A Brief Survey of Vedāntic Oneirology

The Upaniṣads, as one of the trilogy of principal Vedāntic texts, the oldest and the most fundamental of them, have exposed a more or less detailed discussion on dreaming, taking it whether as the factual object of their discourse or as a symbol. However, there has been a debate between different schools of Vedāntic philosophy about oneirology, science of dreams and their interpretation, discussion of nature of the dream state, its reality and unreality. This paper, after a short study of oneirology in the Vedas and Upaniṣads, examines argumentations of four great philosophers of different Vedāntic schools, Gauḍapāda, Śaṅkara, Rāmānuja, and Madhva, pertaining to dreams

Compact Multi-Class Boosted Trees

Gradient boosted decision trees are a popular machine learning technique, in part because of their ability to give good accuracy with small models. We describe two extensions to the standard tree boosting algorithm designed to increase this advantage. The first improvement extends the boosting formalism from scalar-valued trees to vector-valued trees. This allows individual trees to be used as multiclass classifiers, rather than requiring one tree per class, and drastically reduces the model size required for multiclass problems. We also show that some other popular vector-valued gradient boosted trees modifications fit into this formulation and can be easily obtained in our implementation. The second extension, layer-by-layer boosting, takes smaller steps in function space, which is empirically shown to lead to a faster convergence and to a more compact ensemble. We have added both improvements to the open-source TensorFlow Boosted trees (TFBT) package, and we demonstrate their efficacy on a variety of multiclass datasets. We expect these extensions will be of particular interest to boosted tree applications that require small models, such as embedded devices, applications requiring fast inference, or applications desiring more interpretable models.Comment: Accepted for publication in IEEE Big Data 2017 http://cci.drexel.edu/bigdata/bigdata2017/AcceptedPapers.htm

Macroscale multimodal imaging reveals ancient painting production technology and the vogue in Greco-Roman Egypt.

Macroscale multimodal chemical imaging combining hyperspectral diffuse reflectance (400-2500 nm), luminescence (400-1000 nm), and X-ray fluorescence (XRF, 2 to 25 keV) data, is uniquely equipped for noninvasive characterization of heterogeneous complex systems such as paintings. Here we present the first application of multimodal chemical imaging to analyze the production technology of an 1,800-year-old painting and one of the oldest surviving encaustic ("burned in") paintings in the world. Co-registration of the data cubes from these three hyperspectral imaging modalities enabled the comparison of reflectance, luminescence, and XRF spectra at each pixel in the image for the entire painting. By comparing the molecular and elemental spectral signatures at each pixel, this fusion of the data allowed for a more thorough identification and mapping of the painting's constituent organic and inorganic materials, revealing key information on the selection of raw materials, production sequence and the fashion aesthetics and chemical arts practiced in Egypt in the second century AD

Mitochondrial DNA content in paired normal and cancerous breast tissue samples from patients with breast cancer

Introduction: We develop a multiplex quantitative real-time PCR for synchronized analysis of mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) to investigate relative mtDNA abundance in paired normal and cancerous breast tissues. Materials and methods: The amounts of nDNA and mtDNA in 102 tissue samples were quantified for both glyceraldehype-3-phosphodehydrogenase (GAPDH) gene and mtDNA encoded ATPase (MTATP) 8 gene. The average threshold cycle (Ct) number values of the nDNA and mtDNA were used to calculate relative mtDNA content in breast tissues. Results: The median delta Ct (ΔCt) and the median mtDNA content for normal and cancerous breast tissues were 6.73 and 2.54, as well as 106.50 and 5.80 (P=0.000, respectively). The mtDNA content was decreased in 82% of cancerous breast tissues compared with the normal ones. The changes were associated with hormone receptor status. Conclusion: Our finding suggests that decreased mtDNA content in breast cancer may have diagnostic and prognostic value for the diseas

Four novel germline mutations in the MLH1 and PMS2 mismatch repair genes in patients with hereditary nonpolyposis colorectal cancer

Background: Hereditary nonpolyposis colorectal cancer (HNPCC) is the most common cause of early onset hereditary colorectal cancer. In the majority of HNPCC families, microsatellite instability (MSI) and germline mutation in one of the DNA mismatch repair (MMR) genes are found. Materials and methods: The entire coding sequence of MMR genes (MLH1, MLH2, MLH6, and PMS2) was analyzed using direct sequencing. Also, tumor tests were done as MSI and immunohistochemistry testing. Results: We were able to find three novel MLH1 and one novel PMS2 germline mutations in three Iranian HNPCC patients. The first was a transversion mutation c.346A>C (T116P) and happened in the highly conserved HATPase-c region of MLH1 protein. The second was a transversion mutation c.736A>T (I246L), which caused an amino acid change of isoleucine to leucine. The third mutation (c.2145,6 delTG) was frameshift and resulted in an immature stop codon in five codons downstream. All of these three mutations were detected in the MLH1 gene. The other mutation was a transition mutation, c.676G>A (G207E), which has been found in exon six of the PMS2 gene and caused an amino acid change of glycine to glutamic acid. MSI assay revealed high instability in microsatellite for two patients and microsatellite stable for one patient. Conclusion: In all patients, an abnormal expression of the MMR proteins in HNPCC was related to the above novel mutation

A selected pre-amplification strategy for genetic analysis using limited DNA targets

Background: Limited DNA resources or limited DNA targets in predominant backgrounds for genetic tests can lead to misdiagnosis. We developed a strategy to selectively increase the amount of minor targets through a specific pre-amplification procedure. Methods: We used the model of circulating cell free (ccf) male fetal DNA as a minor target in the predominant maternal plasma DNA to evaluate the strategy. The sex determining region (SRY) locus on the Y chromosome was used to identify ccf fetal DNA, and the human glyceraldehydes-3-phosphate dehydrogenase (GAPDH) gene was used to identify ccf total DNA in maternal plasma. We selectively pre-amplified the minor target SRY locus using the Expand Long Template PCR system and assessed the efficiency of the pre-amplification by real-time PCR, for both SRY and GAPDH, to compare the quantities of pre-amplified fetal DNA with those of maternal total DNA without pre-amplification. Results: The selected pre-amplification increased the amount of ccf fetal DNA dramatically (Wilcoxon test: p=0.000, the fold change=11,596). After selected pre-amplification, a proportion of 2.19% of the ccf fetal minor part in the predominant maternal component was changed up to 25,334%. The increased amounts of ccf fetal DNA found with the pre-amplification are not correlated to the amounts found without the procedure (r=−0.017, p=0.949). Conclusions: This strategy may be useful in genetic analysis with limited DNA resources and limited DNA targets in predominant background molecules. However, this approach is not suitable for quantitative assessments, due to the fact that quantitative imbalanced amplification was observed as a result of the pre-amplification procedure. Clin Chem Lab Med 2009;47:288-9

Assessing the value of CAN-gene mutations using MALDI-TOF MS

Purpose: To identify cancer-linked genes, Sjöblom et al. and Wood et al. performed a genome-wide mutation screening in human breast and colorectal cancers. 140 CAN-genes were found in breast cancer, which in turn contained overall 334 mutations. These mutations could prove useful for diagnostic and therapeutic purposes. Methods: We used a MALDI-TOF MS 40-plex assay for testing 40 loci within 21 high-ranking breast cancer CAN-genes. To confirm mutations, we performed single-plex assays and sequencing. Results: In general, the mutation rate of the analyzed loci in our sample cohort was very low. No mutation from the 40 loci analyzed could be found in the 6 cell lines. In tissue samples, a single breast cancer tissue sample showed heterozygosity at locus c.5834G>A within the ZFYVE26 gene (Zinc finger FYVE domain-containing gene 26). Conclusions: Sjöblom et al./Wood et al. already showed that the vast majority of CAN-genes are mutated at very low frequency. Due to the fact that we only found one mutation in our cohort, we therefore assume that at the selected loci, mutations might be low-frequency events and therefore, more rarely detectable. However, further evaluation of the CAN-gene mutations in larger cohorts should be the aim of further studie