Classifying T cell activity in autofluorescence intensity images with convolutional neural networks

The importance of T cells in immunotherapy has motivated developing technologies to improve therapeutic efficacy. One objective is assessing antigen‐induced T cell activation because only functionally active T cells are capable of killing the desired targets. Autofluorescence imaging can distinguish T cell activity states in a non‐destructive manner by detecting endogenous changes in metabolic co‐enzymes such as NAD(P)H. However, recognizing robust activity patterns is computationally challenging in the absence of exogenous labels. We demonstrate machine learning methods that can accurately classify T cell activity across human donors from NAD(P)H intensity images. Using 8260 cropped single‐cell images from six donors, we evaluate classifiers ranging from traditional models that use previously‐extracted image features to convolutional neural networks (CNNs) pre‐trained on general non‐biological images. Adapting pre‐trained CNNs for the T cell activity classification task provides substantially better performance than traditional models or a simple CNN trained with the autofluorescence images alone. Visualizing the images with dimension reduction provides intuition into why the CNNs achieve higher accuracy than other approaches. Our image processing and classifier training software is available at https://github.com/gitter‐lab/t‐cell‐classification .     

低强度林窗式疏伐对云杉人工纯林地表微气候和土壤养分的短期影响

选择高密度云杉人工纯林,模拟天然林窗形成方式,开展了低强度林窗式疏伐试验,监测了地表空气温、湿度和不同土壤层次的养分状况.结果表明：疏伐后第1年,生长季(5-9月)林窗内地表日均温升高而日均湿度降低,林窗内土壤腐殖层(O层)有机质(SOM)和铵态氮(NH₄⁺-N)含量分别增加了19.62%和283.85%,硝态氮(NO₃^--N)和可溶性有机碳(DOC)含量分别减少77.86%和23.60% 而0～10 cm土层SOM、全氮(TN)和NO₃^--N含量分别比对照增加45.77%、37.14%和75.11%;NH₄⁺-N、DOC和全磷(TP)含量分别减少48.56%、33.33%和13.11%.上述结果说明,低强度林窗式疏伐迅速改善了高密度云杉人工纯林地表阴湿的环境,增强了O层土壤微生物活性与土壤矿化过程,促进了土壤养分释放与土壤肥力恢复.     

光照、温度和氮对竹叶眼子菜生长的影响

实验选择长江中下游常见沉水植物竹叶眼子菜(Potamogeton malaianus Mig.),利用正交试验设计,通过室内静态模拟实验研究3种主要环境因子光照强度、温度、总氮浓度及其互作对竹叶眼子菜分苗生长的影响。结果表明:光照强度和温度为影响竹叶眼子菜生长的主效环境因子,且它们的交互作用对竹叶眼子菜生长有较为显著的影响;在2～8mg·L^-1的总氮浓度下,竹叶眼子菜均可以正常生长。观察结果可知,竹叶眼子菜在5320～12000lx光照强度、30℃、4～8mg·L^-1水体总氮浓度的条件下生长良好,竹叶眼子菜生长虽然对光照强度的要求较高,但其叶往往集中在水体表面形成冠层,能在透明度较低的水体中生长,加上对高温及高营养盐的耐受性较好,故推测竹叶眼子菜可作为夏季富营养化水体中恢复和重建沉水植被的先锋工具种。     

Influence of ammonium chloride feeding time and light intensity on the cultivation of Spirulina (Arthrospira) platensis

This study dealt with the influence of both the feeding time and light intensity on the fed-batch culture of the cyanobacterium Spirulina (Arthrospira) platensis using ammonium chloride as a nitrogen source. For this purpose, a 2(2) plus star central composite experimental design combined with response surface methodology was employed, and the maximum cell concentration (X(m)), the cell productivity (P(X)), and the yield of biomass on nitrogen (Y(X/N)) were selected as the response variables. The optimum values of X(m) (1,833 mg L(-1)) and Y(X/N) (5.9 g g(-1)) estimated by the model at light intensity of 13 klux and feeding time of 17.2 days were very close to those obtained experimentally under these conditions (X(m) = 1,771 +/- 41 mg L(-1); Y(X/N) = 5.7 +/- 0.17 g g(-1)). The cell productivity was a decreasing function of the ammonium chloride feeding time and a quadratic function of the light intensity. The protein and lipid contents of dry biomass collected at the end of cultivations were shown to decrease with increasing light intensity.     

放牧对松嫩平原农牧交错区防护林下草地的影响

针对当前防护林草地已成为松嫩平原农牧交错区牲畜主要放牧场的实际情况,分析了不同放牧强度对防护林草地的影响．结果表明,未放牧防护林草地严重退化,与极度放牧防护林草地最为相似．未放牧和极度放牧均抑制了防护林草地的生长,轻度放牧和中度放牧却促进了防护林草地的生长,草地产量和质量均明显提高,并合理地利用了杨树叶资源．未放牧防护林草地质量指数仅为15．51。属严重退化草地范畴;轻度放牧草地质量指数为86．4,随着放牧强度的增加,草地质量逐渐下降．因此,应提倡轻度放牧、中度放牧,防止未放牧和极度放牧现象出现,促进防护林草地生长,并充分利用杨树叶资源增加畜牧业牧草的来源．     

Distribution,Feeding, and Some Physiological Parameters of the Pacific Herring from the Gizhigin and Okhotsk Populations in the North Part of the Sea of Okhotsk in the Spring Season

The distribution of the Pacific herring of various sizes from the Okhotsk and Gizhigin-Kamchatka populations is discussed. The dependence of herring food composition on the condition of the plankton community is demonstrated. In the spring season the feeding rate of juveniles and fattening adult herring depended on the degree of its fatness and on the maturity of the gonads in the prespawning period.     

Peak intensity analysis as a method for estimation of fluorescent probe binding to artificial and natural nanoparticles: Tetramethylrhodamine uptake by isolated mitochondria

A modified version of fluorescence correlation spectroscopy (FCS) closely related to the photon counting histogram (PCH) method, which is used in the case of a mixture of molecules with similar diffusion coefficients, was applied here for analyzing the binding of the potential-sensitive dye tetramethylrhodamine ethyl ester, TMRE, to isolated mitochondria both in energized and deenergized states. Fluorescence time traces of suspensions of TMRE-doped mitochondria representing sequences of peaks of different intensity appeared to be similar to those of fluorescent beads and TMRE-doped latex particles. The experimental data were obtained under stirring conditions which increased the number of events by about three orders of magnitude thus substantially enhancing the resolution of the method. The statistics of the brightness of identical fluorescent particles reflecting their random walk through the confocal volume was described by a simple analytical equation which enabled us to perform the peak intensity analysis (PIA) of TMRE-doped mitochondria. The validity of PIA was tested with fluorescent beads of different sizes and TMRE-doped latex particles. Mitochondrial energization in the presence of TMRE led to the increase in the number and the intensity of the peaks in fluorescence time traces, the PIA of which allowed us to determine mitochondrial membrane potential and additionally a number of mitochondrial particles per ml of the suspension. The value of the membrane potential on a single mitochondrion was estimated to be about 180 mV in agreement with the data related to mitochondrial suspensions. Importantly, the PIA method required less than 1 microgram of mitochondrial protein per measurement.     

Difference in light-induced increase in ploidy level and cell size between adaxial and abaxial epidermal pavement cells of Phaseolus vulgaris primary leaves

Changes in nuclear DNA content and cell size of adaxial andabaxial epidermal pavement cells were investigated using brightlight-induced leaf expansion of Phaseolus vulgaris plants. Inprimary leaves of bean plants grown under high (sunlight) ormoderate (ML; photon flux density, 163 µmol m^–2s^–1) light, most adaxial epidermal pavement cells hada nucleus with the 4C amount of DNA, whereas most abaxial pavementcells had a 2C nucleus. In contrast, plants grown under lowintensity white light (LL; 15 µmol m^–2 s^–1)for 13 d, when cell proliferation of epidermal pavement cellshad already finished, had a 2C nuclear DNA content in most adaxialpavement cells. When these LL-grown plants were transferredto ML, the increase in irradiance raised the frequency of 4Cnuclei in adaxial but not in abaxial pavement cells within 4d. On the other hand, the size of abaxial pavement cells increasedby 53% within 4 d of transfer to ML and remained unchanged thereafter,whereas adaxial pavement cells continuously enlarged for 12d. This suggests that the increase in adaxial cell size after4 d is supported by the nuclear DNA doubling. The differentresponses between adaxial and abaxial epidermal cells were notinduced by the different light intensity at both surfaces. Itwas shown that adaxial epidermal cells have a different propertythan abaxial ones. Key words: Cell enlargement, endopolyploidization, epidermal pavement cells, incident light intensity, leaf expansion, nuclear DNA content, Phaseolus vulgaris     

Changes in the Intensity of Respiration during Ontogenesis of Some Invertebrates

We studied the dynamic of respiration intensity during ontogenesis of flat worms (Dugesia tigrina), molluscs (Anodonta piscinalis and Viviparus viviparus, and insects (Leptinotarsa decemlineata). In planarians that reproduce vegetatively, the intensity of respiration increases just after fission and decreases at the subsequent phases of growth. In A. piscinalis, this index of metabolism increases during embryonic and early larval development and decreases at the later developmental stages. In V. viviparus, which develops in the female genital tract, the intensity of respiration remains unchanged during embryogenesis and decreases during late embryogenesis and subsequent phases of growth. In L. decemlineata, the intensity of respiration increases during embryonic and early larval development and then decreases to undergo cyclic changes times to molts. This index markedly decreases in the pupae, increases in the beginning of imaginal period, and then again decreases.     

Testing the grass-fire cycle: alien grass invasion in the tropical savannas of northern Australia

Abstract. Invasive alien grasses can increase fuel loads, leading to changes in fire regimes of invaded ecosystems by increasing the frequency, intensity and spatial extent of fires. Andropogon gayanus Kunth. (Gamba grass), a tall perennial grass from Africa, is invading ecosystems in the Top End of northern Australia. To determine whether A. gayanus alters savanna fire regimes, we compared fuel loads and fire intensities at invaded sites with those from native grass savannas. Savanna invaded by A. gayanus had fuel loads up to seven times higher than those dominated by native grasses. This higher fuel load supported a fire that was on average eight times more intense than those recorded in native grass savannas at the same time of year (means 15700 ± 6200 and 2100 ± 290 kW m⁻¹, respectively), and was the highest early dry season fire intensities ever recorded in the Northern Territory. These results suggest that A. gayanus is a serious threat to northern Australia's savannas, with the potential to alter vegetation structure and initiate a grass-fire cycle.