GPU-accelerated molecular dynamics simulation of solid covalent crystals

Graphics processing unit (GPU) is becoming a powerful computational tool in science and engineering. In this paper, different from previous molecular dynamics (MD) simulation with pair potentials and many-body potentials, two MD simulation algorithms implemented on a single GPU are presented to describe a special category of many-body potentials – bond order potentials used frequently in solid covalent materials, such as the Tersoff potentials for silicon crystals. The simulation results reveal that the performance of GPU implementations is apparently superior to their CPU counterpart. Furthermore, the proposed algorithms are generalised, transferable and scalable, and can be extended to the simulations with general many-body interactions such as Stillinger–Weber potential and so on.     

Effects of experimental calcium availability,egg parameters and laying order on Great Tit Parus major eggshell pigmentation patterns

Many bird species lay eggs speckled with protoporphyrin‐based spots, however, for most of them the function of eggshell spotting is unknown. A plausible hypothesis is that protoporphyrin might have a structural function in strengthening the eggshell and is therefore deposited when calcium is scarce. In this study, we experimentally provided Great Tit Parus major females with supplemental calcium to examine its effect on the protoporphyrin‐based maculation of their eggs. In addition, we studied variation in eggshell pigmentation patterns in relation to other egg parameters and laying order. Calcium‐supplemented females laid larger eggs but shell thickness was not significantly affected by the treatment. Calcium supplementation may reduce the time and energy females devote to searching for calcium‐rich material, so that they can collect more nutrients and so lay larger eggs. Furthermore, pigment darkness was associated with egg volume and shape, which suggests that female quality and environmental food availability may also influence the shell pigmentation pattern. Within clutches, later‐laid eggs had larger and darker spots that were distributed more unevenly on the shell surface. This within‐clutch pattern could be explained by the increase in egg volume and egg shape and a decline in shell thickness with egg‐laying order, which characteristics were all related to shell‐spotting pattern. Eggs with a coronal ring had thinner shells, but pigment intensity and spot size were not related to shell thickness. Thus, our results suggest that concentrated spotting distribution may have a mechanical function, supporting the structural‐function hypothesis.     

以静脉药物配置中心为平台的静脉用药医嘱干预

目的 以静脉药物配置中心为平台,对用药医嘱进行分析和干预,提高用药医嘱的合理性,促进临床合理用药。方法 对静脉药物配置中心服务的6个病区用药医嘱中的不合理医嘱进行统计分析。结果 不合理医嘱明显减少,用药医嘱合理性大幅度提高差异有显著性（P＜0.01）。结论 通过对用药医嘱干预,能促进临床合理用药,保证患者用药安全。     

华西雨屏区香樟人工林土壤表层细根生物量和碳储量

2010年11月-2011年12月, 研究了华西雨屏区31年生香樟人工林土壤表层(0～30 cm)细根生物量及碳储量.结果表明: 香樟人工林土壤0～30 cm层细根总生物量(活根+死根)和碳储量的平均值分别为1592.29 kg·hm^-2和660.68 kg C·hm^-2,其中活细根贡献率分别为91.1%和91.8%.随着土壤深度的增加,香樟1～5级活细根和死细根的生物量及碳储量均显著减少;随着根序等级的升高,香樟活细根生物量及碳储量显著增加.香樟细根总生物量及碳储量均在秋季最高、冬季最低,死细根生物量及碳储量为冬季最高、夏季最低;1级根和2级根生物量及碳储量均在夏季最高、冬季最低,而3~5级根则为秋季最高、冬季最低.土壤养分和水分的空间异质性是导致细根生物量和碳储量变化的主要原因.     

马尾松和苦槠林根际土壤矿化和根系分解CO2释放的温度敏感性

以中亚热带马尾松林和苦槠林为对象,原位收集根际和非根际土壤、树木不同生态功能的根系,开展15℃、25℃、35℃和45℃恒温培养模拟试验,采用密闭气室碱液吸收法测定53 d内CO2释放的动态变化.结果表明:两种森林类型不同温度下土壤矿化CO2释放速率的根际效应介于1.12 ～3.09,且培养前期高于培养后期;15℃下马尾松林和苦槠林差异不显著,25℃和35℃下前者低于后者,45℃下则相反.不同培养温度下两树种吸收根分解的CO2释放速率均高于过渡根和贮存根,且马尾松均低于苦槠.两种森林类型CO2释放的Q10值均为土壤(1.21 ～1.83)显著高于根系(0.96 ～1.36).两种森林类型土壤矿化CO2释放的Q10值差异不显著,而马尾松根系分解CO2释放的Q10值高于苦槠.推断全球变暖导致的土壤矿化CO2释放的增量将远远高于根系分解,且马尾松林高于苦槠林;地带性顶极群落应对气候变化的抵抗力强于先锋树种群落.     

Stage specific requirement of Gfrα1 in the ureteric epithelium during kidney development

Glial cell line-derived neurotrophic factor (GDNF) binds a coreceptor GDNF family receptor α1 (GFRα1) and forms a signaling complex with the receptor tyrosine kinase RET. GDNF-GFRα1-RET signaling activates cellular pathways that are required for normal induction of the ureteric bud (UB) from the Wolffian duct (WD). Failure of UB formation results in bilateral renal agenesis and perinatal lethality. Gfrα1 is expressed in both the epithelial and mesenchymal compartments of the developing kidney while Ret expression is specific to the epithelium. The biological importance of Gfrα1’s wider tissue expression and its role in later kidney development are unclear. We discovered that conditional loss of Gfrα1 in the WD epithelium prior to UB branching is sufficient to cause renal agenesis. This finding indicates that Gfrα1 expressed in the nonepithelial structures cannot compensate for this loss. To determine Gfrα1’s role in branching morphogenesis after UB induction we used an inducible Gfrα1-specific Cre-deletor strain and deleted Gfrα1 from the majority of UB tip cells post UB induction in vivo and in explant kidney cultures. We report that Gfrα1 excision from the epithelia compartment after UB induction caused a modest reduction in branching morphogenesis. The loss of Gfrα1 from UB-tip cells resulted in reduced cell proliferation and decreased activated ERK (pERK). Further, cells without Gfrα1 expression are able to populate the branching UB tips. These findings delineate previously unclear biological roles of Gfrα1 in the urinary tract and demonstrate its cell-type and stage-specific requirements in kidney development.     

Application of higher order statistics for atrial arrhythmia classification

Atrial fibrillation (AF) and atrial flutter (AFL) are the two common atrial arrhythmia encountered in the clinical practice. In order to diagnose these abnormalities the electrocardiogram (ECG) is widely used. The conventional linear time and frequency domain methods cannot decipher the hidden complexity present in these signals. The ECG is inherently a non-linear, non-stationary and non-Gaussian signal. The non-linear models can provide improved results and capture minute variations present in the time series. Higher order spectra (HOS) is a non-linear dynamical method which is highly rugged to noise. In the present study, the performances of two methods are compared: (i) 3rd order HOS cumulants and (ii) HOS bispectrum. The 3rd order cumulant and bispectrum coefficients are subjected to dimensionality reduction using independent component analysis (ICA) and classified using classification and regression tree (CART), random forest (RF), artificial neural network (ANN) and k-nearest neighbor (KNN) classifiers to select the best classifier. The ICA components of cumulant coefficients have provided the average accuracy, sensitivity, specificity and positive predictive value of 99.50%, 100%, 99.22% and 99.72% respectively using KNN classifier. Similarly, the ICA components of HOS bispectrum coefficients have yielded the average accuracy, sensitivity, specificity and PPV of 97.65%, 98.16%, 98.75% and 99.53% respectively using KNN. So, the ICA performed on the 3rd order HOS cumulants coupled with KNN classifier performed better than the HOS bispectrum method. The proposed methodology is robust and can be used in mass screening of cardiac patients.     

Seasonal dynamics of δ13C of C‐rich fractions from Picea abies (Norway spruce) and Fagus sylvatica (European beech) fine roots

The ^13/12C ratio in plant roots is likely dynamic depending on root function (storage versus uptake), but to date, little is known about the effect of season and root order (an indicator of root function) on the isotopic composition of C‐rich fractions in roots. To address this, we monitored the stable isotopic composition of one evergreen (Picea abies) and one deciduous (Fagus sylvatica), tree species' roots by measuring δ¹³C of bulk, respired and labile C, and starch from first/second and third/fourth order roots during spring and fall root production periods. In both species, root order differences in δ¹³C were observed in bulk organic matter, labile, and respired C fractions. Beech exhibited distinct seasonal trends in δ¹³C of respired C, while spruce did not. In fall, first/second order beech roots were significantly depleted in ¹³C, whereas spruce roots were enriched compared to higher order roots. Species variation in δ ¹³C of respired C may be partially explained by seasonal shifts from enriched to depleted C substrates in deciduous beech roots. Regardless of species identity, differences in stable C isotopic composition of at least two root order groupings (first/second, third/fourth) were apparent, and should hereafter be separated in belowground C‐supply‐chain inquiry.     

Collagen chirality and three‐dimensional orientation studied with polarimetric second‐harmonic generation microscopy

Polarization‐dependent second‐harmonic generation (P‐SHG) microscopy is used to characterize molecular nonlinear optical properties of collagen and determine a three‐dimensional (3D) orientation map of collagen fibers within a pig tendon. C₆ symmetry is used to determine the nonlinear susceptibility tensor components ratios in the molecular frame of reference and , where the latter is a newly extracted parameter from the P‐SHG images and is related to the chiral structure of collagen. The is observed for collagen fibers tilted out of the image plane, and can have positive or negative values, revealing the relative polarity of collagen fibers within the tissue. The P‐SHG imaging was performed using a linear polarization‐in polarization‐out (PIPO) method on thin sections of pig tendon cut at different angles. The nonlinear chiral properties of collagen can be used to construct the 3D organization of collagen in the tissue and determine the orientation‐independent molecular susceptibility ratios of collagen fibers in the molecular frame of reference.      

Dynamic observation and quantification of type I/II collagen in chondrogenesis of mesenchymal stem cells by second‐order susceptibility microscopy

Second‐order susceptibility (SOS) microscopy is used to image and characterize chondrogenesis in cultured human mesenchymal stem cells. SOS analysis shows that the SOS tensor ratios can be used to characterize type I and II collagens in living tissues and that both collagen types are produced at the onset of chondrogenesis. Time‐lapse analysis shows a modulation of extracellular matrix results in a higher rate in increase of type II collagen, as compared to type I collagen. With time, type II collagen content stabilizes at the composition of 70% of total collagen content. SOS microscopy can be used to continuously and noninvasively monitor the production of collagens I and II. With additional development, this technique can be developed into an effective quality control tool for monitoring extracellular matrix production in engineered tissues.