Modeling of halorhodopsin and rhodopsin based on bacteriorhodopsin

Bacteriorhodopsin (BR), halorhodopsin (HR), and rhodopsin (Rh) all belong to the class of seven-helix membrane proteins. For BR, a structural model at atomic resolution is available; for HR, diffraction data are available only down to a resolution of 6 Å in the membrane plane, and for Rh, down to 9 Å. BR and HR are closely related proteins with a sequence homology of 34%, while Rh does not share any sequence homology with BR. An atomic model for HR is derived that is based on sequence alignment and the atomic model for BR and is improved by molecular dynamics simulations. The model structure obtained accounts well for the experimentally observed difference between HR and BR in the projection map, where HR exhibits a higher density in the region between helices D and E. The reason for this difference lies partially in the different side chains and partially in slightly different helix tilts. The scattering amplitudes and phases of the model structure are calculated and agree with the experimental data down to a resolution of about 8 Å. If the helix positions are adopted from the projection map for HR and used as input in the model, this number improves to 7 Å. Analogously, an atomic model for Rh is derived based on the atomic model for BR and subjected to molecular dynamics simulations. Optimal agreement with the experimental projection map for Rh is obtained when the entire model structure is rotated slightly about two axes in the membrane plane. The agreement with the experimental projection map is not as satisfactory as for HR, but the results indicate that even for a nonhomologous, but structurally related, protein such as Rh, an acceptable model structure can be derived from the structure of BR. © 1996 Wiley-Liss, Inc.     

Linear measurement error models with restricted sampling

The relationship between nutrient consumption and chronic disease risk is the focus of a large number of epidemiological studies where food frequency questionnaires (FFQ) and food records are commonly used to assess dietary intake. However, these self-assessment tools are known to involve substantial random error for most nutrients, and probably important systematic error as well. Study subject selection in dietary intervention studies is sometimes conducted in two stages. At the first stage, FFQ-measured dietary intakes are observed and at the second stage another instrument, such as a 4-day food record, is administered only to participants who have fulfilled a prespecified criterion that is based on the baseline FFQ-measured dietary intake (e.g., only those reporting percent energy intake from fat above a prespecified quantity). Performing analysis without adjusting for this truncated sample design and for the measurement error in the nutrient consumption assessments will usually provide biased estimates for the population parameters. In this work we provide a general statistical analysis technique for such data with the classical additive measurement error that corrects for the two sources of bias. The proposed technique is based on multiple imputation for longitudinal data. Results of a simulation study along with a sensitivity analysis are presented, showing the performance of the proposed method under a simple linear regression model.     

Immunologic unresponsiveness of mouse spleen sensitized to allogenic tumors.

CS7BL/6 mice were sensitized with an ip injection of allogeneic P-815 mastocytoma cells. Fifteen days later the spleen cells of the tumor allosensitized mice were cultured and tested for their responsiveness to mitogens and alloantigens, and for their ability to generate cytotoxic cells in vitro. The results indicate that 15 day tumor-sensitized spleen cells are hypo-responsive in mixed lymphocyte culture (MLC) with DBA/2 or AKR as stimulating spleen cells. The cells which are hypo-responsive in MLC can proliferate in response to mitogens and they also can generate cytotoxic cells in vitro. MLC reactivity recovers in about 2–3 months which is $\text{1}\text{1}\text{2}\text{–2}\text{1}\text{2}$ months after the mice have rejected their tumors. The mechanism of MLC hypo-responsiveness was investigated. The results suggest the presence of a suppressor cell which does not appear to be a macrophage or a B-cell. The suppressor cell can be separated from the cytotoxic cell and therefore appears to be a noncytotoxic T-cell.     

Impact of Human,workplace and indoor environmental risk factors on operator’s reliability in control rooms

Abstract

Adequate design of control rooms is very important for increasing the reliability of operators working in them. Therefore, it is necessary to choose the best solution for improving the compliance between operators and elements of control room while dealing with problems of illumination, thermal climate and noise. For this purpose we will analyze the impact of execution time of operator's information processing tasks, motor and logical operator's tasks, operator's functional state, workplace risk factors and indoor environment parameters on operator's reliability in control room. Methodological approaches for these five groups are formed and used for experimental research and to determine the level of their quantitative values. Research results are showing the following levels of reliability for specific indicators: reaction time ‐ very good, coefficient of task complexity ‐ optimal, operator's error caused by stress ‐ very good, workplace risk factor ‐ critical and indoor environment ‐ good. Because the functional appropriateness and efficiency in the operator's workplace were inadequate, the following recommendations and solutions were proposed: signaling and control elements should be placed on the central part of the control desk, because due to poor control desk construction, they cause uneven burden on various operator's body parts.     

Counterpoint to “Infrared cameras overestimate skin temperature during rewarming from cold exposure”

We evaluated the paper by Maley et al. (2020) in this journal “Infrared cameras overestimate skin temperature during rewarming from cold Exposure” for the evidence provided in support of its title and conclusions. Several methodological issues were identified as well as issues with the data interpretation: 1: Only one camera was used but a conclusion was made for ‘cameras’ in general; 2: The camera accuracy (±2 °C) is too low to do a meaningful comparison without using local reference values or an on-site calibrator with higher accuracy; 3: Thermistor measurements are taken as a gold standard while issues such as temperature gradients and taping are known; 4: Both methods are not compared at the same location and a natural, physiological, gradient may be present between their locations; 5. The impact of the sensor and tape on delays in the change of the underlying tissue temperature is not considered; 6: Only a single pixel was used for the analysis, which has been shown to be problematic.We concluded that the paper by Maley et al. does not provide conclusive evidence that infrared cameras overestimate skin temperature during rewarming from cold exposure.     

Testing the stability of transfer functions

In dendroclimatology, testing the stability of transfer functions using cross-calibration verification (CCV) statistics is a common procedure. However, the frequently used statistics reduction of error (RE) and coefficient of efficiency (CE) merely assess the skill of reconstruction for the validation period, which does not necessarily reflect possibly instable regression parameters. Furthermore, the frequently used rigorous threshold of zero which sharply distinguishes between valid and invalid transfer functions is prone to an underestimation of instability. To overcome these drawbacks, we here introduce a new approach – the Bootstrapped Transfer Function Stability test (BTFS). BTFS relies on bootstrapped estimates of the change of model parameters (intercept, slope, and r²) between calibration and verification period as well as the bootstrapped significance of corresponding models. A comparison of BTFS, CCV and a bootstrapped CCV approach (BCCV) applied to 42,000 pseudo-proxy datasets with known properties revealed that BTFS responded more sensitively to instability compared to CCV and BCCV. BTFS performance was significantly affected by sample size (length of calibration period) and noise (explained variance between predictor and predictand). Nevertheless, BTFS performed superior with respect to the detection of instable transfer functions in comparison to CCV.     

Chemical composition and rumen degradability of three corn hybrids treated with insecticides against the European corn borer (Ostrinia nubilalis)

This experiment determined the chemical composition, rumen degradability (aNDF in stalks and starch in kernels) and in vitro gas production of kernels from three corn hybrids treated (TT) or not treated (control, CTR) with insecticides against the European corn borer (ECB, Ostrinia nubilalis). Two whole-plant silage hybrids belonging to the FAO rating 600 and 700 maturity class (S600 and S700, respectively) and one selected for grain production (G600, FAO rating 600, Dekalb-Monsanto Agricoltura S.p.A., Lodi, Italy) were sown in two main plots (TT and CTR) of an experimental field. Two subsequent treatments of pyrethroids (25 and 1.2 g/ha of cyfluthrin and deltamethrin, respectively) were applied to the TT plots. The insecticide treatment reduced the number of damaged plants (4.5 broken plants/plot versus 0.3 broken plants/plot, P<0.01) and increased the total grain yield by 11% (13.8 t/ha versus 12.4 t/ha), while hybrids did not differ. ECB larvae which bored into the stalk tunnels modified the chemical composition of stalks and kernels. In stalks, total sugars content (i.e. glucose, fructose, sucrose) was about twice that in TT versus CTR plants (123 g/kg versus 60 g/kg DM, P<0.01), while aNDF content was higher in CTR stalks (765 versus 702 g/kg DM, P<0.01). DM degradability after 48 h of incubation of stalks was higher in TT than in CTR, both in vitro (0.360 versus 0.298, P<0.01) and in situ (0.370 versus 0.298, P<0.05), while there were no differences in aNDF degradability. Kernels from TT plots contained less DM (615 g/kg versus 651 g/kg, P<0.01) and more CP (84 g/kg and 78 g/kg DM, P<0.05) than those from CTR plots, while in situ rumen starch disappearance and in vitro gas production were similar. Corn hybrid selected for yield of grain (G600) differed from S600 and S700 due to a higher (P<0.01) content of aNDF, ADF and lignin(sa) in the stalks, and a higher starch content (696 g/kg versus 674 and 671 g/kg DM, P<0.01) and CP (87 g/kg versus 77 and 76 g/kg DM, P<0.05) in grain. The G600 hybrid produced stalks with a lower (P<0.01) aNDF rumen degradability than the S600 and S700.