Influence of force fields on the selective diffusion of para-xylene over ortho-xylene in 10-ring zeolites

A molecular dynamics study of diffusion of p-xylene and o-xylene has been performed over three different pure silica 10-ring zeolites, MFI, SFG and TUN. The shape selective properties of the frameworks of these three materials have been tested using four different types of force fields commonly used based on united atom, rigid-ion and core-shell approximations. The performance of each force field is analysed in order to find which force fields can give sufficiently accurate estimations that allow to select appropriate zeolites for selective separation of para/ortho xylene. This performance was found to depend on the quality of the structural properties of the zeolite, in particular the size and shape of the 10 rings which act as bottlenecks for the diffusion. The computational results allow us to define some optimum characteristics for the selective diffusion of p-xylene.     

秸秆全量还田对稻田土壤溶解有机碳含量和水稻产量的影响

以南粳44为供试材料,在粘土和砂土土壤中,设置麦秸秆不还田和全量还田(6000 kg·hm^-2)及3种施氮量(0、225、300 kg·hm^-2)试验,研究了麦秸秆全量还田的腐解率和有机碳释放量动态变化,及其对稻田0～45 cm土壤溶解有机碳(DOC)含量和水稻产量的影响.结果表明： 麦秸秆还田的前期(0～30 d)其腐解率和有机碳释放量最高,腐解率为35.0%(粘土)和31.7%(砂土),有机碳释放率为34.1%(粘土)和33.1%(砂土);30 d后两者均减小.施用氮肥可显著促进秸秆腐解和有机碳释放量,粘土中麦秸秆腐解率和有机碳释放量明显大于砂土.麦秸秆还田后土壤DOC含量逐渐增加,至25 d达最大值,粘土和砂土分别为60.18和56.62 mg·L^-1,此后逐渐减小并趋于稳定.麦秸秆还田处理15 cm处土壤DOC含量显著高于未还田处理,但两者在30和45 cm处土壤DOC含量差异不显著,说明秸秆还田主要增加了稻田0～15 cm土层DOC含量.与不施氮处理相比,施氮处理土壤DOC含量降低,2种施氮处理间差异不显著.秸秆还田减少了水稻前期分蘖发生量,显著降低了有效穗数,增加了穗粒数、结实率和千粒重,显著提高了水稻产量.     

南方稻田活性氮损失途径及其影响因素

基于文献数据,研究了南方不同稻区水稻生长期氧化亚氮排放(N₂O排放)、硝态氮或铵态氮淋洗(N淋洗)、硝态氮或铵态氮径流(N径流)、氨挥发(NH₃挥发)的差异及其影响因素.结果表明: N₂O排放、N淋洗和N径流主要发生在长江流域单季稻区,损失量分别为1.89、6.4和10.4 kg N·hm^-2,损失率分别为0.8%、3.8%和5.3%,较高施氮量和稻田土壤干湿交替可能是主要原因;NH₃挥发主要发生在华南晚稻,损失量和损失率分别为54.9 kg N·hm^-2和35.2%,晚稻生长期较高的温度可能是NH₃挥发较大的主要原因.田间优化管理措施减少某一途径氮损失的同时可能会增加另一种途径氮素损失,实际生产中应综合考虑田间管理措施对各种活性氮损失的影响,活性氮损失量随着水稻产量水平的提高而增加,主要是因为施氮量也在逐渐增加.随着氮肥偏生产力的增加,N₂O排放、N淋洗和N径流损失率逐渐下降,因此,努力减小单位产量的氮损失,是协同提高作物产量和氮肥利用效率的重要途径.     

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10, represented sequences of three large RNA structures with limited or no homology with previously solved RNA molecules. A lariat-capping ribozyme, as well as riboswitches complexed to adenosylcobalamin and tRNA, were predicted by seven groups using RNAComposer, ModeRNA/SimRNA, Vfold, Rosetta, DMD, MC-Fold, 3dRNA, and AMBER refinement. Some groups derived models using data from state-of-the-art chemical-mapping methods (SHAPE, DMS, CMCT, and mutate-and-map). The comparisons between the predictions and the three subsequently released crystallographic structures, solved at diffraction resolutions of 2.5–3.2 Å, were carried out automatically using various sets of quality indicators. The comparisons clearly demonstrate the state of present-day de novo prediction abilities as well as the limitations of these state-of-the-art methods. All of the best prediction models have similar topologies to the native structures, which suggests that computational methods for RNA structure prediction can already provide useful structural information for biological problems. However, the prediction accuracy for non-Watson–Crick interactions, key to proper folding of RNAs, is low and some predicted models had high Clash Scores. These two difficulties point to some of the continuing bottlenecks in RNA structure prediction. All submitted models are available for download at http://ahsoka.u-strasbg.fr/rnapuzzles/.     

Learning generative models for protein fold families

We introduce a new approach to learning statistical models from multiple sequence alignments (MSA) of proteins. Our method, called GREMLIN (Generative REgularized ModeLs of proteINs), learns an undirected probabilistic graphical model of the amino acid composition within the MSA. The resulting model encodes both the position-specific conservation statistics and the correlated mutation statistics between sequential and long-range pairs of residues. Existing techniques for learning graphical models from MSA either make strong, and often inappropriate assumptions about the conditional independencies within the MSA (e.g., Hidden Markov Models), or else use suboptimal algorithms to learn the parameters of the model. In contrast, GREMLIN makes no a priori assumptions about the conditional independencies within the MSA. We formulate and solve a convex optimization problem, thus guaranteeing that we find a globally optimal model at convergence. The resulting model is also generative, allowing for the design of new protein sequences that have the same statistical properties as those in the MSA. We perform a detailed analysis of covariation statistics on the extensively studied WW and PDZ domains and show that our method out-performs an existing algorithm for learning undirected probabilistic graphical models from MSA. We then apply our approach to 71 additional families from the PFAM database and demonstrate that the resulting models significantly out-perform Hidden Markov Models in terms of predictive accuracy.     

水稻土中铁还原菌多样性

微生物介导的异化Fe(III) 还原是非硫厌氧环境中Fe(III) 还原生成Fe(II) 的主要途径,然而相关的铁还原菌还不是很清楚,特别是在水稻土中.本文采用富集培养的方法,以乙酸和氢气作为电子供体,水铁矿和针铁矿作为电子受体,通过末端限制性片段长度多态性（T-RFLP）技术和16S rRNA基因克隆测序相结合的分子生物学方法研究了水稻土中铁还原菌的多样性.结果表明：无论是以乙酸或氢气为电子供体,水铁矿或针铁矿为电子受体,地杆菌（Geobacter）和梭菌（Clostridiales）是富集到的主要微生物群落;乙酸为电子供体时,富集到的主要微生物群落还包括红环菌（Rhodocyclaceae）;因此,除地杆菌外,梭菌和红环菌很可能也是水稻土中重要的铁还原菌.     

Environmental factors associated with the distribution of floodwater mosquito eggs in irrigated fields in Wrocław,Poland

A survey of distribution patterns of floodwater mosquito eggs related to environmental conditions such as moisture and plant associations was conducted by using soil samples from irrigated fields in Wroc?aw, Poland. Mosquito egg distribution was determined by repeatedly flooding the soil samples with aerated water at a temperature of 25° C. Under laboratory conditions, hatching in installments of Aedes caspius (Pallas) and Aedes vexans (Meigen) were commonly observed. The results show that ～75% of the larvae of Ae. caspius and Ae. vexans hatched after the first flooding under summer‐like conditions, whereas, following the second and third flooding, the numbers of hatched larvae were significantly lower. In our study, within one intermediate flooded field, a total of 66 plant species was identified and classified into six communities. All vegetation types were associated by varied egg densities and showed differences both in richness and Shannon‐Wiener diversity index as well as in ecological indices for moisture, soil reaction, and nutrient level. Small changes in elevation along the slope within the study area showed a large difference in the distribution of mosquito eggs. The highest average egg density was observed in zones with high occurrence of Phalaris arundinacea, usually prevalent in intermediate flooded and fertile areas. Knowledge of the indicators for the distribution of floodwater mosquito eggs in temporary breeding sites may be essential for organizing a successful, integrated mosquito control program with special regard to microbial control agents.     

Skin temperature increase caused by a mobile phone: a methodological infrared camera study

Mobile phone users often complain about burning sensations or a heating of the ear region. The increase in temperature may be due to thermal insulation by the phone, heating of the mobile phone resulting from its electrical power dissipation, and radio frequency (RF) exposure. The main objective of this study was to use infrared (IR) camera techniques to find how much each of these factors contributes to the increase in skin temperature resulting from the use of one GSM 900 phone. One subject, a healthy male, took part in the study. He was holding the phone in a normal position when the phone was switched off, when it was switched on but with the antenna replaced by a 50 Omega load to eliminate the RF exposure, and when it was transmitting RF fields. The output power could be fixed, and the minimal and the maximal power levels of the phone were used. The study was designed as a double blind experiment. The changes in temperature after 15 and 30 min of mobile phone use were calculated on the exposed side of the head relative to the unexposed side. The insulation and the electrical power dissipation led to statistically significant rises in the skin temperature, while the RF exposure did not.     

Effect of weak, interrupted sinusoidal low frequency magnetic field on neural regeneration in rats: functional evaluation

A study of the effect of weak, interrupted sinusoidal low frequency magnetic field (ISMF) stimulation on regeneration of the rat sciatic nerve was carried out. In the experiment, 60 Wistar rats were used: 24 rats underwent unilateral sciatic nerve transection injury and immediate surgical nerve repair, 24 rats underwent unilateral sciatic nerve crush injury, and the remaining 12 rats underwent a sham surgery. Half of the animals (n = 12) with either sciatic nerve lesion were randomly chosen and exposed between a pair of Helmholtz coils for 3 weeks post-injury, 4 h/day, to an interrupted (active period to pause ratio = 1.4 s/0.8 s) sinusoidal 50 Hz magnetic field of 0.5 mT. The other half of the animals (n = 12) and six rats with sham surgery were used for two separate controls. Functional recovery was followed for 6 weeks for the crush injuries and 7(1/2) months for the transection injuries by video assisted footprint analysis in static conditions and quantified using a recently revised static sciatic index (SSI) formula. We ascertained that the magnetic field influence was weak, but certainly detectable in both injury models. The accuracy of ISMF influence detection, determined by the one-way repeated measures ANOVA test, was better for the crush injury model: F(1, 198) = 9.0144, P = .003, than for the transection injury model: F(1, 198) = 6.4826, P = .012. The Student-Newman-Keuls range test for each response day yielded significant differences (P < .05) between the exposed and control groups early in the beginning of functional recovery and later on from the points adjacent to the beginning of the plateau, or 95% of functional recovery, and the end of observation. These differences probably reflect the ISMF systemic effect on the neuron cell bodies and increased and more efficient reinnervation of the periphery.     

Decreased plasma levels of nitric oxide metabolites, angiotensin II, and aldosterone in spontaneously hypertensive rats exposed to 5 mT static magnetic field

Previously, we found that whole body exposure to static magnetic fields (SMF) at 10 mT (B(max)) and 25 mT (B(max)) for 2-9 weeks suppressed and delayed blood pressure (BP) elevation in young, stroke resistant, spontaneously hypertensive rats (SHR). In this study, we investigated the interrelated antipressor effects of lower field strengths and nitric oxide (NO) metabolites (NO(x) = NO(2)(-) + NO(3)(-)) in SHR. Seven-week-old male rats were exposed to two different ranges of SMF intensity, 0.3-1.0 mT or 1.5-5.0 mT, for 12 weeks. Three experimental groups of 20 animals each were examined: (1) no exposure with intraperitoneal (ip) saline injection (sham-exposed control); (2) 1 mT SMF exposure with ip saline injection (1 mT); (3) 5 mT SMF exposure with ip saline injection (5 mT). Arterial BP, heart rate (HR), skin blood flow (SBF), plasma NO metabolites (NO(x)), and plasma catecholamine levels were monitored. SMF at 5 mT, but not 1 mT, significantly suppressed and retarded the early stage development of hypertension for several weeks, compared with the age matched, unexposed (sham exposed) control. Exposure to 5 mT resulted in reduced plasma NO(x) concentrations together with lower levels of angiotensin II and aldosterone in SHR. These results suggest that SMF may suppress and delay BP elevation via the NO pathways and hormonal regulatory systems.