SuperPCA: A Superpixelwise PCA Approach for Unsupervised Feature Extraction of Hyperspectral Imagery

As an unsupervised dimensionality reduction method, principal component analysis (PCA) has been widely considered as an efficient and effective preprocessing step for hyperspectral image (HSI) processing and analysis tasks. It takes each band as a whole and globally extracts the most representative bands. However, different homogeneous regions correspond to different objects, whose spectral features are diverse. It is obviously inappropriate to carry out dimensionality reduction through a unified projection for an entire HSI. In this paper, a simple but very effective superpixelwise PCA approach, called SuperPCA, is proposed to learn the intrinsic low-dimensional features of HSIs. In contrast to classical PCA models, SuperPCA has four main properties. (1) Unlike the traditional PCA method based on a whole image, SuperPCA takes into account the diversity in different homogeneous regions, that is, different regions should have different projections. (2) Most of the conventional feature extraction models cannot directly use the spatial information of HSIs, while SuperPCA is able to incorporate the spatial context information into the unsupervised dimensionality reduction by superpixel segmentation. (3) Since the regions obtained by superpixel segmentation have homogeneity, SuperPCA can extract potential low-dimensional features even under noise. (4) Although SuperPCA is an unsupervised method, it can achieve competitive performance when compared with supervised approaches. The resulting features are discriminative, compact, and noise resistant, leading to improved HSI classification performance. Experiments on three public datasets demonstrate that the SuperPCA model significantly outperforms the conventional PCA based dimensionality reduction baselines for HSI classification. The Matlab source code is available at https://github.com/junjun-jiang/SuperPCAComment: 13 pages, 10 figures, Accepted by IEEE TGR

An integrated paper-based microfluidic platform for screening of early-stage Alzheimer's disease by detecting Aβ42.

Alzheimer's disease (AD) is the leading cause of dementia worldwide, and the development of early screening methods can address its significant health and social consequences. In this paper, we present a rotary-valve assisted paper-based immunoassay device (RAPID) for early screening of AD, featuring a highly integrated on-chip rotary micro-valve that enables fully automated and efficient detection of the AD biomarker (amyloid beta 42, Aβ42) in artificial plasma. The microfluidic paper-based analytical device (μPAD) of the RAPID pre-stores the required assay reagents on a μPAD and automatically controls the liquid flow through a single valve. Once the test sample is added, the test reagents are sequentially transferred to the test area in the order set by the enzyme-linked immunosorbent assay (ELISA) protocol. In addition, the RAPID can remotely control the operation of the μPAD valve via a micro-servomotor, quantify the signals generated, display the results, and wirelessly transmit the data to a smartphone. To calibrate the RAPID, we performed a sandwich ELISA for Aβ42 in artificial plasma, and obtained a low limit of detection (LOD) of 9.6 pg mL-1, a coefficient of determination (COD) of 0.994, and an individual assay time of ∼30 minutes. In addition, we simulated 24 artificial samples to quantify Aβ42 protein concentrations in artificial plasma samples. The results show good consistency between the conventional ELISA and RAPID detection. The experimental results demonstrate that the RAPID is expected to promote further popularization of the screening of early-stage AD

Identifying a few foot-and-mouth disease virus signature nucleotide strings for computational genotyping

<p>Abstract</p> <p>Background</p> <p>Serotypes of the Foot-and-Mouth disease viruses (FMDVs) were generally determined by biological experiments. The computational genotyping is not well studied even with the availability of whole viral genomes, due to uneven evolution among genes as well as frequent genetic recombination. Naively using sequence comparison for genotyping is only able to achieve a limited extent of success.</p> <p>Results</p> <p>We used 129 FMDV strains with known serotype as training strains to select as many as 140 most serotype-specific nucleotide strings. We then constructed a linear-kernel Support Vector Machine classifier using these 140 strings. Under the leave-one-out cross validation scheme, this classifier was able to assign correct serotype to 127 of these 129 strains, achieving 98.45% accuracy. It also assigned serotype correctly to an independent test set of 83 other FMDV strains downloaded separately from NCBI GenBank.</p> <p>Conclusion</p> <p>Computational genotyping is much faster and much cheaper than the wet-lab based biological experiments, upon the availability of the detailed molecular sequences. The high accuracy of our proposed method suggests the potential of utilizing a few signature nucleotide strings instead of whole genomes to determine the serotypes of novel FMDV strains.</p

Parasphaerolaimus jintiani Cai 2017, n. sp.

&lt;i&gt;Parasphaerolaimus jintiani&lt;/i&gt; n. sp. &lt;p&gt;(Figs. 4&ndash;5, Table 2)&lt;/p&gt; &lt;p&gt; &lt;b&gt;Type material.&lt;/b&gt; Male holotype, slide 20110907. The specimen was collected from mangrove wetland nature reserve of the Zhangjiang Estuary in the northern South China Sea, coordinates: 23.930&deg; N, 117.417&deg; E, surface sediment layer (0&ndash;10 cm), muddy sediment. Paratypes, three females and one juvenile, slide 20110908, slide 20110909 and slide 20110998. Specimens were also collected from the same location, coordinates: 23.923&deg; &ndash; 23.932&deg; N, 117.413&deg;&ndash;24.415&deg; E, surface sediment layer (0&ndash;10 cm), muddy sediment.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Etymology.&lt;/b&gt; The species is named after the elder son of the first author Sujing Fu.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Description.&lt;/b&gt; Male body stout. Cuticle faintly striated with lateral longitudinal unstriated band extending from about the middle of the pharynx to the anterior two-thirds of the tail. Internal labial papillae, six external labial setae (3 &micro;m) and four cephalic setae (5 &micro;m) in one circle, situated posterior to the level of the distal end of the first cuticularised articulated plates. Somatic setae about 6 &micro;m long, numerous in the pharyngeal region and sparse elsewhere. Amphids circular with a posterior break. Buccal cavity in two parts. The anterior portion large, 93 &micro;m deep and 73 &micro;m wide, with six strongly cuticularised articulated plates (196 &micro;m long in total), posterior portion, 40 &micro;m deep and 22 &micro;m wide, with strongly cuticularised rim. Posterior portion of buccal cavity surrounded by pharyngeal tissue. Pharynx cylindrical. Cardia triangular. Nerve ring not observed. Secretory-excretory system not observed.&lt;/p&gt; &lt;p&gt;Anterior testis single, outstretched. Spicules, slightly arcuate, with swollen proximal ends and pointed distal ends. Gubernaculum without apophyses, parallel to the spicules. Tail conico-cylindrical, with caudal glands. Long and sparse caudal setae present sub-ventrally, three very long terminal setae, 32 &micro;m long.&lt;/p&gt; &lt;p&gt; Females &lt;b&gt;s&lt;/b&gt; imilar to males but with a shorter body length and weaker maximum body diameter, smaller mean value of a and smaller amphid diameters. Reproductive system monodelphic, with anterior ovary situated at the right of intestine. Female gonad consisting of about nine oocytes with granular cytoplasm and clear nucleus. Posterior to the oocytes region is a sequence of developing eggs and shelled embryos. One uterus can contain about nine fertilized eggs and embryos, and sometimes a few hatched juveniles. Vagina situated far posteriorly and about 91 &micro;m from the anal opening. No vulvar glands observed.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Diagnosis.&lt;/b&gt; &lt;i&gt;Parasphaerolaimus jintiani&lt;/i&gt; &lt;b&gt;n. sp.&lt;/b&gt; is characterized by a relatively long body (1286&ndash;2490 &micro;m), buccal cavity consisting of six strongly cuticularised articulating plates anteriorly and strongly cuticularised rim posteriorly, cuticle with lateral longitudinal unstriated bands, gubernaculum without apophyses and parallel with spicules. Tail conico-cylindrical with three long terminal setae.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Differential diagnosis.&lt;/b&gt; &lt;i&gt;Parasphaerolaimus jintiani&lt;/i&gt; &lt;b&gt;n. sp.&lt;/b&gt; can be differentiated from the seven species &lt;i&gt;P. paradoxus&lt;/i&gt;, &lt;i&gt;P. antiae&lt;/i&gt;, &lt;i&gt;P. brevisetosus&lt;/i&gt;, &lt;i&gt;P. crassus&lt;/i&gt;, &lt;i&gt;P. dispar&lt;/i&gt;, &lt;i&gt;P. lodosus&lt;/i&gt; and &lt;i&gt;P. polaris&lt;/i&gt; by the presence of lateral longitudinal unstriated bands or alae on cuticle. Furthermore, large values of V-index are known for some other species in the Sphaerolaimidae family, such as V = 69% in &lt;i&gt;P. antiae&lt;/i&gt;, V = 55.5%&ndash;67.1% in &lt;i&gt;P. pilosus&lt;/i&gt;, V = 62% &amp; 71% in &lt;i&gt;Sphaerolaimus kleini&lt;/i&gt; Jensen, 1992, V = 76.6%&ndash;79.6% in &lt;i&gt;S. pacificus&lt;/i&gt; Allg&eacute;n, 1947 and V = 83% in &lt;i&gt;P. lodosus&lt;/i&gt;, but not as great as in &lt;i&gt;Parasphaerolaimus jintiani&lt;/i&gt; &lt;b&gt;n. sp.&lt;/b&gt; which has very high V-index (85%). Position of the vulva very close to the anus in the new species is unique for the family. The new species has a buccal cavity similar to &lt;i&gt;P. paradoxus&lt;/i&gt; but differs from this species by shorter cervical setae (6 &micro;m &lt;i&gt;vs&lt;/i&gt; 24&ndash;34 &micro;m), swollen proximal ends of spicules and gubernaculum without apophyses. The new species differs from &lt;i&gt;P. antiae&lt;/i&gt; which has irregularly shaped plates in the buccal cavity. In addition, &lt;i&gt;Parasphaerolaimus jintiani&lt;/i&gt; &lt;b&gt;n. sp.&lt;/b&gt; can be distinguished from other species of &lt;i&gt;Parasphaerolaimus&lt;/i&gt; by much longer spicules (109 &micro;m) and gubernaculum (48 &micro;m).&lt;/p&gt;Published as part of &lt;i&gt;Cai, Lizhe, 2017, Two new ovoviviparous species of the family Selachinematidae and Sphaerolaimidae (Nematoda, Chromadorida &amp; Monhysterida) from the northern South China Sea, pp. 95-110 in Zootaxa 4317 (1)&lt;/i&gt; on pages 101-104, DOI: 10.11646/zootaxa.4317.1.4, &lt;a href="http://zenodo.org/record/880136"&gt;http://zenodo.org/record/880136&lt;/a&gt

Bendiella Leduc 2013

Genus &lt;i&gt;Bendiella&lt;/i&gt; Leduc, 2013 &lt;p&gt; &lt;b&gt;Diagnosis&lt;/b&gt; (modified from Leduc 2013). Cuticle with lateral differentiation consisting of longitudinal rows of larger punctuations. Outer labial sensillae and cephalic setae in one circle, cephalic setae slightly longer than outer labial sensillae. Buccal cavity consisting of two parts: anterior portion of buccal cavity funnel-shaped, with twelve cuticularised rhabdions, posterior portion of buccal cavity narrower, surrounded by three Y-shaped pairs of slender rhabdions, tail long.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Type species:&lt;/b&gt; &lt;i&gt;Bendiella thalassa&lt;/i&gt; Leduc, 2013&lt;/p&gt; &lt;p&gt; &lt;b&gt;Other species:&lt;/b&gt; &lt;i&gt;Bendiella vivipara&lt;/i&gt; &lt;b&gt;n. sp.&lt;/b&gt;&lt;/p&gt;Published as part of &lt;i&gt;Cai, Lizhe, 2017, Two new ovoviviparous species of the family Selachinematidae and Sphaerolaimidae (Nematoda, Chromadorida &amp; Monhysterida) from the northern South China Sea, pp. 95-110 in Zootaxa 4317 (1)&lt;/i&gt; on page 96, DOI: 10.11646/zootaxa.4317.1.4, &lt;a href="http://zenodo.org/record/880136"&gt;http://zenodo.org/record/880136&lt;/a&gt

Parasphaerolaimus Ditlevsen 1918

Genus &lt;i&gt;Parasphaerolaimus&lt;/i&gt; Ditlevsen, 1918 &lt;p&gt; &lt;b&gt;Diagnosis&lt;/b&gt; (modified from Fonseca &amp; Bezerra 2014). Sphaerolaimidae. Buccal cavity has six anterior and three posterior, circularly arranged elements. The anterior-most part of the inner pharyngeal wall transformed into six plates. Longitudinal ribs of the lip region in all juvenile stages correspond to a uniform pattern that differs from that of the adults. Eight groups of subcephalic setae present in all juvenile stages and adults.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Type species&lt;/b&gt;: &lt;i&gt;Parasphaerolaimus paradoxus&lt;/i&gt; Ditlevsen, 1918&lt;/p&gt; &lt;p&gt; = &lt;i&gt;Sphaerolaimus paradoxus&lt;/i&gt; (Ditlevsen, 1918) Filipjev, 1946&lt;/p&gt;Published as part of &lt;i&gt;Cai, Lizhe, 2017, Two new ovoviviparous species of the family Selachinematidae and Sphaerolaimidae (Nematoda, Chromadorida &amp; Monhysterida) from the northern South China Sea, pp. 95-110 in Zootaxa 4317 (1)&lt;/i&gt; on page 101, DOI: 10.11646/zootaxa.4317.1.4, &lt;a href="http://zenodo.org/record/880136"&gt;http://zenodo.org/record/880136&lt;/a&gt

Bendiella vivipara Cai 2017, n. sp.

&lt;i&gt;Bendiella vivipara&lt;/i&gt; n. sp. &lt;p&gt;(Figs. 1 &ndash;3, Table 1)&lt;/p&gt; &lt;p&gt; &lt;b&gt;Type material.&lt;/b&gt; Male holotype, slide 20140901. Specimen collected from Beibu Gulf, South China Sea in August 2011, coordinates: 21.191&deg; N, 109.562&deg; E, water depth 9.5 m, surface sediment layer (0&ndash;10 cm), muddy sediment.&lt;/p&gt; &lt;p&gt;Paratypes, three males, slide 20140702&ndash;slide 20140704, specimens collected from Beibu Gulf, South China Sea in August 2011, coordinates: 20.788&deg; N, 109.535&deg; E, water depth 10.2 m, surface sediment layer (0&ndash;10 cm), muddy sediment; three females (slide 20140305&ndash;slide 20140307, coordinates: 21.226&deg; N, 108.751&deg; E, water depth 16 m, surface sediment layer (0&ndash;10 cm), muddy sediment.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Etymology.&lt;/b&gt; The species name is related to viviparity of the female.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Description.&lt;/b&gt; Males. Body cylindrical, anterior end blunt, not set off. Cuticle transversely striated with transverse rows of punctations, lateral differentiation of cuticle beginning at a short distance posterior to the amphids down to the tail, consisting of 2&ndash;4 longitudinal rows of larger dots (two rows anteriorly, four rows from posterior end of pharynx to anterior intestine and three rows posteriorly to anterior intestine to the level of cloacal). Somatic setae short and sparse, irregularly spaced. Amphid spiral with five turns, inner labial papillae short, six outer labial papillae smaller than inner labial papillae situated on the same level with the four cephalic setae. Buccal cavity large, consisting of two parts including a wide anterior and a narrower posterior portion. Anterior portion of buccal cavity cylindrical with twelve cuticularised rhabdions, posterior buccal cavity surrounded by three &ldquo;V&rdquo; shaped pairs of rhabdions. About twelve denticles which are extensions of the anterior rhabdions present at the border of anterior and posterior portions of the buccal cavity. Pharynx larger around the stoma, and slightly wider towards its base but without a posterior bulb. Nerve ring not distinct, cardia short and triangular. Secretoryexcretory system with renette cell present, ampulla and pore at about 58% of the pharynx from the anterior end. Intestinal cells contain masses of granules.&lt;/p&gt; &lt;p&gt;Male with paired outstretched testes, anterior testis on right of intestine, posterior testis on left of intestine. Three conoid precloacal papillae, the anterior one situated about 38 &micro;m from cloacal opening. Arcuate paired spicules of similar length, tapering distally. Gubernaculum comprising a pair of lateral pieces without apophyses, about 24 &micro;m long. Tail with an anterior conoid and posterior cylindrical part. Sparse setae irregularly distributed on the tail. Spinneret 10 &micro;m long.&lt;/p&gt; &lt;p&gt;Adult females similar to males. Reproductive system didelphic with two reflexed ovaries. The anterior ovary contains three to four embryos indicative of an ovoviviparous mode of reproduction. Vulva with thick walls situated slightly anterior of median body. Intestine blind. Anus not observed.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Diagnosis.&lt;/b&gt; &lt;i&gt;Bendiella vivipara&lt;/i&gt; &lt;b&gt;n. sp.&lt;/b&gt; is characterized by having an amphideal fovea with five turns, the anterior portion of buccal cavity surrounded by 12 cuticularised rhabdions, each with one pair of pointed projections at the posterior extremity, forming 12 denticles between the two chambers. The posterior chamber is an inverted pyramid surrounded by three V-shaped pairs of cuticularised rhabdions. The new species lacks a posterior pharyngeal bulb, and has a conico-cylindroid tail. Males have plain arcuate spicules, the gubernaculum is arcuate, without apophyses, in addition, they have three papillose precloacal supplements and female is ovoviviparous.&lt;/p&gt; &lt;p&gt; &lt;b&gt;Differential diagnosis.&lt;/b&gt; &lt;i&gt;Bendiella vivipara&lt;/i&gt; &lt;b&gt;n. sp.&lt;/b&gt; is morphologically close to &lt;i&gt;Bendiella thalassa&lt;/i&gt; Leduc, 2013 in the structure of the buccal cavity, the head sensillae pattern and the shape of the long tail. Both species have a lateral differentiation of the cuticle, i.e. longitudinal rows of larger dots. The new species differs from &lt;i&gt;Bendiella thalassa&lt;/i&gt; in a smaller number of amphidial fovea turns (five turns &lt;i&gt;vs&lt;/i&gt; 5.25 turns), the presence of three precloacal supplements and an ovoviviparous mode of reproduction.&lt;/p&gt;Published as part of &lt;i&gt;Cai, Lizhe, 2017, Two new ovoviviparous species of the family Selachinematidae and Sphaerolaimidae (Nematoda, Chromadorida &amp; Monhysterida) from the northern South China Sea, pp. 95-110 in Zootaxa 4317 (1)&lt;/i&gt; on pages 96-100, DOI: 10.11646/zootaxa.4317.1.4, &lt;a href="http://zenodo.org/record/880136"&gt;http://zenodo.org/record/880136&lt;/a&gt

FIGURE 4. Parasphaerolaimus jintiani n in Two new ovoviviparous species of the family Selachinematidae and Sphaerolaimidae (Nematoda, Chromadorida & Monhysterida) from the northern South China Sea

FIGURE 4. Parasphaerolaimus jintiani n. sp. A: Entire male, showing lateral longitudinal unstriated band on CutiCle. B: Entire female. C: Anterior body region of female. D: Male head. E: Female head. F: Female posterior body region. G: Male posterior body region

FIGURE 2. Bendiella vivipara n in Two new ovoviviparous species of the family Selachinematidae and Sphaerolaimidae (Nematoda, Chromadorida & Monhysterida) from the northern South China Sea

FIGURE 2. Bendiella vivipara n. sp. Light miCrographs. A: Anterior body region of an ovoviviparous female. B: CutiCle of male, showing amphid. C: BuCCal Cavity of a female showing paired rhabdions in buCCal Cavity. D: BuCCal Cavity of a female, showing dentiCles in buCCal Cavity. E: Posterior body region of pharynx, Cardia, and anterior body region of intestine of male. F: Vulva region. Arrow shows position of vulva