 to 4.9-fold) more active compounds (i.e., albiflorin, liquiritin, pentagalloylglucose, isoliquiritin apioside, isoliquiritin, liquiritigenin, and glycyrrhizin) than JGT-W. The ethanol extracts of JGT inhibited hydrogen peroxide-induced cell death and intracellular reactive oxygen species generation more effectively than the water extract of JGT in a dose-dependent manner. For the first time, these results suggest that ethanol extract of JGT is relatively more efficacious at protecting against oxidative stress-induced muscle cell death.
Dental 3D-Printing: Transferring Art from the Laboratories to the Clinics

The rise of three-dimensional (3D) printing technology has changed the face of dentistry over the past decade. 3D printing is a versatile technique that allows the fabrication of fully automated, tailor-made treatment plans, thereby delivering personalized dental devices and aids to the patients. It is highly efficient, reproducible, and provides fast and accurate results in an affordable manner. With persistent efforts among dentists for refining their practice, dental clinics are now acclimatizing from conventional treatment methods to a fully digital workflow to treat their patients. Apart from its clinical success, 3D printing techniques are now employed in developing haptic simulators, precise models for dental education, including patient awareness. In this narrative review, we discuss the evolution and current trends in 3D printing applications among various areas of dentistry. We aim to focus on the process of the digital workflow used in the clinical diagnosis of different dental conditions and how they are transferred from laboratories to clinics. A brief outlook on the most recent manufacturing methods of 3D printed objects and their current and future implications are also discussed.
Enhanced Separation of Polyethylene Glycol from Bovine Serum Albumin Using Electro-Ultrafiltration

Electric field-enhanced separation of polyethylene glycol (PEG) from an aqueous electrolyte solution of bovine serum albumin has been carried out. Experimental results show significant improvements in both the permeate flux and the PEG transmission with the application of a suitable d.c. electric field. A mass transfer model based on film theory is proposed for prediction of permeate flux and observed retention of PEG. The model uses a single parameter, namely real retention (Rr2) of the PEG which is evaluated by optimizing the experimental values of steady state permeate flux and the permeate concentration. Model predictions are in good agreement with the experimental data.
Thermoreversible Radial Growth of Micellar Assembly for Hydrogel Formation Using Zwitterionic Oligopeptide Copolymer

Amphiphilic block copolymers can self-assemble into micelles in water and can further form thermosensitive gels. Here, we explored Pluronic F127 ABA triblock copolymer of poly(ethylene glycol) (PEG; A) and poly(propylene glycol) (PPG; B), modified with telechelic ionic peptides, either anionic Gly-Phe-Gly-Asp (GFGD) or zwitterionic Gly-Arg-Gly-Leu (GRGL) or Gly-Arg-Gly-Asp (GRGD). All block copolymers formed micelles, but only those bearing zwitterionic peptides formed thermoreversible nanoassembly of micellar aggregates. These aggregates facilitate to form a gel at high polymer concentrations, thus making the sol-to-gel transition temperature lower than F127 and FGM. An increase in the sol-to-gel transition temperature and a decrease in the gel modulus have been a concern for biomedical applications of hydrophobically modified Pluronics. Current zwitterionic modified Pluronic F127, on the contrary, decreased the sol-to-gel transition temperature without loss of the gel modulus. The gelation, evidenced by.
Morphology and thermal behavior of organo‐bentonite clay/poly(styrene‐co‐methacrylic acid)/poly(isobutyl methacrylate‐co‐4‐vinylpyridine) nanocomposites

Poly(styrene-co-methacrylic acid) containing 29 mol % of methacrylic acid (SMA-29) and poly(isobutyl methacrylate-co-4-vinylpyridine) containing 20 mol % of 4-vinylpyridine (IBM4VP-20) were synthesized, characterized, and used to elaborate binary and ternary nanocomposites of different ratios with a 3% by weight hexadecylammonium-modified bentonite from Maghnia (Algeria) by casting method from tetrahydrofuran (THF) solutions. The morphology and the thermal behavior of these binary and ternary elaborated nanocomposites were investigated by X-ray diffraction, scanning electron microscopy, FTIR spectroscopy, differential scanning calorimetry, and thermogravimetry. Polymer nanocomposites and nanoblends of different morphologies were obtained. The effect of the organoclay and its dispersion within the blend matrix on the phase behavior of the miscible SMA29/IBM4VP20 blends is discussed. The obtained results showed that increasing the amount of SMA29 in the IBM4VP20/SMA29 blend leads to near exfoliated nanostructure with significantly improved thermal stability. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
The role of sulphur in ZDDP‐induced reaction films formed in the presence of ZDDP: Contribution of electron spectroscopic imaging technique

The anti-wear action of zinc dithiophosphate (ZDDP), extensively used in engine oils, is here studied by analysis of wear particles generated during a friction test between two ferrous substrates. It is known in this case that the interfacial film is complex, and contains elements from surfaces, environment and degradation products of the additive. This paper deals with the presence and the form of sulphur species in the constitution of this film. Analytical Transmission Electron Microscopy (TEM, STEM, EDS and EELS filtered images) of particles shows that sulphur is in the form of small crystallites of iron sulphide Fe7S8, embedded in an amorphous phosphate matrix. Wear tests performed at different normal loads show the variation of the P/S ratio in the particles. The results are discussed.
mer -Mediated Resistance and Volatilization of Hg(II) Under Anaerobic Conditions

The response of the mercury-resistant denitrifier, Pseudomonas stutzeri strain OX, and its sensitive derivative OX1 to HgCl 2 was examined under aerobic and anaerobic conditions to evaluate the potential role of the transformations mediated by the mercury resistance operon ( mer ) in the geochemical cycling of mercury. The resistance of strain OX to increasing concentrations of Hg(II) under anaerobic conditions resulted in a tri-phasic dose-response curve. Between 0.1 and 5 w M Hg(II), OX was as sensitive to Hg(II) as anaerobically grown OX1. No further growth inhibition was observed for OX between 5 and 25 w M Hg(II) under anaerobic conditions. At concentrations > 30 w M Hg(II), OX exhibited greater tolerance to Hg(II) under anaerobic versus aerobic conditions. Similarly, the sensitive strain OX1 was able to tolerate a 6-fold higher Hg(II) concentration under anaerobic than under aerobic conditions. When grown anaerobically, the maximal apparent 203 8Hg(II) volatilization rates by strain OX were decreased relative to those seen in aerobically grown cultures. Induction of mercuric reductase (MR) under anaerobic versus aerobic conditions depended on the Hg(II) concentration; at 0.1 w M, 203 Hg volatilization was lower anaerobically, whereas at 25 w M, MR activity was similar under both conditions. Additionally, an OX1 derivative carrying a merR-lacZ fusion produced > 20 times more g -galactosidase under aerobic than under anaerobic conditions when induced with < 0.5 w M Hg(II). These results suggest that (1) anaerobiosis affects Hg(II) transport into the cell and (2) the levels of mer expression are influenced by both the redox conditions and the concentration of Hg(II). Thus, mer -mediated activities are expected to affect mercury geochemistry in anoxic environments at higher concentrations of Hg(II) than in oxic environments. The implications of these findings to methylmercury accumulation in aquatic environments are discussed.
Characterizing vesicle leakage by fluorescence lifetime measurements

The membrane leakage assay based on vesicles loaded with self-quenching dyes has been widely used for quantifying the activity of antibiotic peptides and other compounds that induce membrane pores or leaks. Here we show that this assay can be substantially improved if it is based on time-resolved decay curves rather than steady-state intensities only. A bi- or triexponential fit of calcein fluorescence decays allows for a parallel quantification of the free and (one or two) entrapped dye fractions and their effective local concentrations (governing the lifetime). The advantages of this technique are that it (i) allows the distinguishing of all-or-none from graded leakage for each sample, (ii) reveals the heterogeneity of graded leakage, (iii) truly quantifies the released dye rather than providing an empiric dequenching value, and (iv) is independent of many errors that may affect the intensity. We introduce the method by studying graded leakage caused by the detergent C12EO8.
Topical Treatment of Psoriasis Vulgaris: The Swiss Treatment Pathway

Topical treatment is crucial for the successful management of plaque psoriasis. Topicals are used either as a stand-alone therapy for mild psoriasis or else in combination with UV or systemic treatment for moderate-to-severe disease. For the choice of a suitable topical treatment, the formulation matters and not just the active substances. This expert opinion paper was developed via a non-structured consensus process by Swiss dermatologists in hospitals and private practices to illustrate the current treatment options to general practitioners and dermatologists in Switzerland. Defining treatment goals together with the patient is crucial and increases treatment adherence. Patients’ personal preferences and pre-existing experiences should be considered and their satisfaction with treatment and outcome regularly assessed. During the induction phase of “classical” mild-to-moderate psoriasis, the fixed combination of topical calcipotriol (Cal) 50 μg/g and betamethasone dipropionate (BD) 0.5 mg/g once daily is frequently used for 4–8 weeks. During the maintenance phase, a twice weekly (proactive) management has proved to reduce the risk of relapse. Of the fixed combinations, Cal/BD aerosol foam is the most effective formulation. However, the individual choice of formulation should be based on a patient’s preference and the location of the psoriatic plaques. Tailored recommendations are given for the topical management of specific areas (scalp, facial, intertriginous/genital, or palmoplantar lesions), certain symptoms (hyperkeratotic or hyperinflammatory forms) as well as during pregnancy or a period of breastfeeding. As concomitant basic therapy, several emollients are recommended. If topical treatment alone does not appear to be sufficient, the regimen should be escalated according to the Swiss S1-guideline for the systemic treatment of psoriasis.
Calibrating Nonconvex Penalized Regression for Logistic Model in Ultra-high Dimension

Calibrating Nonconvex Penalized Regression for Logistic Model in Ultra-high Dimension Semin Choi The Department of Statistics The Graduate School Seoul National University In high dimensional linear regression, penalized regression methods are used for estimation and variable selection simultaneously. The LASSO is a penalized regression method which is easy to compute the solution, but the LASSO solution is hard to satisfy the variable selection consistency. Nonconvex penalized regression
Resection of cerebellar tumours causes widespread and functionally relevant white matter impairments

Several diffusion tensor imaging studies reveal that white matter (WM) lesions are common in children suffering from benign cerebellar tumours who are treated with surgery only. The clinical implications of WM alterations that occur as a direct consequence of cerebellar disease have not been thoroughly studied. Here, we analysed structural and diffusion imaging data from cerebellar patients with chronic surgical lesions after resection for benign cerebellar tumours. We aimed to elucidate the impact of focal lesions of the cerebellum on WM integrity across the entire brain, and to investigate whether WM deficits were associated with behavioural impairment in three different motor tasks. Lesion symptom mapping analysis suggested that lesions in critical cerebellar regions were related to deficits in savings during an eyeblink conditioning task, as well as to deficits in motor action timing. Diffusion imaging analysis of cerebellar WM indicated that better behavioural performance was associated with higher fractional anisotropy (FA) in the superior cerebellar peduncle, cerebellum's main outflow path. Moreover, voxel‐wise analysis revealed a global pattern of WM deficits in patients within many cerebral WM tracts critical for motor and non‐motor function. Finally, we observed a positive correlation between FA and savings within cerebello‐thalamo‐cortical pathways in patients but not in controls, showing that saving effects partly depend on extracerebellar areas, and may be recruited for compensation. These results confirm that the cerebellum has extended connections with many cerebral areas involved in motor/cognitive functions, and the observed WM changes likely contribute to long‐term clinical deficits of posterior fossa tumour survivors.
Fluorescent probes and bioconjugation chemistries for single-molecule fluorescence analysis of biomolecules

Fluorescence-based detection of single biomolecules in solution and at room temperature has opened new avenues for understanding biological mechanisms. Single-molecule fluorescence spectroscopy (SMFS) of biomolecules requires careful selection of fluorophores, sites of incorporation, and labeling chemistries. SMFS-compatible fluorophores should permit extended, uninterrupted observations of fluorescence with high signal-to-noise ratios; more stringent considerations apply for specific methodologies, such as fluorescence resonance energy transfer and fluorescence anisotropy. Strategies for site-specific in vitro labeling of small proteins exploit the reactivity of the amino acid cysteine (Cys), allowing incorporation of one or more fluorophores; labeling of closely spaced Cys residues using bis-functionalized fluorophores allows probing of the orientation of individual protein domains. For in vitro labeling of large proteins, the options include peptide ligation, intein-mediated labeling, puromycin-based labeling, unnatural amino acid mutagenesis, and reconstitution from individual subunits or subunit fragments. For in vivo analysis, one can use proteins that are labeled in vitro and then incorporated in cells; genetic encoding of specific protein sequences can also lead to in vivo labeling, either by in vivo targeting by fluorophores or by biosynthesis of protein fusions with natural fluorophores such as the green fluorescent protein. The existing methods, along with others under development, will bring SMFS to the mainstream and advance significantly our understanding of vital biological processes.
Effects of androgenic properties of progestin combined with ethinyl estradiol on vascular endothelial reactivity, plasma lipids and free radical production in women with endometriosis

Endothelial reactivity is inhibited and oxidative stress is enhanced in women with endometriosis. Testosterone may adversely affect lipids and endothelium. We investigated the effects of androgenic properties of progestins combined with ethinyl estradiol (EE) on endothelial function, lipids and free radical production in such women.