Searching by parts: Towards fine-grained image retrieval respecting species correlation

Most of the existing works on fine-grained image categorization and retrieval focus on finding similar images from the same species and often give little importance to inter-species similarities. However, these similarities may carry species correlations such as the same ancestors or similar habits, which are helpful in taxonomy and understanding biological traits. In this paper, we devise a new fine-grained retrieval task that searches for similar instances from different species based on body parts. To this end, we propose a two-step strategy. In the first step, we search for visually similar parts to a query image using a deep convolutional neural network (CNN). To improve the quality of the retrieved candidates, structural cues are introduced into the CNN using a novel part-pooling layer, in which the receptive field of each part is adjusted automatically. In the second step, we re-rank the retrieved candidates to improve the species diversity. We achieve this by formulating a novel ranking function that balances between the similarity of the candidates to the queried parts, while decreasing the similarity to the query species. We provide experiments on the benchmark CUB200 dataset and Columbia Dogs dataset, and demonstrate clear benefits of our schemes.     

DISTRIBUTION AND SYSTEMATICS OF THE FRESHWATER GENUS TUOMEYA (RHODOPHYTA,BATRACHOSPERMACEAE)1

Twenty-seven populations of Tuomeya, including the types of Tuomeya fluviatilis Harvey and Baileya americana Kützing, were analyzed from the entire known range of the genus: northern Newfoundland to northern Florida and east of the Mississippi River. Key morphological features were examined in detail since it has been recently proposed that Tuomeya should be reduced to a section of the genus Batrachospermum. Our observations confirmed the presence of several characteristics unique to Tuomeya: gametophyte development from a basal mass of undifferentiated cells rather than a chantransia stage, pseudoparenchymatous growth, and carpogonia with obliquely to perpendicularly attached trichogynes. Based on these findings, we conclude that the genus Tuomeya should be retained. Using multivariate morphometrics, two groupings were found that differed significantly in plant length (X = 14.1 and 24.1 mm, respectively). However, since there was no other morphometric, environmental, or geographic basis for separation of the groupings, only one species is recognized, T. americana (Kützing) Papenfuss. Populations tend to occur in large streams (>2.8 m wide) with low ion content (≤ 100 μS · cm^?1).     

人体超微弱发光图像中的信号检验

用近期研制的具有单光子探测能力的超高灵敏度成像系统获得了人体体表生物超微弱发光的强度数据。为分析图像中的信号检验,二项分布被用于人手不同时间累积发光图像中的信号显著性检验,证实人手存在超微弱生物发光,手指的发光强度在３００～５５０ｐｈｏｔｏｎｓ／ｓ范围内,全手的发光强度在８５０～１２００ｐｈｏｔｏｎｓ／ｓ范围内。     

SEXUAL DIFFERENTIATION OF GRIFFITHSIA (CERAMIALES, RHODOPHYTA): NUCLEAR PLOIDY LEVEL OF MIXED-PHASE PLANTS IN G. JAPONICA1

Mixed-phase plants of Griffithsia japonica Okamura spontaneously occurred in a laboratory culture. Four female plants produced tetrasporangia and spermatangia in addition to their normal female reproductive structures (bisexual/mixed-phase plants), and four male plants produced tetrasporangia as well as spermatangia (male/mixed-phase plants). To determine the nuclear ploidy level of these mixed-phase plants, relative nuclear sizes of male, female, tetrasporangial, and mixed-phase plants were measured using a microscopic image analysis system. Haploid gametophytes could be distinguished from diploid tetrasporophytes by relative nuclear sizes, with the later having nuclei twice the size of the former. Relative nuclear sizes of the mixed-phase plants were similar to those of the haploid plants. Thus, the mixed-phase plants were determined to be haploid. Haploid mixed-phase plants of G. japonica have a potential to produce male, female and tetrasporangial reproductive structures. Sex determination models are discussed to explain "haploid" mixed-phase phenomena in red algae .     

Image analysis, neural networks, and the taxonomic impediment to biodiversity studies

The taxonomic impediment to biodiversity studies may be influenced radically by the application of new technology, in particular, desktop image analysers and neural networks. The former offer an opportunity to automate objective feature measurement processes, and the latter provide powerful pattern recognition and data analysis tools which are able to 'learn' patterns in multivariate data. The coupling of these technologies may provide a realistic opportunity for the automation of routine species identifications. The potential benefits and limitations of these technologies, along with the development of automated identification systems are reviewed.     

SINGLE-CELL PIGMENTATION OF PORPHYRA LINEARIS ANALYZED BY FOURIER TRANSFORM MULTI-PIXEL SPECTROSCOPY AND IMAGE ANALYSIS1

The novel method of Fourier transform multi-pixel spectroscopy was used for the nondestructive analysis of and comparison of pigmentation in different regions of live thalli of the red alga Porphyra linearis. Because the thallus in this alga consists of a monolayer of nonoverlapping cells, we were able to analyze the pigmentation of single cells by combining light absorbance with natural fluorescence data. From the image of each cell in the vegetative male and female reproductive and holdfast regions, more than 4 ± 10⁴ fluorescence and absorbance spectra were obtained. Specific pigments in the different regions were localized by the use of a software program of similarity mapping followed by image construction. The reconstructed images revealed subcellular localization of each pigment according to specific spectroscopic fingerprints. The results showed that the vegetative and female reproductive cell types had a significantly higher content of phycoerythrin than of phycocyanin, and quite similar chlorophyll a levels. Most of the holdfast cells were poorly pigmented, but had more chlorophyll a than phycoerythrin or phycocyanin. The male reproductive cells contained only traces of pigments. Thus, by using Fourier transform multipixel spectroscopy, we were able to characterize the pigmentation of different regions of the thallus and follow the distribution patterns of the different pigments on the subcellular level along the differentiation gradient of the alga.     

Regio- and stereo-specific nitrile hydrolysis by the nitrile hydratase from Rhodococcus AJ270

Abstract Acid phosphatase activity was measured in individual cells by determining their optical densities through a scanning confocal laser microscope. The naphthol AS-TR (3-hydroxy-2-naphtoic acid 4'-chloro-2'-methylanilide) phosphate-hexazotized para-rosanilin method was used to visualise the acid phosphatase content in the light microscope. Evidence was obtained that the amount of enzyme varied in exponential growth phase cells as the fission age increased. By comparing the acid phosphatase activity with the rate of food vacuole formation, it appeared that the amount of enzyme inside the cells decreased in early clonal life, whereas the rate of food uptake increased. It was assumed that the reduction of acid phosphatase content could lead to a more extended life of vacuoles and to a decreased membrane recycling rate. In turn, the reduced supply of membrane available for food vacuole formation could partly be responsible for the decrease of the food uptake rate observed after the initial increase.     

Inhibition of ceruloplasmin and other copper oxidases by thiomolybdate

The dietary antagonism between copper and molybdate salts prompted a study of the inhibition of copper enzymes by thiomolybdate (TM). TM strongly inhibited the oxidase activity of five copper oxidase with I50% values in the 1-5 microM range. The mechanism of the TM effect on the copper oxidase, ceruloplasmin (Cp) (E.C. 1.16.3.1), was studied in detail. In Vmax vs. E plots, TM gave parallel data suggesting irreversibility but a large number of TM molecules per Cp were required. The inhibition of Cp by TM could not be reversed by dialysis. Isolation of TM-inhibited Cp on Sephadex G-10 did not yield any active Cp molecules. Cu(II) did not restore any inhibited oxidase activity. Gel electrophoresis supported the covalent binding of Cp by TM without any extensive change in protein structure. EPR results confirmed that Cu(II) is reduced to Cu(I) after reaction with TM. However, the Mo(VI) in MoS4(2-) did not change in oxidation number. Analysis of the TM-Cp compound accounted for all six Cu atoms as found in native Cp. The data suggest the covalent binding of sulfide to Cp copper. TM also inhibited the activity of ascorbate oxidase, cytochrome oxidase, superoxide dismutase, and tyrosinase. However, no inhibition of carbonic anhydrase, a zinc enzyme, was observed at 1 mM TM.     

Structural properties of the zinc site in Cu,Zn-superoxide dismutase; Perturbed angular correlation of gamma ray spectroscopy on the Cu, 111Cd-superoxide dismutase derivative

The Zn(II) site of the dimeric Cu(II),Zn(II)-superoxide dismutase from Saccharomyces cerevisiae has been examined by means of perturbed angular correlation of gamma rays (PAC) on the Cu(II),Cd(II)- and Cu(I),Cd(II)-superoxide dismutase. The PAC spectrum for the Cu(II),Cd(II) enzyme reveals two different, pH independent, coordination geometries for the Cd site. Removal of Cu(II) does not affect the PAC spectrum, which suggests that Cu(II) and Cd(II) do not share a common histidine side chain as ligand. The results are consistent with either an equilibrium between two coordination geometries for Cd(II) in each subunit or a difference in the structure of the Cd(II) site in the two subunits. In contrast, in the reduced enzyme only one structure is present, identical for the two subunits.     

Structural changes in thin filaments of crab striated muscle.

Low angle X-ray diffraction patterns were recorded from crab leg muscle in living resting state and in rigor (glycerol-extracted). Both resting and rigor patterns showed a series of layer-lines arising from a helical arrangement of actin subunits in the thin filaments. In the resting state, the crossover repeat of the long-pitch actin helices was 36.6 nm, and the symmetry of the genetic actin helix was an intermediate between $\text{26}\text{12}$ and $\text{28}\text{13}$. When the muscle went into rigor, the crossover repeat changed to 38.3 nm and the helical symmetry to $\text{28}\text{13}$.In the living resting pattern, six other reflections were observed on the meridian and in the near-meridional region. These were indexed as orders of 2 × 38.2 nm and could be assigned to troponin molecules; the spacings and the intensity distributions of these reflections could be explained by the model proposed by Ohtsuki (1974) for the arrangement of troponin molecules in the thin filaments.The muscle in rigor gave meridional and near-meridional reflections at orders of 2 × 38.3 nm. These were identified as the same series of reflections as was assigned to troponin in the living resting pattern, but were more intense and could be seen up to higher orders. We consider that the myosin heads attached to the thin filament at regular intervals along its axis also contribute to these reflections in the rigor pattern.