Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics.

Cancer is driven by genomic alterations, but the processes causing this disease are largely performed by proteins. However, proteins are harder and more expensive to measure than genes and transcripts. To catalyze developments of methods to infer protein levels from other omics measurements, we leveraged crowdsourcing via the NCI-CPTAC DREAM proteogenomic challenge. We asked for methods to predict protein and phosphorylation levels from genomic and transcriptomic data in cancer patients. The best performance was achieved by an ensemble of models, including as predictors transcript level of the corresponding genes, interaction between genes, conservation across tumor types, and phosphosite proximity for phosphorylation prediction. Proteins from metabolic pathways and complexes were the best and worst predicted, respectively. The performance of even the best-performing model was modest, suggesting that many proteins are strongly regulated through translational control and degradation. Our results set a reference for the limitations of computational inference in proteogenomics. A record of this paper's transparent peer review process is included in the Supplemental Information

Calculation method of side backlash in meshing gears of a harmonic gear

W pracy przedstawiono metodę wyznaczania luzu obwodowego dla przyjętego zarysu ewolwentowego koła podatnego i sztywnego przekładni falowej. W pierwszej części pracy scharakteryzowano parametry geometryczne przekładni. Następnie dla współpracujących kół zębatych zdefiniowano luz obwodowy, przedstawiono założenia do modelu matematycznego wyznaczania luzu obwodowego, omówiono algorytm metody rozwiązania równań modelu matematycznego. We wnioskach zawarto wyniki badań symulacyjnych. Opracowana metoda zostanie wykorzystana w dalszych badaniach do określenia w strefie kontaktu zazębiających się kół rozkładu nacisków i odkształceń.The article contains information about the calculation method of side backlash for harmonic gear with involute profile. The first part of the paper contains a description of main geometric parameters of this kind of gear. After that a definition of side backlashes was defined with the main foundations of mathematical model of the method with algorithm. The summary contains conclusions. The presented method will be used in further research of tooth contact

Effect of Annealing and Irradiation on the Optical Properties of Oxide Crystals

We described results of the effect of annealing and irradiation treatments on the optical properties of Y$\text{}_{3}$Al$\text{}_{5}$O$\text{}_{12}$, YAlO$\text{}_{3}$, SrLaGa$\text{}_{3}$O$\text{}_{7}$, LiNbO$\text{}_{3}$, Gd$\text{}_{3}$Ga$\text{}_{5}$O$\text{}_{12}$, LaGaO$\text{}_{3}$, ZnSe, and LiF single crystals. Changes in absorption and luminescence are presented. Recharging processes of uncontrolled impurities (e.g. Fe$\text{}^{3+}$, Fe$\text{}^{2+}$, and Mn$\text{}^{2+}$), and active ions (e.g. Nd$\text{}^{3+}$, Dy$\text{}^{3+}$, Cr$\text{}^{4+}$, Cr$\text{}^{3+}$, and Ce$\text{}^{3+}$), as well as types of color centers produced in the crystals after a particular irradiation or annealing treatment are presented

Post-implantation defects instability under 1 MeV electron irradiation in GaAs

The influence of 1 MeV electron irradiation on the stability of post-implantation defects in GaAs has been investigated. The n-type GaAs wafers of orientation were implanted with 150 keV As+ ions below the amorphization threshold at RT using the implantation dose of 2×1013 ions cm–2 at a constant flux of 0.1 žA cm–2. Then the implanted samples were irradiated with a scanned beam of 1 MeV electrons from a Van de Graaff accelerator in a dose range (0.5–5.0)×1017 cm–2 at 320 K. RBS and channeling spectroscopy of 1.7 MeV 4He+ ions were used to determine the depth distribution of defect concentration before and after 1 MeV irradiations. New results of an "oscillatory" behaviour of the damage level as a function of 1 MeV electron fluence are presented

Angular dependence of post-implantation damage recovery under 1 MeV electron irradiation in GaAs

The angular dependence of post-implantation defects removal in GaAs irradiated with 1 MeV electrons from a Van de Graaff accelerator has been investigated. The possible way of enhancing defect annealing consists in ionization created by electron irradiation. In this paper new results of a damage level behaviour dependent on 1 MeV electron beam angle irradiation are presented. GaAs single crystals of orientation were implanted with 150 keV As+ ions at RT and then irradiated with a scanning beam of 1 MeV electrons at some selected angles. Rutheford Backscattering Spectroscopy (RBS) of 1.7 MeV 4He+ ions were used to determine the depth distribution of defect concentration before and after electron irradiation. The results relate clearly the ionization intensity created by the electron beam with angle of incidence with respect to the GaAs orientation

Damage Production in As Implanted GaAs1−x\text{}_{1-x}Px\text{}_{x}

Post-implantation damage in GaAs$\text{}_{1-x}$P$\text{}_{x}$ compounds (x = 0, 0.15, 0.39, 0.65, and 1) implanted with 150 keV As ions in the dose range 1 × 10$\text{}^{13}$ -8 × 10$\text{}^{13}$ cm$\text{}^{-2}$ at 120 K was investigated. The depth distribution of damage and the degree of amorphization were measured by Rutherford backscattering 1.7 MeV He$\text{}^{+}$ channeling technique. The critical damage dose and the critical energy density necessary for amorphization were determined. It is shown that GaAsP is easier to amorphize (lower critical damage dose) than the binary crystals (GaAs, GaP) at low temperatures

Phosphorus fertiliser equivalent value of dairy processing sludge-derived STRUBIAS products using ryegrass (Lolium perenne L.) and spring wheat (Triticum aestivum)

Struvite, biochar and ash products (collectively known as STRUBIAS) products derived from different waste streams are used as fertilisers in agriculture. Raw dairy processing sludge (DPS) shows promise as bio-based fertilisers, but their secondary STRUBIAS-derived products need testing as fertilisers. The objective of this ryegrass (Lolium perenne L.) and wheat (Triticum aestivum) pot trial was to calculate their phosphorus mineral fertiliser equivalency (P-MFE) using the apparent P method for Fe-DPS and DPS-derived struvites (Struvite 1 ¿ 4), hydrochars (HC1 ¿ 3) and ash. Results showed that the products can be divided into two groups: (1) a range of products that can (i.e., Struvite 1 ¿ 3) and (2) cannot (i.e., Struvite 4, HC1 ¿ 3, ash and Fe-DPS) be considered as fertilisers. In the first group, the P-MFE ranged from 66.8 to 76.7% for ryegrass and from 77.9 to 93.5% for spring wheat grain. In the second group, the P-MFE ranged from 7.8 to 58.3% for ryegrass and from -34.5 to -151.3% for spring wheat grain. Processing solutions could overcome problems. These may include the avoidance of Fe dosing salts (in the case of struvite) by using biological methods of P removal or the utilisation of oxalic acid during struvite precipitation, which removes Fe from the process chain and produces higher yields. Future policy and research must be aware that not all STRUBIAS products are suitable as fertilisers and therefore need to be tested individually.This project (REFLOW) has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 814258. Open access funding provided by IReL.peer-reviewe