Confusing finding of quantitative fluorescent polymerase chain reaction analysis in invasive prenatal genetic diagnosis: A case report.

BACKGROUND: Quantitative fluorescent polymerase chain reaction (QF-PCR) is a rapid prenatal diagnostic method for abnormalities on chromosomes 21, 18, and 13 and sex chromosomal aneuploidy. However, the value of QF-PCR in diagnosing chromosomal structural abnormalities is limited. In this article, we report a confusing QF-PCR finding in a pregnant woman who underwent amniocentesis. CASE SUMMARY: The short tandem repeat marker AMXY (Xp22.2/Yp11.2) located on the sex chromosome exhibited a trisomic biallelic pattern, indicating that the karyotype of the fetus might be 47,XYY. Chromosome analysis performed on cultured amniocytes showed a normal male karyotype of the fetus. Copy number variation sequencing confirmed a 500 kb duplication at Yp11.2-Yp11.2 (chrY:6610001_ 7110000) and a 250 kb duplication at Yp11.2-Yp11.2 (chrY:7110001_7360000). CONCLUSION: In conclusion, the comprehensive application of different methods could achieve a higher detection rate and accuracy for the prenatal diagnosis of chromosomal disorders through chromosomal testing.

CNSeg: A dataset for cervical nuclear segmentation.

BACKGROUND AND OBJECTIVE: Nuclear segmentation in cervical cell images is a crucial technique for automatic cytopathology diagnosis. Experimental evaluation of nuclear segmentation methods with datasets is helpful in promoting the advancement of nuclear segmentation techniques. However, public datasets are not enough for a reasonable and comprehensive evaluation because of insufficient quantity, single data source, and low segmentation difficulty. METHODS: Therefore, we provide the largest dataset for cervical nuclear segmentation (CNSeg). It contains 124,000 annotated nuclei collected from 1,530 patients under different conditions. The image styles in this dataset cover most practical application scenarios, including microbial infection, cytopathic heterogeneity, overlapping nuclei, etc. To evaluate the performance of segmentation methods from different aspects, we divided the CNSeg dataset into three subsets, namely the patch segmentation dataset (PatchSeg) with nuclei images collected under complex conditions, the cluster segmentation dataset (ClusterSeg) with cluster nuclei, and the domain segmentation dataset (DomainSeg) with data from different domains. Furthermore, we propose a post-processing method that processes overlapping nuclei single ones. RESULTS AND CONCLUSION: Experiments show that our dataset can comprehensively evaluate cervical nuclear segmentation methods from different aspects. We provide guidelines for other researchers to use the dataset. https://github.com/jingzhaohlj/AL-Net.

AL-Net: Attention Learning Network Based on Multi-Task Learning for Cervical Nucleus Segmentation.

Cervical nucleus segmentation is a crucial and challenging issue in automatic pathological diagnosis due to uneven staining, blurry boundaries, and adherent or overlapping nuclei in nucleus images. To overcome the limitation of current methods, we propose a multi-task network based on U-Net for cervical nucleus segmentation. This network consists of a primary task and an auxiliary task. The primary task is employed to predict nuclei regions. The auxiliary task, which predicts the boundaries of nuclei, is designed to improve the feature extraction of the main task. Furthermore, a context encoding layer is added behind each encoding layer of the U-Net. The output of each context encoding layer is processed by an attention learning module and then fused with the features of the decoding layer. In addition, a codec block is used in the attention learning module to obtain saliency-based attention and focused attention simultaneously. Experiment results show that the proposed network performs better than the state-of-the-art methods on the 2014 ISBI dataset, BNS, MoNuSeg, and our nucluesSeg dataset.

[Diagnostic Cut-Off Value of RDW for Screening Thalassemia and the Combined Determination of MCV, MCH, HBA 2 and RDW].

OBJECTIVE: To explore the value of red cell distribution width (RDW), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH) and hemoglobin (Hb) A2 combined determination scheme for screening thalassemia. METHODS: The RDW levels of thalassemia group and healthy control group were detected and compared. The efficiency of RDW for screening thalassemia was evaluated by receiver operating characteristic (ROC) curve. The diagnostic cut-off value of RDW was also acquired by Youden index. Then, 3 groups for thalassemia screening scheme were set, including MCV+MCH+HBA 2, MCV+MCH+RDW(>16.0)+HBA 2 and MCV+MCH+RDW(>15.15)+HBA 2. The performances of the 3 groups were evaluated through screening 621 clinical suspected cases of thalassemia. RESULTS: The RDW level in thalassemia group was significantly higher than that in healthy control group (P<0.05). The diagnostic cut-off value for screening thalassemia was RDW>15.15, when the Youden index was the biggest among all data. The sensitivity, specificity, positive predictive value, negative predictive value, false negative rate and consistency rate of MCV+MCH+RDW(>15.15)+HBA 2 group was 75.46%, 48.83%, 26.50%, 89.06%, 24.54%, and 54.06%, respectively. CONCLUSION: The diagnostic cut-off value of RDW for thalassemia screening has been established. The group of MCV(<82.0 fl)+MCH(<27.0 pg)+HBA 2(<2.5% or ≥3.5%)+RDW(>15.15) has a best efficiency among the 3 groups to screen thalassemia.

Endocytosis Is a Key Mode of Interaction between Extracellular ß-Amyloid and the Cell Membrane.

Interactions between amyloid-ß peptide (Aß) and the cell membrane include interaction with membrane lipids and binding to membrane receptors, both of which are considered to be the toxicity mechanisms of Aß. However, it is unclear whether both mechanisms lead to cytotoxicity. Thus, we aimed to analyze these two mechanisms of Aß42 interaction with cell membranes under different Aß aggregation states. To this end, model membrane experiments were conducted. Quantitative analysis of Aß42 monomers or oligomers bound to the membrane of neuro-2a cells was also performed, and laser confocal microscopy was employed to assess endocytosis of FITC-Aß42 monomers or oligomers by neuro-2a cells. We found that the binding capacity of Aß42 to membrane lipids was weak and that the amount of Aß42 bound to membrane lipids was low. Moreover, clathrin-mediated endocytosis of Aß42 oligomers by neuro-2a cells was observed. Endocytosis serves as a key mode of interaction between extracellular Aß42 and neurons. These findings provide insights into the mechanisms underlying Aß oligomer metabolism.

An Overlapping Cell Image Synthesis Method for Imbalance Data.

DNA ploidy analysis of cells is an automation technique applied in pathological diagnosis. It is important for this technique to classify various nuclei images accurately. However, the lack of overlapping nuclei images in training data (imbalanced training data) results in low recognition rates of overlapping nuclei images. To solve this problem, a new method which synthesizes overlapping nuclei images with single-nuclei images is proposed. Firstly, sample selection is employed to make the synthesized samples representative. Secondly, random functions are used to control the rotation angles of the nucleus and the distance between the centroids of the nucleus, increasing the sample diversity. Then, the Lambert-Beer law is applied to reassign the pixels of overlapping parts, thus making the synthesized samples quite close to the real ones. Finally, all synthesized samples are added to the training sets for classifier training. The experimental results show that images synthesized by this method can solve the data set imbalance problem and improve the recognition rate of DNA ploidy analysis systems.

Correction to: Transcriptome profiling of genes related to light-induced anthocyanin biosynthesis in eggplant (Solanum melongena L.) before purple color becomes evident.

After publication of the original article [1] it was noted that in Additional file 1: Table S1, and Fig. 1, specific primer sequences were incorrect, and taken from Sme2.5_02154.1_g00001.1 rather than Sme2.5_13923.1_g00001.1.

Transcriptome profiling of genes related to light-induced anthocyanin biosynthesis in eggplant (Solanum melongena L.) before purple color becomes evident.

BACKGROUND: The anthocyanins are highly enriched in eggplants (Solanum melongena L.) with purple peel. However, our previous study showed that anthocyanins biosynthesis in eggplant cultivar 'Lanshan Hexian' was completely regulated by light and color becomes evident at most 2 days after exposure to light. In the present investigation, transcriptome study was made to explore the underlying molecular mechanisms of light-induced anthocyanin biosynthesis in eggplant (Solanum melongena L.) before color becomes evident. RESULTS: RNA-Seq was performed for four time points (0, 0.5, 4 and 8 h after bags removal) where concerted changes happened. A total of 32,630 genes or transcripts were obtained by transcriptome sequencing, from which 1956 differentially expressed genes (DEGs) were found. Gene Ontology analysis showed that the 1956 DEGs covered a wide range of cellular components, molecular functions and biological processes. All the DEGs were further divided into 26 clusters based on their distinct expression patterns. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis found out 24 structural anthocyanin biosynthesis genes which distributing in seven clusters. In addition, 102 transcription factors, which exhibited highly dynamic changes in response to light, were found in the seven clusters. Three photoreceptors, UV Resistance Locus 8 (UVR8), Cryptochrome 3 (CRY3) and UVR3, were identified as DEGs. The light signal transduction elements, COP1 and two SPAs, might be responsible for anthocyanin biosynthesis regulation. CONCLUSION: Based on the transcriptome data, the anthocyanin biosynthesis structural genes, transcription factors, photoreceptors and light signal transduction elements were quickly screened which may act as the key regulatory factors in anthocyanin biosynthesis pathway. By comparing the transcriptome data with our previous studies, 869 genes were confirmed to participate in the light-induced anthocyanin biosynthesis. These results expand our knowledge of light-induced anthocyanin biosynthesis in plants, which allowing for fruit coloration to be improved under low-light conditions in future.

Ethyl 4-chloro-3,5-dinitro-benzoate.

In the title compound, C(9)H(7)ClN(2)O(6), the nitro groups and the ester group make dihedral angles of 44.0 (1), 89.6 (1) and 164.1 (1)°, respectively, with the benzene ring. In the crystal, mol-ecules are linked through weak C-H⋯O hydrogen-bonding inter-actions. Mol-ecules are stacked via π-π inter-actions about inversion centers, with a centroid-centroid distance of 3.671 (2) Å.

Ethyl 2-(2-methyl-4-nitro-1H-imidazol-1-yl)acetate.

In the title compound, C(8)H(11)N(3)O(4), the dihedral angle between the imidazole ring and the ethyl acetate plane is 103.1 (8)°. The crystal packing is stabilized by weak inter-molecular C-H⋯O and C-H⋯N hydrogen bonds.

Glycine ethyl ester hydro-chloride.

In the crystal structure of the title compound, C(4)H(10)NO(2) (+)·Cl(-) (systematic name: 3-eth-oxy-3-oxopropan-1-aminium chlor-ide), there are strong inter-molecular N-H⋯Cl, C-H⋯Cl and C-H⋯O hydrogen-bonding inter-actions between the free chloride anion and the organic cation, resulting in a two-dimensional supra-molecular network in the ab plane.

2-Chloro-ethyl 4-nitro-benzoate.

The title compound, C(9)H(8)ClNO(4), crystallizes with two mol-ecules in the asymmetric unit. In each mol-ecule, the carboxyl-ate group is nearly coplanar with the benzene ring, forming dihedral angles of 2.4 (1) and 4.9 (1)°. In the crystal, mol-ecules are linked through weak C-H⋯O and C-H⋯Cl hydrogen bonds. A short O⋯N contact of 2.7660 (19) Šoccurs between the nitro groups of adjacent mol-ecules.

2-(Carbazol-9-yl)acetic acid.

In the title compound, C(14)H(11)NO(2), the tricyclic aromatic ring system is essentially planar [maximum deviation = 0.025 (2) Å]. The dihedral angle between the two benzene rings is 2.8 (5)°, while the carboxyl group forms a dihedral angle of 88.5 (1)° with the pyrrole ring. Inter-molecular O-H⋯O hydrogen bonds may contribute to the overall stabilization of the crystal structure.

Methyl 4-nitro-benzoate.

In the mol-ecule of the title compound, C(8)H(7)NO(4), the nitro group is approximately coplanar with the benzene ring [dihedral angle = 0.6 (1)°], while the dihedral angle between the methoxy-carbonyl group and the benzene ring is 8.8 (1)°. In the crystal structure, weak inter-molecular aromatic C-H⋯O(carbox-yl) and C-H⋯O(nitro) hydrogen-bonding inter-actions are present.

5,6,7,8-Tetra-hydro-naphthalene-1-carboxylic acid.

In the mol-ecule of the title compound, C(11)H(12)O(2), the cyclo-hexane ring adopts a half-chair conformation. In the crystal structure, mol-ecules are linked into centrosymmetric dimers by pairs of O-H⋯O hydrogen bonds, and the dimers are linked together by π-π inter-actions [centroid-centroid distance = 3.8310 (13) Å] and C-H⋯O bonds.

Diethyl 5-amino-2,4,6-triiodo-isophthalate.

The title compound, C(12)H(12)I(3)NO(4), crystallizes with two mol-ecules in an asymmetric unit. In one of the mol-ecules, the conformation of the O-C-O-C in one ester group is cis and trans in the other. The corresponding conformations for both the ester groups in the other mol-ecule are trans. The I atoms and the benzene rings in the two mol-ecules are approximately coplanar, the I atoms deviating by 0.219 (14), 0.056 (15) and -0.143 (14) Šfrom the mean plane of the benzene ring in one mol-ecule and 0.189 (14), -0.162 (15) and -0.068 (14) Šin the other. The planes of the ester groups are almost orthogonal to those of the benzene rings in both mol-ecules, forming dihedral angles of 88.1 (4), 72.2 (4), 73.0 (4) and 86.6 (4)°. The mean planes of the benzene rings in the two mol-ecules are inclined at 74.6 (4)° with respect to each other. In the crystal, inter-molecular I⋯O inter-actions [3.138 (7) and 3.144 (7) Å] link the mol-ecules into infinite chains along the a axis. In addition, non-classical C-H⋯O hydrogen bonds are observed.

4,7-Diphenyl-2,9-bis-(trichloro-meth-yl)-1,10-phenanthroline.

In the title compound, C(26)H(14)Cl(6)N(2), the phenanthroline ring system is essentially planar, with an r.m.s. deviation of 0.048 (6) Å, and makes dihedral angles of 64.8 (14) and 66.6 (6)° with the two terminal phenyl rings. One of the trichloro-methyl groups is disordered over two positions, with occupancies of 0.42 (2) and 0.58 (2).

Methyl 4-chloro-3,5-dinitro-benzoate.

In the mol-ecule of the title compound, C(8)H(5)ClN(2)O(6), the two nitro groups and the ester group make dihedral angles of 29.6 (1)°, 82.3 (1)° and 13.7 (1)°, respectively, with the benzene ring. In the crystal structure weak C-H⋯O inter-actions are present.

2-Isopropoxyphenyl N-methyl-carbamate.

In the title compound, C(11)H(15)NO(3), the mean planes of the carboxamide and isopropyl groups are inclined at 109.9 (1) and 128.7 (2)°, respectively, to the mean plane of the phen-oxy group. In the crystal structure, mol-ecules are stacked along the b axis, without any π-π inter-actions. The stacked columns are linked together by inter-molecular N-H⋯O hydrogen bonds, with an N⋯O distance of 2.842 (2) Å.