A Leaf Recognition Algorithm for Plant Classification Using Probabilistic Neural Network

In this paper, we employ Probabilistic Neural Network (PNN) with image and data processing techniques to implement a general purpose automated leaf recognition algorithm. 12 leaf features are extracted and orthogonalized into 5 principal variables which consist the input vector of the PNN. The PNN is trained by 1800 leaves to classify 32 kinds of plants with an accuracy greater than 90%. Compared with other approaches, our algorithm is an accurate artificial intelligence approach which is fast in execution and easy in implementation.Comment: 6 pages, 3 figures, 2 table

Stain-free histopathology by programmable supercontinuum pulses

The preparation, staining, visualization, and interpretation of histological images of tissue is well-accepted as the gold standard process for the diagnosis of disease. These methods were developed historically, and are used ubiquitously in pathology, despite being highly time and labor intensive. Here we introduce a unique optical imaging platform and methodology for label-free multimodal multiphoton microscopy that uses a novel photonic crystal fiber source to generate tailored chemical contrast based on programmable supercontinuum pulses. We demonstrate collection of optical signatures of the tumor microenvironment, including evidence of mesoscopic biological organization, tumor cell migration, and (lymph-)angiogenesis collected directly from fresh ex vivo mammary tissue. Acquisition of these optical signatures and other cellular or extracellular features, which are largely absent from histologically processed and stained tissue, combined with an adaptable platform for optical alignment-free programmable-contrast imaging, offers the potential to translate stain-free molecular histopathology into routine clinical use

Identification of COUP-TFII Orphan Nuclear Receptor as a Retinoic Acid–Activated Receptor

The chicken ovalbumin upstream promoter-transcription factors (COUP-TFI and II) make up the most conserved subfamily of nuclear receptors that play key roles in angiogenesis, neuronal development, organogenesis, cell fate determination, and metabolic homeostasis. Although the biological functions of COUP-TFs have been studied extensively, little is known of their structural features or aspects of ligand regulation. Here we report the ligand-free 1.48 Å crystal structure of the human COUP-TFII ligand-binding domain. The structure reveals an autorepressed conformation of the receptor, where helix α10 is bent into the ligand-binding pocket and the activation function-2 helix is folded into the cofactor binding site, thus preventing the recruitment of coactivators. In contrast, in multiple cell lines, COUP-TFII exhibits constitutive transcriptional activity, which can be further potentiated by nuclear receptor coactivators. Mutations designed to disrupt cofactor binding, dimerization, and ligand binding, substantially reduce the COUP-TFII transcriptional activity. Importantly, retinoid acids are able to promote COUP-TFII to recruit coactivators and activate a COUP-TF reporter construct. Although the concentration needed is higher than the physiological levels of retinoic acids, these findings demonstrate that COUP-TFII is a ligand-regulated nuclear receptor, in which ligands activate the receptor by releasing it from the autorepressed conformation

Advances in Molecular Quantum Chemistry Contained in the Q-Chem 4 Program Package

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller–Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube

Real-time Monitoring for the Next Core-Collapse Supernova in JUNO

Core-collapse supernova (CCSN) is one of the most energetic astrophysical events in the Universe. The early and prompt detection of neutrinos before (pre-SN) and during the SN burst is a unique opportunity to realize the multi-messenger observation of the CCSN events. In this work, we describe the monitoring concept and present the sensitivity of the system to the pre-SN and SN neutrinos at the Jiangmen Underground Neutrino Observatory (JUNO), which is a 20 kton liquid scintillator detector under construction in South China. The real-time monitoring system is designed with both the prompt monitors on the electronic board and online monitors at the data acquisition stage, in order to ensure both the alert speed and alert coverage of progenitor stars. By assuming a false alert rate of 1 per year, this monitoring system can be sensitive to the pre-SN neutrinos up to the distance of about 1.6 (0.9) kpc and SN neutrinos up to about 370 (360) kpc for a progenitor mass of 30$M_{\odot}$ for the case of normal (inverted) mass ordering. The pointing ability of the CCSN is evaluated by using the accumulated event anisotropy of the inverse beta decay interactions from pre-SN or SN neutrinos, which, along with the early alert, can play important roles for the followup multi-messenger observations of the next Galactic or nearby extragalactic CCSN.Comment: 24 pages, 9 figure

Potential of Core-Collapse Supernova Neutrino Detection at JUNO

JUNO is an underground neutrino observatory under construction in Jiangmen, China. It uses 20kton liquid scintillator as target, which enables it to detect supernova burst neutrinos of a large statistics for the next galactic core-collapse supernova (CCSN) and also pre-supernova neutrinos from the nearby CCSN progenitors. All flavors of supernova burst neutrinos can be detected by JUNO via several interaction channels, including inverse beta decay, elastic scattering on electron and proton, interactions on C12 nuclei, etc. This retains the possibility for JUNO to reconstruct the energy spectra of supernova burst neutrinos of all flavors. The real time monitoring systems based on FPGA and DAQ are under development in JUNO, which allow prompt alert and trigger-less data acquisition of CCSN events. The alert performances of both monitoring systems have been thoroughly studied using simulations. Moreover, once a CCSN is tagged, the system can give fast characterizations, such as directionality and light curve

Detection of the Diffuse Supernova Neutrino Background with JUNO

As an underground multi-purpose neutrino detector with 20 kton liquid scintillator, Jiangmen Underground Neutrino Observatory (JUNO) is competitive with and complementary to the water-Cherenkov detectors on the search for the diffuse supernova neutrino background (DSNB). Typical supernova models predict 2-4 events per year within the optimal observation window in the JUNO detector. The dominant background is from the neutral-current (NC) interaction of atmospheric neutrinos with 12C nuclei, which surpasses the DSNB by more than one order of magnitude. We evaluated the systematic uncertainty of NC background from the spread of a variety of data-driven models and further developed a method to determine NC background within 15\% with {\it{in}} {\it{situ}} measurements after ten years of running. Besides, the NC-like backgrounds can be effectively suppressed by the intrinsic pulse-shape discrimination (PSD) capabilities of liquid scintillators. In this talk, I will present in detail the improvements on NC background uncertainty evaluation, PSD discriminator development, and finally, the potential of DSNB sensitivity in JUNO

Neutrino Physics with JUNO

The Jiangmen Underground Neutrino Observatory (JUNO), a 20 kton multi-purposeunderground liquid scintillator detector, was proposed with the determinationof the neutrino mass hierarchy as a primary physics goal. It is also capable ofobserving neutrinos from terrestrial and extra-terrestrial sources, includingsupernova burst neutrinos, diffuse supernova neutrino background, geoneutrinos,atmospheric neutrinos, solar neutrinos, as well as exotic searches such asnucleon decays, dark matter, sterile neutrinos, etc. We present the physicsmotivations and the anticipated performance of the JUNO detector for variousproposed measurements. By detecting reactor antineutrinos from two power plantsat 53-km distance, JUNO will determine the neutrino mass hierarchy at a 3-4sigma significance with six years of running. The measurement of antineutrinospectrum will also lead to the precise determination of three out of the sixoscillation parameters to an accuracy of better than 1\%. Neutrino burst from atypical core-collapse supernova at 10 kpc would lead to ~5000inverse-beta-decay events and ~2000 all-flavor neutrino-proton elasticscattering events in JUNO. Detection of DSNB would provide valuable informationon the cosmic star-formation rate and the average core-collapsed neutrinoenergy spectrum. Geo-neutrinos can be detected in JUNO with a rate of ~400events per year, significantly improving the statistics of existing geoneutrinosamples. The JUNO detector is sensitive to several exotic searches, e.g. protondecay via the $p\to K^++\bar\nu$ decay channel. The JUNO detector will providea unique facility to address many outstanding crucial questions in particle andastrophysics. It holds the great potential for further advancing our quest tounderstanding the fundamental properties of neutrinos, one of the buildingblocks of our Universe

2009

ABSTRACT © F e r r a t a S t o r t i F o u n d a t i o n BCL2 translocations are more frequently found in the GCB subtype, whereas 18q21 locus amplification is more common in the ABC subtype of DLBCL. 3, Design and Methods Patients We studied 327 cases of previously untreated de novo DLBCL, diagnosed between January 2002 and October 2009, and collected as part of the International DLBCL Rituxan-CHOP Consortium Program Study. These cases were analyzed for Bcl-2 protein expression, and BCL2 and MYC gene abnormalities, and gene expression profiling (GEP) was performed. All cases were reviewed by a group of hematopathologists (SMM, MAP, MBM, AT, and KHY), and the diagnoses were confirmed based on World Health Organization classification criteria. Patients with transformation from low grade lymphoma, those with composite follicular lymphoma, primary mediastinal large B-cell lymphoma, primary cutaneous and primary central nervous system DLBCL were excluded from the analysis due to the unique biological features of these types of lymphoma. All patients were adults who were negative for human immunodeficiency virus and had sufficient clinical data and clinical follow-up. Patients in this study were treated with R-CHOP (n=291, 89%) or R-CHOP-like regimens (n=36, 11%; CHOP scheme adopting different anthracyclines i.e. novantrone or epirubicin). All patients with advanced stage disease received six (92%) or eight (8%) cycles, every 21 days, with or without radiotherapy for residual disease or initial bulky disease; localized cases received at least three cycles followed by radiotherapy or six cycles without radiotherapy. The current study was approved by each of the participating centers' Institutional Review Boards, and the overall collaborative study was approved by the Institutional Review Board at The University of Texas MD Anderson Cancer Center in Houston, Texas, USA. Immunohistochemistry for Bcl-2 and cut-off determination Bcl-2 protein expression was evaluated in all patients using a monoclonal anti-Bcl-2 antibody (Clone-124, Dako, Carpinteria, CA, USA) and standard immunohistochemical methods. The formalin-fixed, paraffin-embedded tissue slides underwent deparaffinization and heat-induced antigen retrieval techniques. An endogenous biotin-blocking kit (Ventana) was used to decrease background staining. Following antigen retrieval and primary antibody incubation, the reaction was completed in a Ventana ES instrument using a diaminobenzidine immunoperoxidase detection kit (Ventana). Immunoreactivity was determined without knowledge of the patients' survival, clinical data, or GEP data. The samples were analyzed independently by a group of four hematopathologists/pathologists in addition to the hematopathologist of each of the contributing centers, and disagreements were resolved by joint review at a multi-headed microscope. An average of 300-400 cells in four to five fields were counted in the tissue microarray cores. A percentage of tumor cell staining ≥50% was considered positive after receiver operating characteristic (ROC) curve analysis was implemented to assess the discriminatory accuracy of Bcl-2 protein in recognizing patients with different overall survival (OS) and progression-free survival (PFS). The 50% value was established from the analysis of the area under the ROC curve (AUROC) and had the maximum specificity and sensibility for OS and PFS discrimination in our patients (AUROC=0.564, P=0.017 for OS and AUROC=0.564, P=0.015 for PFS). 31 Gene expression profiling analysis RNA was extracted from 327 formalin-fixed, paraffin-embedded tissue samples using a HighPure Paraffin RNA Extraction Kit (Roche Applied Science). Fifty nanograms of RNA were transcribed into cDNA, linearly amplified using the WT-Ovation™ FFPE System (Nugen), and biotin-labeled using FL-Ovation™ cDNA Biotin Module V2 (Nugen) in all cases. For GeneChip hybridization, 5 μg of WT-Ovation amplified cDNA were applied to HG-U133 Plus 2.0 GeneChips (Affymetrix) and hybridized overnight. GeneChips were washed, stained, and scanned using the Fluidic Station 450 and GeneChip Scanner 3000 (Affymetrix) according to the manufacturer's recommendations. For data analysis and classification, the microarray DQN (trimmed mean of differences of perfect match and mismatch intensities with quantile normalization) signals were generated and normalized to the quantiles of beta distribution with parameters p=1.2 and q=3 as previously described. 32 A Bayesian model was also utilized to determine the class probability. The classification model was built on the 47 paired formalin-fixed, paraffin-embedded tissue sample dataset previously generated with a confidence rate of 90-100% in fresh frozen tissue and 92-100% in formalin-fixed, paraffinembedded tissue. The same methodology developed during this study has been validated and demonstrated to be applicable by using the LLMPP dataset in the Gene Expression Omnibus (GEO) database GSE#10846 that has 181 CHOP-treated and 233 R-CHOP-treated DLBCL patients with fresh-frozen samples. 3, Validation set To validate our observations in predicting survival in an independent series of cases, we analyzed a second group of 120 archival DLBCL cases studied similarly to the first cohort except for MYC analysis that was not available (GCB 49%, ABC 40%, unclassified 11%; BCL2 translocations in 18%; Bcl-2 overexpression in 54%). All these patients had been treated with R-CHOP and the same selection criteria as those for the first cohort were applied. The clinical characteristics at presentation of the patients in the validation set were not significantly different from those of the patients in the test set. Statistical analysis Following pre-defined criteria, 33 PFS was measured from the time of diagnosis to the time of progression or death from any cause. OS was measured from the time of diagnosis to last followup or death from any cause. Only patients with a follow-up of longer than 12 months were included in the survival analysis. The actuarial probabilities of PFS and OS were determined using the Kaplan-Meier method, and differences were compared using the log-rank test. A Cox proportional-hazards model was used for multivariate analysis. The χ 2 test or Mann-Whitney test was applied to assess differences between variables. The interobserver agreement for FISH was assessed using the κ statistic; a κ value of >0.75 implied excellent agreement. All statistical calculations, except for ROC and the κ statistic which were performed with SPSS 18.0 (SPSS Inc., Chicago, IL, USA), were conducted using StatView (Abacus Concepts, Berkeley, CA, USA). Results Patients' characteristics and outcome The median age of the patients at diagnosis was 62 years (range, 18-86). Their clinical characteristics are reported in BCL2 and MYC genes in the subgroups defined by gene expression profiling Sixty patients (18.3%) had DLBCL with BCL2 gene translocations, and 50 (15.3%) had BCL2 gene amplifications. The presence of BCL2 translocations was not associated with any clinical prognostic variable at diagnosis, except for Ann Arbor Stage (70% versus 49% with stage III-IV, P=0.004), as shown in The OS and PFS rates of patients with BCL2 translocations were similar to those of patients without BCL2 translocations, irrespectively of MYC status. When we restricted the analysis to the GCB subtype, patients with BCL2 translocations alone, in the absence of MYC breaks, had a significantly worse outcome than GCB patients without BCL2 translocations (3-year PFS of 53% versus 76%, respectively; P=0.0002). The outcome of patients with BCL2 rearranged GCB subtype was similar to that of the patients with the ABC subtype of DLBCL (52%, P=0.30), but still better than that of the patients with double hit lymphomas (P<0.0001, The presence of MYC breaks alone in the 19 patients without concomitant BCL2 translocations was not associated with impaired PFS (P=0.70) or OS (P=0.66) in the whole cohort, but was associated with inferior OS (P=0.03), but not PFS (P=0.22), in patients with GCB-DLBCL (only 9 with isolated MYC breaks). As shown in BCL2 gains were not prognostic in any of the subgroups of patients. Particular consideration of high-level amplifications was of no additional prognostic value. Bcl-2 protein expression, clinical characteristics, fluorescence in situ hybridization and gene expression profiling None of the common clinical characteristics of our patients at the time of presentation was significantly associated with Bcl-2 protein expression except age, with older patients more often being Bcl-2 positive (≥60 years old, P=0.02). Bcl-2 protein expression in GEP-and FISHdefined subgroups is shown in © F e r r a t a S t o r t i F o u n d a t i o n patients without the BCL2 translocation (range, 0-100%; median 60%). Bcl-2 protein expression was significantly associated with worse PFS (P=0.01) and OS (P=0.02) in the whole cohort, but when patients were divided according to GEPdefined subtypes, we observed that higher Bcl-2 expression was associated with significantly inferior PFS in the GCB subgroup (P=0.04), but not in the ABC subgroup (P=0.57), as shown in Multivariate analysis Multivariate analysis of all 137 patients with the GCB subtype of DLBCL showed that BCL2 translocations (HR 0.40, 95% CI: 0.18-0.89; P=0.02), but not Bcl-2 expression (HR 1.01, 95% CI: 0.45-2.21; P=0.98), MYC breaks (HR 0.25, 95% CI: 0.10-0.59; P=0.001), and IPI score (HR 0.41, 95% CI: 0.20-0.84; P=0.01), were independently associated with patients' outcome. Results were not modified after each molecular feature was computed with age as a continuous parameter. C. Visco et al. 258 haematologica | 2013; 98(2) Overall survival Progression-free survival Four-hundred and forty-four genes were found to be differentially expressed (>1.5 fold and P<0.005) in DLBCL patients with or without BCL2 translocations including both GCB and ABC subtypes. In the GCB group, however, only 43 genes were differentially expressed among patients with and without BCL2 translocations ( Interestingly, a number of genes overexpressed in the BCL2 translocated group are involved in the control of angiogenesis and the inflammatory response (AIMP1, PPIA, and ALOX), while others are involved in promoting apoptosis or regulating B-cell signaling (STK17A, RAL-GPS2, NCOA3, STRBP, and ZNF117). 35-37 C. Visco et al. 260 haematologica | 2013; 98(2) © F e r r a t a S t o r t i F o u n d a t i o n Discussion We addressed the clinical impact of BCL2 aberrations and their relationship to Bcl-2 protein expression in a large series of patients with DLBCL homogeneously treated with R-CHOP, with known MYC gene status and molecularly characterized according to GEP analysis. We were able to establish the role of the BCL2 gene in different subtypes of DLBCL, irrespectively of concomitant MYC aberrations. We found that isolated BCL2 translocations, in the absence of MYC breaks, were associated with a poor outcome in the subset of patients with GCB-DLBCL, and that the prognosis of these patients was similar to that of patients with ABC-DLBCL. The concomitant presence of MYC breaks (double hit lymphoma) further worsened the outcome of these patients. The role of Bcl-2 protein expression appeared dependent on its association with BCL2 translocations, as outlined by multivariate analysis and survival curves As determined by FISH break apart probe analysis, the overall frequency of BCL2 translocations in de novo DLBCL was 18.3%. The BCL2 translocations were almost exclusively associated with GCB-DLBCL, found in 34.5% of cases The impact of BCL2 translocations on survival in our series could not be explained by differences in the clinical features of the patients because there was no association between the presence of BCL2 translocations and IPI risk groups (P=0.90, A C B FIGURE A COLORI SOLO ONLINE © F e r r a t a S t o r t i F o u n d a t i o n with isolated BCL2 or MYC lesions. Confirming previous findings, In this series, Bcl-2 protein was overexpressed in half of the patients with GCB-DLBCL and in 72% of patients with ABC-DLBCL 18,39 However, Bcl-2 overexpression had prognostic value only in the GCB subtype, as already observed by others in the era of R-CHOP therapy. Iqbal et al. 22 Secondly, Bcl-2 protein expression in Iqbal's study was significantly associated with adverse clinical prognostic factors (stage III-IV, elevated lactate dehydrogenase, high IPI risk group) in GCB-DLBCL, which was not the case in our study. Finally, no mention was made about exclusion of possibly confounding DLBCL subtypes such as double hit lymphoma, primary cutaneous or primary central nervous system DLBCL. We also acknowledge that different findings in the literature regarding BCL2 rearrangements or protein expression could very well be related to lack of uniformity between different studies in terms of Bcl-2 staining and scoring. Moreover, patients' characteristics in the different series, differences in the management of the cases as they were not in clinical trials, data collection regarding outcome, and sometimes short follow-up times may also have contributed to different results. Our GEP analysis revealed that patients with BCL2 translocations substantially differed with respect to important recurrent oncogenic events, which may contribute to the adverse outcome of the subgroup of GCB-DLBCL patients with BCL2 translocations. Up-regulation of the BCL11A gene occurred exclusively in the group of patients with BCL2 translocations We confirm that the outcome of GCB-DLBCL patients should be interpreted in the context of abnormalities of the MYC and BCL2 genes. While the MYC rearrangement is quite rare, it is rarely found as the sole genetic abnormality, and its clinical relevance is mainly related to a double hit mechanism, BCL2 rearrangements are present in a considerable fraction of patients with the GCB subtype who have similar outcomes to those of patients with the ABC subtype. Our results confirm that the GCB and ABC subtypes of DLBCL have distinct pathogeneses, and support the rationale for further classification of different subgroups. © F e r r a t a S t o r t i F o u n d a t i o n Funding CV is a hematologist supported by Sa

Optimasi Portofolio Resiko Menggunakan Model Markowitz MVO Dikaitkan dengan Keterbatasan Manusia dalam Memprediksi Masa Depan dalam Perspektif Al-Qur`an

Risk portfolio on modern finance has become increasingly technical, requiring the use of sophisticated mathematical tools in both research and practice. Since companies cannot insure themselves completely against risk, as human incompetence in predicting the future precisely that written in Al-Quran surah Luqman verse 34, they have to manage it to yield an optimal portfolio. The objective here is to minimize the variance among all portfolios, or alternatively, to maximize expected return among all portfolios that has at least a certain expected return. Furthermore, this study focuses on optimizing risk portfolio so called Markowitz MVO (Mean-Variance Optimization). Some theoretical frameworks for analysis are arithmetic mean, geometric mean, variance, covariance, linear programming, and quadratic programming. Moreover, finding a minimum variance portfolio produces a convex quadratic programming, that is minimizing the objective function ðð¥with constraintsð ð 𥠥 ðandð´ð¥ = ð. The outcome of this research is the solution of optimal risk portofolio in some investments that could be finished smoothly using MATLAB R2007b software together with its graphic analysis