CPEM: Accurate cancer type classification based on somatic alterations using an ensemble of a random forest and a deep neural network

With recent advances in DNA sequencing technologies, fast acquisition of large-scale genomic data has become commonplace. For cancer studies, in particular, there is an increasing need for the classification of cancer type based on somatic alterations detected from sequencing analyses. However, the ever-increasing size and complexity of the data make the classification task extremely challenging. In this study, we evaluate the contributions of various input features, such as mutation profiles, mutation rates, mutation spectra and signatures, and somatic copy number alterations that can be derived from genomic data, and further utilize them for accurate cancer type classification. We introduce a novel ensemble of machine learning classifiers, called CPEM (Cancer Predictor using an Ensemble Model), which is tested on 7,002 samples representing over 31 different cancer types collected from The Cancer Genome Atlas (TCGA) database. We first systematically examined the impact of the input features. Features known to be associated with specific cancers had relatively high importance in our initial prediction model. We further investigated various machine learning classifiers and feature selection methods to derive the ensemble-based cancer type prediction model achieving up to 84% classification accuracy in the nested 10-fold cross-validation. Finally, we narrowed down the target cancers to the six most common types and achieved up to 94% accuracy

Efficient Photoacoustic Conversion in Optical Nanomaterials and Composites

Photoacoustic pulses generated by pulsed laser irradiation have the characteristics of high frequency and wide bandwidth, which are desirable for imaging and sensing. Efficient photoacoustic composites have been developed for fabricating photoacoustic transmitters capable of generating high‐amplitude ultrasound. Here, recent advances in photoacoustic transmitters are reviewed from an application perspective, starting with the fundamental aspects of photoacoustic generation. The topics discussed include various composite materials for photoacoustic generation, and their applications such as high‐amplitude therapy, imaging and sensing, and photoacoustic waveform control.Photoacoustic transmitters using pulsed laser irradiation onto optical nanomaterials have been developed for generating strong photoacoustic pulses, enabling interesting applications. Recent advances in photoacoustic transmitters are reviewed from an application perspective, starting with the fundamental aspects of photoacoustic generation.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147165/1/adom201800491_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147165/2/adom201800491.pd

Towards Generating Secure Keys for Braid Cryptography

Braid cryptosystem was proposed in CRYPTO 2000 as an alternate public-key cryptosystem. The security of this system is based upon the conjugacy problem in braid groups. Since then, there have been several attempts to break the braid cryptosystem by solving the conjugacy problem in braid groups. In this paper, we first survey all the major attacks on the braid cryptosystem and conclude that the attacks were successful because the current ways of random key generation almost always result in weaker instances of the conjugacy problem. We then propose several alternate ways of generating hard instances of the conjugacy problem for use braid cryptography

Učinci gama-zračenja na folikule jajnika

In order to observe the morphological and endocrinological changes of the rat and mouse ovarian follicles by gamma-radiation, rats were whole-body irradiated with doses of 3.2 Gy and 8.0 Gy and mice with 2.9 Gy and 7.2 Gy. Sections of ovaria were examined by light microscopy. Concentrations of progesterone, testosterone, and estradiol in ovarian homogenate were determined by radioimmunoassay techniques. Gamma-radiation resulted in the increased percentage of atretic follicles in the groups killed on day 0, day 4, and day 8 after irradiation. The decrease in granulosa cell viability was found in animals killed on day 4 after irradiation. The finding of the high ratio of testosterone to estradiol compared to that of progesterone to testosterone suggests that aromatase activity — steroid biosynthesis from testosterone to estradiol — in granulosa cell could be affected by gamma-radiation.U radu su procjenjivane strukture i endokrinološke promjene u folikulima jajnika štakorica i mišica izazvane gama-zračenjem. Štakorice su bile izložene zračenju od 3,2 Gy ili 8,0 Gy, a mišice od 2,9 Gy ili 7,2 Gy. Životinje su usmrćene dana 0, dana 4, odnosno dana 8 nakon ozračenja. Rezovi debljine 7 µm pripremljeni su za mikroskopiranje. Koncentracije progesterona, testosterona i estradiola u homogenatu jajnika određene su specifičnim radioimunoesejem. Gama-zračenje uzrokovalo je povećanje broja atretičnih folikula u obje skupine životinja usmrćenih 4 odnosno 8 dana nakon ozračivanja. Gama-zračenje također je smanjilo životni vijek granuloza stanica u skupinama usmrćenim 4. dan nakon ozračivanja. Utvrđeno povećanje omjera testosterona prema estradiolu u usporedbi s omjerom progesterona prema testosteronu upućuje na to da gama-zračenje utječe na aktivnost aromataze u steroidnoj biosintezi testosterona u estradiol u granuloza stanicama

Materials and extracellular matrix rigidity highlighted in tissue damages and diseases: Implication for biomaterials design and therapeutic targets

Rigidity (or stiffness) of materials and extracellular matrix has proven to be one of the most significant extracellular physicochemical cues that can control diverse cell behaviors, such as contractility, motility, and spreading, and the resultant pathophysiological phenomena. Many 2D materials engineered with tunable rigidity have enabled researchers to elucidate the roles of matrix biophysical cues in diverse cellular events, including migration, lineage specification, and mechanical memory. Moreover, the recent findings accumulated under 3D environments with viscoelastic and remodeling properties pointed to the importance of dynamically changing rigidity in cell fate control, tissue repair, and disease progression. Thus, here we aim to highlight the works related with material/matrix-rigidity-mediated cell and tissue behaviors, with a brief outlook into the studies on the effects of material/matrix rigidity on cell behaviors in 2D systems, further discussion of the events and considerations in tissue-mimicking 3D conditions, and then examination of the in vivo findings that concern material/matrix rigidity. The current discussion will help understand the material/matrix-rigidity-mediated biological phenomena and further leverage the concepts to find therapeutic targets and to design implantable materials for the treatment of damaged and diseased tissues

Replication of the genetic effects of IFN regulatory factor 5 (IRF5) on systemic lupus erythematosus in a Korean population

Recently, two studies provided convincing evidence that IFN regulatory factor 5 (IRF5) gene polymorphisms are significantly associated with systemic lupus erythematosus (SLE) in several white populations. To replicate the association with SLE in an Asian population, we examined the genetic effects in our SLE cohort from a Korean population. A total of 1,565 subjects, composed of 593 cases and 972 controls, were genotyped using the TaqMan® (Applied Biosystems, Foster City, CA, USA) method. The genetic effects of polymorphisms on the risk of SLE were evaluated using χ2 tests and a Mantel–Haenszel meta-analysis. Statistical analysis revealed results in the Korean population were similar to the previous reports from white populations. The rs2004640 T allele had a higher frequency in SLE cases (0.385) than controls (0.321; odds ratio (OR) = 1.32, P = 0.0003). In combined analysis, including all seven independent cohorts from the three studies so far, robust and consistent associations of the rs2004640 T allele with SLE were observed. The estimate of risk was OR = 1.44 (range, 1.34–1.55), with an overall P = 1.85 × 10-23 for the rs2004640 T allele. The haplotype (rs2004640T–rs2280714T) involved in both the alternative splice donor site and the elevated expression of IRF5 also had a highly significant association with SLE (pooled, P = 2.11 × 10-16). Our results indicate that the genetic effect on the risk of SLE mediated by IRF5 variants can be generally accepted in both white and Asian populations

Switching Magnetism and Superconductivity with Spin-Polarized Current in Iron-Based Superconductor

We have explored a new mechanism for switching magnetism and superconductivity in a magnetically frustrated iron-based superconductor using spin-polarized scanning tunneling microscopy (SPSTM). Our SPSTM study on single crystal Sr$_2$VO$_3$FeAs shows that a spin-polarized tunneling current can switch the Fe-layer magnetism into a non-trivial $C_4$ (2$\times$2) order, not achievable by thermal excitation with unpolarized current. Our tunneling spectroscopy study shows that the induced $C_4$ (2$\times$2) order has characteristics of plaquette antiferromagnetic order in Fe layer and strongly suppressed superconductivity. Also, thermal agitation beyond the bulk Fe spin ordering temperature erases the $C_4$ state. These results suggest a new possibility of switching local superconductivity by changing the symmetry of magnetic order with spin-polarized and unpolarized tunneling currents in iron-based superconductors.Comment: 33 pages, 16 figure

Incipient piezoelectrics and electrostriction behavior in Sn-doped Bi-1/2( Na0.82K0.18)(1/2) TiO3 lead-free ceramics

Dielectric, ferroelectric, piezoelectric, and strain properties of lead-free Sn-doped Bi-1/2(Na0.82K0.18)(1/2)TiO3 (BNKT) were investigated. A crossover from a nonergodic relaxor to an ergodic relaxor state at room temperature, accompanied by a giant electric-field-induced strain, was observed at 5 at. % Sn doping. Switching dynamics monitored during a bipolar poling cycle manifested that the observed giant strain originates from incipient piezoelectricity. When Sn doping level reached 8 at. %, BNKT exhibited an electrostrictive behavior with a highly temperature-insensitive electrostrictive coefficient of Q(11) = 0.023 m(4)open3