Miracle-dz/UniFAR-FTUs huggingface dataset:
Constructive Prediction of Potential RNA Aptamers for a Protein Target

Aptamers are short single-stranded nucleic acids that bind to target molecules with high affinity and selectivity. Aptamers are generally identified in vitro by performing SELEX (systematic evolution of ligands by exponential enrichment). Complementing the SELEX process, several computational methods have been proposed in the search for aptamers. However, many of these methods cannot be applied for finding new aptamers, either because they are classifiers for determining whether an RNA and protein interact with each other, or because they are limited to a specific target only. Hence, we developed a new random forest (RF) model for finding potential RNA aptamers for a protein target. From an extensive analysis of protein-RNA complexes including RNA aptamers-protein complexes, we identified key features of interacting RNA and protein molecules, and structural constraints on RNA aptamers. The potential RNA aptamers predicted by our method reveal similar secondary and protein-binding structures as the actual RNA aptamers. The RF model showed a reliable performance in both cross validations and independent testing. The key features of interacting RNA and protein molecules and the structural constraints identified in our study were effective in finding potential aptamers for a protein target. Although preliminary, our results are promising, and we believe this approach will be useful in reducing time and money spent on in vitro experiments by substantially limiting the size of the initial pool of nucleic acid sequences.
Immunological ignorance is an enabling feature of the oligo-clonal T cell response to melanoma neoantigens

Significance Recent work implicates tumor neoantigens as the primary target of the antitumor immune response based on the correlates of tumor mutational burden and tumoral CD8+ T cell density. We provide evidence that, despite ubiquitous sharing of clonal and subclonal neoantigens among tumors, the CD8+ response is limited to a small (<10%) subset of antigens and is typically mono-/oligoclonal in nature. Vaccination promotes an increase in neoantigen breath and T cell clonotype diversity, suggesting ineffective neoantigen cross-presentation as the primary mechanism for immunological ignorance. Our findings support the notion that therapeutic vaccination is necessary as an adjunct to checkpoint inhibitor treatment, since most T cell clones specific for melanoma neoantigens are naïve and often below the limit of detection. The impact of intratumoral heterogeneity (ITH) and the resultant neoantigen landscape on T cell immunity are poorly understood. ITH is a widely recognized feature of solid tumors and poses distinct challenges related to the development of effective therapeutic strategies, including cancer neoantigen vaccines. Here, we performed deep targeted DNA sequencing of multiple metastases from melanoma patients and observed ubiquitous sharing of clonal and subclonal single nucleotide variants (SNVs) encoding putative HLA class I-restricted neoantigen epitopes. However, spontaneous antitumor CD8+ T cell immunity in peripheral blood and tumors was restricted to a few clonal neoantigens featuring an oligo-/monoclonal T cell-receptor (TCR) repertoire. Moreover, in various tumors of the 4 patients examined, no neoantigen-specific TCR clonotypes were identified despite clonal neoantigen expression. Mature dendritic cell (mDC) vaccination with tumor-encoded amino acid-substituted (AAS) peptides revealed diverse neoantigen-specific CD8+ T responses, each composed of multiple TCR clonotypes. Isolation of T cell clones by limiting dilution from tumor-infiltrating lymphocytes (TILs) permitted functional validation regarding neoantigen specificity. Gene transfer of TCRαβ heterodimers specific for clonal neoantigens confirmed correct TCR clonotype assignments based on high-throughput TCRBV CDR3 sequencing. Our findings implicate immunological ignorance of clonal neoantigens as the basis for ineffective T cell immunity to melanoma and support the concept that therapeutic vaccination, as an adjunct to checkpoint inhibitor treatment, is required to increase the breadth and diversity of neoantigen-specific CD8+ T cells.
Investigation on Hardness of Gravity Die Cast Secondary Al-10Si Piston Alloy with Trace Addition of Sr, Fe and Mn

This paper investigates the effect of minor elements on Brinell hardness properties of Al-10Si alloy. This investigation was carried out with the aim of improving the properties of recycled cast Al-Si alloys so as to enhance their performance. The research therefore came up with the most suitable level of element composition that gives the recycled Al-Si alloys enhanced mechanical properties. The results obtained are deemed beneficial to the local foundries that utilize scrap aluminium alloys to cast their products both for commercial and domestic purposes. Al-Si alloys were produced using gravity die casting process upon which strontium, iron and manganese were added in varying proportions. T6 heat treatment procedures were also carried out on the obtained casting in order to determine the effects of heat treatment on Al-Si alloys. Addition of Sr at weight levels of 0.025%, 0.048% and 0.06% increased the Brinell hardness by 4.64%, 11.42% and 14.57% respectively. The results on addition of Fe at 0.50% and 0.78% weight levels showed improved alloy hardness by 3.48% and 2.15% respectively. Addition of Fe combined with Mn at levels of 0.50% Fe and 0.25% Mn resulted in hardness increase of 8.61% while a combination at 0.78% Fe and 0.39% Mn levels resulted in increasing the material hardness by 6.46%. Upon heat treating the base alloy material, its hardness value improved compared to its non-heat treated value. T6 heat treated alloys with 0.025%, 0.048% and 0.06% Sr levels showed hardness increment by 7.83%, 14.94% and 25.30% respectively. In addition, the heat treated alloys with Fe levels at 0.50% and 0.78% resulted in increased hardness by 5.42% and 4.46% respectively. On the other hand, when the Fe levels were neutralized with Mn at ratio of 2:1, the heat treated alloys bearing 0.50% and 0.78% Fe resulted in hardness increase by 12.05% and 10% respectively.
Tyrosinase Inhibitory Activity Within Hexane Extract of Ten Screened Plants From Kurdistan Province of Iran

Objective: Tyrosinase as the key enzyme in melanin biosynthesis, involves in determining the color of mammalian skin and hair. A variety of dermatological disorders, come up from an unnecessary level of epidermal pigmentation. Plants are low-cost and rich sources of active compounds. Methods: More than seventy native plants collected from the central region of Kurdistan province collected. Inhibitory effect of hexane extracts from aerial parts of them was tested on tyrosinase activity. All extracts were screened for their tyrosinase inhibitory activity at 1, 0.1, 0.01, 0.001 µg/ml concentrations. Assay method was based on Microplate spectrophotometric study of absorption in 492 nm, arbutin and kojic acid were used as positive controls. Results: Among the evaluated hexane extracts, only 10 cases showed more than 50% tyrosinase inhibitory activities, including Gundelia Tourneforti L. , Astragalus vegetus Bunge, Vicia hyrcanica Fisch. & C.A. Mey, Campanula involucrate Auch.ex DC, Isatis cappadocica Desv, Sanguisorba minor Scop. , Eremostachys laevigata Bunge, Ballota nigra L. , Aristolochia bottae Jaub. &Spach, Astragalus caryolobus Bge, and among them Gundelia Tournefortii L. L. , showed considerable inhibition with IC50 of 0.173 µg/ml. These results suggest that the most effective plant extracts, especially that of Gundelia Tourneforti L. be worthy of further investigation.
Variability of Storm-Relative Helicity during VORTEX

In this paper, storm-relative helicity (SRH) and low-level vertical shear of the horizontal wind fields were investigated on the mesoscale and stormscale in regions where tornadoes occurred for four case studies using data collected during the Verification of the Origin of Rotation in Tornadoes Experiment. A primary finding was that SRH was highly variable in both time and space in all of the cases, suggesting that this parameter might be difficult to use to predict which storms might become tornadic given the available National Weather Service upper-air wind data. Second, it was also found that the shear between the lowest mean 500-m wind and the 6-km wind was fairly uniform over vast regions in all of the four cases studied; thus, this parameter provided little guidance other than that there was possibly enough shear to support supercells. It was contended that forecasters will need to monitor low-level features, such as boundaries or wind accelerations, which might augment streamwise vorticity ingested into storms. Finally, it was suggested that one reason why one storm might produce a tornado while a nearby one does not might be due to the large variations in SRH on very small spatial and temporal scales. In other words, only those storms that move into regions, small or large, with sufficient SRH might produce tornadoes.
Effects of low temperature on the mechanical properties of glass fibre–epoxy composites: static tension, compression, R = 0.1 and R =− 1 fatigue of ±45° laminates

Effects of cold climate exposure on structures made of composite materials are scarcely documented. As a result, even if exceptional wind conditions prevail in some cold regions, uncertainties related to composite materials durability at low temperatures may hinder development of wind energy projects in those regions. Therefore, as part of the Wind Energy Strategic Network (WESNet) of the Natural Sciences and Engineering Research Council (NSERC) of Canada, efforts were made to evaluate the effects of cold climate exposure on the mechanical properties of glass–epoxy composites. Tensile and compressive quasi-static tests as well as tensile (R = 0.1) and fully reversed (R =− 1) fatigue tests were performed on vacuum-infused [±45]2s glass–epoxy composites at −40°C and 23°C. Results for quasi-static tests show an increase of tensile, compressive and shear strengths and moduli at low temperatures. It is also demonstrated that for the stress range under scrutiny, fatigue performance is improved at −40°C for both the R = 0.1 and R =− 1 loading cases. Moreover, the failure mode for R =− 1 fatigue changed from compressive failure due to buckling of delaminated plies to tensile failure, suggesting a more efficient use of the material. However, if R =− 1 fatigue results at low temperature are extrapolated towards the very low stresses that are also part of wind turbine blades fatigue load spectrum, fatigue life may be degraded compared with that at ambient temperature. Finally, evidence of visco-elastic behaviour leading to changes in s − N curve slope parameter are reported. Copyright © 2015 John Wiley & Sons, Ltd.
An evaluation of talimogene laherparepvec for the treatment of melanoma

ABSTRACT Introduction: Intralesional therapies have emerged as effective immune therapies for locally advanced and metastatic melanoma. Talimogene laherparepvec (T-VEC), an oncolytic virus derived from the herpes simplex 1 (HSV-1) virus, is the first and only FDA approved intralesional therapy for recurrent, unresectable cutaneous, subcutaneous or nodal metastases from melanoma. Areas covered: We discuss results from clinical trials of T-VEC including data on safety, biodistribution, and viral shedding, which established the current treatment protocol and basis for FDA approval. Data are presented from early implementation of T-VEC in clinical practice. We explore the use of T-VEC in the neoadjuvant setting and in combination with anti-CTLA-4 and PD-1 therapies, including available evidence to support a mechanism for the observed synergistic effect. Expert opinion: Intralesional T-VEC is effective for unresectable stage III and IVa melanoma, with early clinical results comparing favorably to response rates from clinical trials. Clinical applications will likely increase as more data become available on its use in the neoadjuvant setting and in combination with other systemic immune therapies. We expect the fields of intralesional therapy and viral oncotherapy to expand as we better understand how to manipulate the tumor microenvironment and host immune response to cancer.
Propagation and forcing of high frequency sea level variability in the eastern equatorial Pacific

approved: David B. Enftld Sea level and wind data from coastal and island stations from Buenaventura, Colombia (14°N) to Callao, Peru (12°S) have been analyzed for the 1979-1984 time period, to describe the seasonal and interannual variations in the characteristics of short time scale variability (1-2 weeks). Autoand cross spectral analyses are used to make comparisons between Austral summers and winters as well as interannual comparisons between the 1982-1983 El Ni? io/Southern Oscillation (ENSO) period and non-ENSO years. The principal results show weak evidence of local forcing of the sea level by the alongshore wind during the whole year without significant differences between summer and winter seasons. The alongshore coherence and phase spectra between the sea level series show evidence of poleward propagating fluctuations at speeds of 2.6-3.0 ms1 during winter, but no propagation is evident during summer. There is also a large energy increase in coastal sea level, especially in the 8-11 day band, during the 1982-1983 ENSO episode. Redacted for privacy This increase is associated with a non-dispersive, poleward propagation of events at speeds of 3.11-3.6 ms1. The propagating fluctuations are superimposed on a weak, locally forced variability. The only plausible source for the observed coastal fluctuations appears to be trapped waves in the equatorial waveguide. Additional equatorial data from subsurface pressure gauges in the Galapagos Islands and inverted echo sounders at 3°N,95°W, 3°N,85°W and 2°S,85°W are used to explore the possibility that the coastal signal during the 1982-1983 ENSO episode is connected to the arrival of energy in the form of equatorially trapped Rossby-gravity (Yanai) and Kelvin waves, and to determine the respective contributions of the two wave types. Cross spectral analyses, frequency domain EOF analysis and the characteristics of equatorial waves demonstrate that equatorially trapped Yanai waves are the principal source of the propagating signals in the coastal sea levels during the 1982-1983 ENSO. During the 1982-1983 ENSO, between 64% and 91% of the coastal SLH variability in the 8-11 day period band is associated with antisymmetric variability across the equator. Phase in this band is zonally invariant along the equator but is poleward propagating along the coast, consistent with the conversion of stationary, equatorial lanai waves into coastal trapped waves. Propagation and Forcing of High Frequency Sea Level Variability in the Eastern Equatorial Pacific
Analysis of the pedaling biomechanics of master’s cyclists: A preliminary study

The crank torque represents the kinetics of the propulsive torque within the crank cycle. These kinetics are one of the important determinants of cycling performance. At our knowledge, works in literature concerning the pedaling pattern of master cyclist is lacking although this group of cyclists concerns the majority of practitioners. The purpose of this experimentation is to study the biomechanics of cycling in masters cyclists during an incremental test. Eleven trained masters cyclists (53.5 ± 4.1 years) have participated at this study. The results indicate that the master cyclists have a significant asymmetry (30 ± 8 to 23 ± 13 %) during the pedaling exercise at all power output level tested in this study (100, 150, 200 and 250 W). The present preliminary study suggests that the pedaling pattern asymmetry observed in the master cyclists should be taken into account to prevent knee or muscle overuse injuries.
Smoking is an important factor that affects peripheral blood progenitor cells yield in healthy male donors

Smoking could reduce the CD34+ cells in peripheral blood of healthy individual. This study aimed to investigate the correlation between smoking load and the effect of peripheral blood hematopoietic progenitor cells (PBPCs) mobilization by granulocyte colony‐stimulating factor (G‐CSF) alone in healthy donors.
Effects of Post Annealing on the Electrical Properties of ZnO Thin Films Transistors

This paper reports the effects of post-annealing of ZnO thin films on their microstructure and the device performance of the transistors fabricated from the films. From X-ray diffraction and transmission electron microscopy characterization, we uncovered that the grain size increased with the annealing temperature escalating and that the film stress shifted from compressive to tensile due to the grain size increment. Electrical characterization revealed that the grain size increase damaged the device performance by drastically lifting the off-current level. By annealing the devices in an ambient (instead of air), we were able to suppress the off-current while improving the electron mobility.
tree / H *-cubing : Improved Data Cube Structure and Cubing Method for OLAP on Data Stream

Data cube plays an important role in multi-dimensional, multi-level data analysis. Meeting on-line analysis requirements of data stream, several cube structures have been proposed for OLAP on data stream, such as stream cube, flowcube, S-cube. Since it is costly to construct data cube and execute ad-hoc OLAP queries, more research works should be done considering efficient data structure, query method and algorithms. Stream cube uses H-cubing to compute selected cuboids and store the computed cells in an H-tree, which form the cuboids along popular-path. However, the H-tree layoutis disorderly and H-cubing method relies too much on popular path.In this paper, first, we propose H*-tree, an improved data structure, which makes the retrieval operation in tree structure more efficient. Second, we propose an improved cubing method, H*-cubing, with respect to computing the cuboids that cannot be retrieved along popular-path when an ad-hoc OLAP query is executed. H*-tree construction and H*-cubing algorithms are given. Performance study turns out that during the construction step, H*-tree outperforms H-tree with a more desirable trade-off between time and memory usage, and H*-cubing is better adapted to ad-hoc OLAP querieswith respect to the factors such as time and memory space.
Fasting in the ureotelic Lake Magadi tilapia, Alcolapia grahami, does not reduce its high metabolic demand, increasing its vulnerability to siltation events

Abstract Lake Magadi, Kenya, is one of the most extreme aquatic environments on Earth (pH~10, anoxic to hyperoxic, high temperatures). Recently, increased water demand and siltation have threatened the viable hot springs near the margins of the lake where Alcolapia grahami, the only fish surviving in the lake, live. These Lake Magadi tilapia largely depend on nitrogen-rich cyanobacteria for food and are 100% ureotelic. Their exceptionally high aerobic metabolic rate, together with their emaciated appearance, suggests that they are energy-limited. Therefore, we hypothesized that during food deprivation, Magadi tilapia would economize their energy expenditure and reduce metabolic rate, aerobic performance and urea-N excretion. Surprisingly, during a 5-day fasting period, routine metabolic rates increased and swimming performance (critical swimming speed) was not affected. Urea-N excretion remained stable despite the lack of their N-rich food source. Their nitrogen use switched to endogenous sources as liver and muscle protein levels decreased after a 5-day fast, indicating proteolysis. Additionally, fish relied on carbohydrates with lowered muscle glycogen levels, but there were no signs indicating use of lipid stores. Gene expression of gill and gut urea transporters were transiently reduced as were gill rhesus glycoprotein Rhbg and Rhcg-2. The reduction in gill glutamine synthetase expression concomitant with the reduction in Rh glycoprotein gene expression indicates reduced nitrogen/ammonia metabolism, most likely decreased protein synthesis. Additionally, fish showed reduced plasma total CO2, osmolality and Na+ (but not Cl−) levels, possibly related to reduced drinking rates and metabolic acidosis. Our work shows that Lake Magadi tilapia have the capacity to survive short periods of starvation which could occur when siltation linked to flash floods covers their main food source, but their seemingly hardwired high metabolic rates would compromise long-term survival.
Ionosphere plasma bubbles and density variations induced by pre‐earthquake rock currents and associated surface charges

[1] Recent ionospheric observations indicate that the total electron content (TEC) may anomalously decrease or increase up to 5–20% before the occurrence of big earthquakes. The ionospheric density variations can be caused by earth surface charges/currents produced from electric currents associated with the stressed rock. We formulate a coupling model for the stressed rock-Earth surface charges-atmosphere-ionosphere system. The stressed-rock acts as the dynamo to provide the currents for the coupling system. The electric fields and currents in the atmosphere and the lower boundary of ionosphere are obtained by solving the current continuity equation, ∇ • J = 0, where J is the current density. A three-dimensional ionosphere simulation code is then used to study the ionospheric dynamics based on the obtained electric fields and currents. The simulation results show that a current density Jrock = 0.2–10 μA/m2 in an earthquake fault zone is required to cause daytime TEC variations of 2–25%. The simulation results also show that a current density Jrock = 0.01–1 μA/m2 can lead to nighttime TEC variations of 1–30% as well as the formation of a nighttime plasma bubble (equatorial spread F) extending over the whole magnetic flux tube containing the earthquake epicenter. We suggest that observations of daytime and nighttime TEC variations and a nighttime plasma bubble within the affected region can be used as precursors for earthquake prediction.
Utilization of Waste Leather Powders for Highly Effective Removal of Dyes from Water

As a natural polymer, leather and its associated industries are known to be the leading economic sector in many countries. However, the huge amounts of leather waste generated from the leather industry causes severe environmental pollution. Herein, cow leather (CL) powders were prepared using a homemade machine and used as a low-cost adsorbent for the effective removal of reactive dyes from wastewater. The as-prepared CL powders exhibited dot-like, rod-like, and fiber-like morphologies. A Fourier transform infrared analysis and an x-ray diffraction analysis demonstrated that the CL powders retained the main structure of the protein contained in it. In addition, an improvement in thermal stability was also observed for the CL powders. Dye adsorption experiments indicate that the CL powders showed the highly effective removal of C.I. Reactive Red 120 (RR120), C.I. Reactive Yellow 127 (RY127), and C.I. Reactive Blue 222 (RB222) with the adsorption capacity of 167.0, 178.9, and 129.6 mg·g−1, respectively. The Langmuir, pseudo-second order, and intraparticle diffusion models could well depict the adsorption equilibrium and kinetics of CL powders toward the investigated reactive dyes. The as-prepared CL powders can be used as a potential adsorbent in the treatment of dye contaminated wastewater. Future studies will mainly focus on the application of the adsorbed CL powders for the pigment printing of textile materials.