Full field spatially-variant image-based resolution modelling reconstruction for the HRRT

Accurate characterisation of the scanner's point spread function across the entire field of view (FOV) is crucial in order to account for spatially dependent factors that degrade the resolution of the reconstructed images. The HRRT users' community resolution modelling reconstruction software includes a shift-invariant resolution kernel, which leads to transaxially non-uniform resolution in the reconstructed images. Unlike previous work to date in this field, this work is the first to model the spatially variant resolution across the entire FOV of the HRRT, which is the highest resolution human brain PET scanner in the world. In this paper we developed a spatially variant image-based resolution modelling reconstruction dedicated to the HRRT, using an experimentally measured shift-variant resolution kernel. Previously, the system response was measured and characterised in detail across the entire FOV of the HRRT, using a printed point source array. The newly developed resolution modelling reconstruction was applied on measured phantom, as well as clinical data and was compared against the HRRT users' community resolution modelling reconstruction, which is currently in use. Results demonstrated improvements both in contrast and resolution recovery, particularly for regions close to the edges of the FOV, with almost uniform resolution recovery across the entire transverse FOV. In addition, because the newly measured resolution kernel is slightly broader with wider tails, compared to the deliberately conservative kernel employed in the HRRT users' community software, the reconstructed images appear to have not only improved contrast recovery (up to 20% for small regions), but also better noise characteristics.     

Rule-based modeling and simulations of the inner kinetochore structure

Background

Combinatorial complexity is a central problem when modeling biochemical reaction networks, since the association of a few components can give rise to a large variation of protein complexes. Available classical modeling approaches are often insufficient for the analysis of very large and complex networks in detail. Recently, we developed a new rule-based modeling approach that facilitates the analysis of spatial and combinatorially complex problems. Here, we explore for the first time how this approach can be applied to a specific biological system, the human kinetochore, which is a multi-protein complex involving over 100 proteins.

Results

Applying our freely available SRSim software to a large data set on kinetochore proteins in human cells, we construct a spatial rule-based simulation model of the human inner kinetochore. The model generates an estimation of the probability distribution of the inner kinetochore 3D architecture and we show how to analyze this distribution using information theory. In our model, the formation of a bridge between CenpA and an H3 containing nucleosome only occurs efficiently for higher protein concentration realized during S-phase but may be not in G1. Above a certain nucleosome distance the protein bridge barely formed pointing towards the importance of chromatin structure for kinetochore complex formation. We define a metric for the distance between structures that allow us to identify structural clusters. Using this modeling technique, we explore different hypothetical chromatin layouts.

Conclusions

Applying a rule-based network analysis to the spatial kinetochore complex geometry allowed us to integrate experimental data on kinetochore proteins, suggesting a 3D model of the human inner kinetochore architecture that is governed by a combinatorial algebraic reaction network. This reaction network can serve as bridge between multiple scales of modeling. Our approach can be applied to other systems beyond kinetochores.     

A Comparative Study on the Power of van Lieshout and Baddeley's J-Function

Summary functions such as the empty space function F and the nearest neighbour distance distribution function G are often used as test statistics for point patterns. Van Lieshout and Baddeley recently proposed an alternative statistic, the J-function, which is defined as J = (1 — G)/(1 — F). Theoretical advantages of the J-function over the F- and G-statistics are that it measures the type, strength and range of interaction, and that it can be evaluated explicitly for a larger class of models. In this simulation study we investigate empirically how the power of tests based on J compares to that of tests based on F and G.     

公共空间安全感研究：以上海城市街景感知为例

在文献基础上梳理了街道安全感影响因素,并采用上海样本检验了“街道眼”等西方街道安全理论。邀请30位学生和30位市民对上海5个不同发展时期社区的300张百度街景图片进行安全感评定。实验发现绿视率、管理程度、车道数等都对安全感起着显著作用,并分别建立了单双车道和多车道街道空间的安全感回归模型。其中发现绿视率（单双车道相关系数R=0.728,p<0.01;多车道相关系数R=0.471,p<0.01）、管理程度（单双车道相关系数R=0.766,p<0.01;多车道相关系数R=0.450,p<0.01）、车道数量因素（相关系数R=0.502,p<0.01）对安全感均有显著的积极作用,界面透明度（单双车道相关系数R=0.222,p<0.01）、独立自行车道（相关系数R=0.309,p<0.01）及设计美感（相关系数R=0.432,p<0.01）等因素在单双车道空间中具有积极影响,而助动车与自行车（单双车道相关系数R=-0.327,p<0.01;多车道相关系数R=-0.281,p<0.01）在对安全感知评价具有消极影响,机动车（单双车道相关系数R=0.251,p<0.01;多车道相关系数R=-0.327,p<0.01）在单双车道与多车道空间中呈现相反的作用。     

Free and total thyroid hormones in humans at extreme altitude

Alterations in circulatory levels of total T₄ (TT₄), total T₃ (TT₃), free T₄ (FT₄), free T₃ (FT₃), thyrotropin (TSH) and T₃ uptake (T₃U) were studied in male and female sea-level residents (SLR) at sea level, in Armed forces personnel staying at high altitude (3750 m) for prolonged duration (acclimatized lowlanders, ALL) and in high-altitude natives (HAN). Identical studies were also performed on male ALL who trekked to an extreme altitude of 5080 m and stayed at an altitude of more than 6300 m for about 6 months. The total as well as free thyroid hormones were found to be significantly higher in ALL and HAN as compared to SLR values. Both male as well as female HAN had higher levels of thyroid hormones. The rise in hormone levels in different ALL ethnic groups drawn from amongst the southern and northern parts of the country was more or less identical. In both HAN and ALL a decline in FT₃ and FT₄ occurred when these subjects trekked at subzero temperatures to extreme altitude of 5080 m but the levels were found to be higher in ALL who stayed at 6300 m for a prolonged duration. Plasma TSH did not show any appreciable change at lower altitudes but was found to be decreased at extreme altitude. The increase in thyroid hormones at high altitude was not due to an increase in hormone binding proteins, since T₃U was found to be higher at high altitudes. A decline in TSH and hormone binding proteins and an increase in the free moiety of the hormones is indicative of a subtle degree of tissue hyperthyroidism which may be playing an important role in combating the extreme cold and hypoxic environment of high altitudes.     

对6个国外城市街道规划设计导则的解析——“如何规划步行友好的城市街道开放空间？”

本文将“如何通过街道规划设计,营建步行友好的城市开放空间环境,提高居民生活质量？”作为研究视角,抽取了6个国外城市街道规划设计导则中与“如何规划设计步行友好的城市开放空间？”密切相关的内容,根据相关导则编制的逻辑将内容进行提炼、归纳和重组。针对中国通过改善街道步行环境建设高品质城市的诉求以及相关导则中缺少对使用者需求关注的现状,提出了将需求调查纳入规划规定环节、从环境特征角度出发进行街道分类与定位、关注地域特征与集约性生态设施的环境营造方法以及提升步行道功能多样性和空间相容性的建议。     

阴道微生态与高危型人乳头瘤病毒感染及宫颈病变的相关性

目的 探究阴道微生态与高危型人乳头瘤病毒(HR HPV)感染以及宫颈病变之间的相关性,为后续研究提供参考。 方法 选择2018年1月至2019年6月就诊于石河子大学医学院第一附属医院妇科门诊,同时行爱必维(细菌性阴道病五项联合测定试剂盒)检测、HR HPV检测及宫颈组织病理检查的343名妇女作为研究对象,分析相关检测数据并探究阴道微生态与HR HPV感染以及宫颈病变的相关性。 结果 过氧化氢阳性、唾液酸苷酶阳性、白细胞酯酶阳性、乳杆菌数量减少及阴道清洁度3~4度的妇女感染HR HPV及发生宫颈病变的可能性显著大于过氧化氢阴性、唾液酸苷酶阴性、白细胞酯酶阴性、乳杆菌数量较多及阴道清洁度1~2度的妇女,差异均有统计学意义(均P结论 阴道微生态失衡与HR HPV感染以及宫颈病变有一定关联,纠正阴道微生态失衡可一定程度上预防HR HPV感染及宫颈病变。     

A combined A431 cell membrane chromatography and online high performance liquid chromatography/mass spectrometry method for screening compounds from total alkaloid of Radix Caulophylli acting on the human EGFR

We have developed an online analytical method that combines A431 cell membrane chromatography (A431/CMC) with high performance liquid chromatography and mass spectrometry (LC/MS) for identifying active components from Radix Caulophylli acting on human EGFR. Retention fractions on A431/CMC model were captured onto an enrichment column and the components were directly analyzed by combining a 10-port column switcher with an LC/MS system for separation and preliminary identification. Using Sorafenib tosylate as a positive control, taspine and caulophine from Radix Caulophylli were identified as the active molecules which could act on the EGFR. This A431/CMC-online-LC/MS method can be applied for screening active components acting on EGFR from traditional Chinese medicines exemplified by Radix Caulophylli and will be of great utility in drug discovery using natural medicinal herbs as a source of novel compounds.     

Towards automated production and drug sensitivity testing using scaffold-free spherical tumor microtissues

Although the relevance of three-dimensional (3-D) culture has been recognized for years and exploited at an academic level, its translation to industrial applications has been slow. The development of reliable high-throughput technologies is clearly a prerequisite for the industrial implementation of 3-D models. In this study the robustness of spherical microtissue production and drug testing in a 96-well hanging-drop multiwell plate format was assessed on a standard 96-well channel robotic platform. Microtissue models derived from six different cell lines were produced and characterized according to their growth profile and morphology displaying high-density tissue-like reformation and growth over at least 15 days. The colon cancer cell line HCT116 was chosen as a model to assess microtissue-based assay reproducibility. Within three individual production batches the size variations of the produced microtissues were below 5%. Reliability of the microtissue-based assay was tested using two reference compounds, staurosporine and chlorambucil. In four independent drug testings the calculated IC(50) values were benchmarked against 2-D multiwell testings displaying similar consistency. The technology presented here for the automated production of a variety of microtissues for efficacy testing in a standard 96-well format will aid the implementation of more organotypic models at an early time point in the drug discovery process.