Miracle-dz/UniFAR-FTUs huggingface dataset:
CD274 (PDL1) and JAK2 genomic amplifications in pulmonary squamous‐cell and adenocarcinoma patients

CD274 (PDL1) and JAK2 (9p24.1) gene amplifications have been recently described in pulmonary carcinomas in association with programmed death‐ligand 1 (PD‐L1) expression. Furthermore, PTEN loss has been explored preclinically in relation to PD‐L1 expression. Our aim was to determine whether these genomic alterations affect PD‐L1 expression levels in non‐small‐cell lung cancer.
Pricing European options and currency options by time changed mixed fractional Brownian motion with transaction costs

This study investigates a new formula for option pricing with transaction costs in a discrete time setting. The value of the financial assets is based on time-changed mixed fractional Brownian motion (MFBM) model. The pricing method is obtained for European call option using the time-changed MFBM model in a discrete time setting. Particularly, the minimal value Cmin(t,St) of an option respect to transaction costs is obtained. Furthermore, the new model for pricing currency option is presented by utilizing the time-changed MFBM model. In addition, the impact of time step Δt, Hurst parameter H and transaction costs α are also investigated, which substantiate that these parameters play a significant role in our pricing formula. Finally, the empirical studies and the simulation findings corroborate the theoretical bases and indicate the time-changed MFBM is a satisfactory model.
Characterization of Resistance, Evaluation of the Attractiveness of Plant Odors, and Effect of Leaf Color on Different Onion Cultivars to Onion Thrips (Thysanoptera: Thripidae)

ABSTRACT Onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae), is a worldwide pest of onion, Allium cepa L. In field studies on onion resistance conducted in 2007 and 2008 using 49 cultivars, 11 showed low leaf damage by T. tabaci. In laboratory studies, the 11 cultivars, along with two susceptible checks and four additional cultivars, were evaluated to characterize resistance to T. tabaci and to determine if color and/or light reflectance were associated with resistance to T. tabaci. No-choice tests were performed with adults and the numbers of eggs and larvae were counted on each cultivar after three and 10 d, respectively. In choice tests in which all cultivars were planted together in a circle in a single pot, 100 adults were released and the number of adults on each plant was evaluated 24 h later. The behavioral response of walking T. tabaci adults to plant odors was studied in a glass Y-tube olfactometer. The reflectance spectrum of leaves was measured using a UV-VTS spectrophotometer. Results indicate that resistant cultivars showed an intermediate-high antibiotic effect to T. tabaci and all of them showed a very strong antixenotic effect. There were no significant preferences in the response of walking T. tabaci adults to plant odors. The two susceptible cultivars had the highest values of leaf reflectance for the first (275–375 nm) and second (310–410 nm) theoretical photopigment-system of T. tabaci, and these values were significantly different from most resistant cultivars. These results suggest a strong response of T. tabaci to onion cultivars with higher reflectance in the ultraviolet range (270–400 nm). Overall, these results appear promising in helping to identify categories of resistance to T. tabaci in onions that can be used in breeding programs.
A glycosylphosphatidylinositol protein anchor from procyclic stage Trypanosoma brucei: lipid structure and biosynthesis.

Cells of the insect (procyclic) stage of the life cycle of the African trypanosome, Trypanosoma brucei, express an abundant stage‐specific glycosylated phosphatidylinositol (GPI) anchored glycoprotein, the procyclic acidic repetitive protein (PARP). The anchor is insensitive to the action of bacterial phosphatidylinositol‐specific phospholipase C (PI‐PLC), suggesting that it contains an acyl‐inositol. We have recently described the structure of a PI‐PLC resistant glycosylphosphatidylinositol, PP1, which is specific to the procyclic stage, and have presented preliminary evidence that the phosphatidylinositol portion of the protein‐linked GPI on PARP has a similar structure. In this paper we show, by metabolic labelling with [3H]fatty acids, that the PARP anchor contains palmitate esterified to inositol, and stearate at sn‐1, in a monoacylglycerol moiety, a structure identical to PP1. Using pulse‐chase labelling, we show that both fatty acids are incorporated into the GPI anchor from a large pool of metabolic precursors, rather than directly from acyl‐CoA. We also demonstrate that the addition of the GPI anchor moiety to PARP is dependent on de novo protein synthesis, excluding the possibility that incorporation of fatty acids into PARP can occur by a remodelling of pre‐existing GPI anchors. Finally we show that the phosphatidylinositol (PI) species that are utilized for GPI biosynthesis are a subpopulation of the cellular PI molecular species. We propose that these observations may be of general validity since several other eukaryotic membrane proteins (e.g. human erythrocyte acetylcholine esterase and decay accelerating factor) have been reported to contain palmitoylated inositol residues.
Effects of mutations within the 3' orf open reading frame region of human T-cell lymphotropic virus type III (HTLV-III/LAV) on replication and cytopathogenicity

Mutations that eliminated the ability of the human T-cell lymphotropic virus type III to produce the 27-kilodalton 3' orf product did not eliminate the ability of the virus to replicate in and kill T4+ cells. A mutant carrying a mutation that deleted carboxy-terminal sequences from the envelope gene as well as the 3' orf sequences retained the ability to kill T4+ lymphocytes, but had a retarded replication rate.
Hypomethylation associated enhanced transcription of trefoil factor-3 mediates tamoxifen-stimulated oncogenicity of ER+ endometrial carcinoma cells

Tamoxifen (TAM) is widely used as an adjuvant therapy for women with breast cancer (BC). However, TAM possesses partial oestrogenic activity in the uterus and its use has been associated with an increased incidence of endometrial carcinoma (EC). The molecular mechanism for these observations is not well understood. Herein, we demonstrated that forced expression of Trefoil factor 3 (TFF3), in oestrogen receptor-positive (ER+) EC cells significantly increased cell cycle progression, cell survival, anchorage-independent growth, invasiveness and tumour growth in xenograft models. Clinically, elevated TFF3 protein expression was observed in EC compared with normal endometrial tissue, and its increased expression in EC was significantly associated with myometrial invasion. TAM exposure increased expression of TFF3 in ER+ EC cells and its elevated expression resulted in increased oncogenicity and invasiveness. TAM-stimulated expression of TFF3 in EC cells was associated with hypomethylation of the TFF3 promoter sequence and c-JUN/SP1-dependent transcriptional activation. In addition, small interfering (si) RNA-mediated depletion or polyclonal antibody inhibition of TFF3 significantly abrogated oncogenicity and invasiveness in EC cells consequent to TAM induction or forced expression of TFF3. Hence, TAM-stimulated upregulation of TFF3 in EC cells was critical in promoting EC progression associated with TAM treatment. Importantly, inhibition of TFF3 function might be an attractive molecular modality to abrogate the stimulatory effects of TAM on endometrial tissue and to limit the progression of EC.
Principles of branch dynamics governing shape characteristics of cerebellar Purkinje cell dendrites

Neurons develop dendritic arbors in cell type-specific patterns. Using growing Purkinje cells in culture as a model, we performed a long-term time-lapse observation of dendrite branch dynamics to understand the rules that govern the characteristic space-filling dendrites. We found that dendrite architecture was sculpted by a combination of reproducible dynamic processes, including constant tip elongation, stochastic terminal branching, and retraction triggered by contacts between growing dendrites. Inhibition of protein kinase C/protein kinase D signaling prevented branch retraction and significantly altered the characteristic morphology of long proximal segments. A computer simulation of dendrite branch dynamics using simple parameters from experimental measurements reproduced the time-dependent changes in the dendrite configuration in live Purkinje cells. Furthermore, perturbation analysis to parameters in silico validated the important contribution of dendritic retraction in the formation of the characteristic morphology. We present an approach using live imaging and computer simulations to clarify the fundamental mechanisms of dendrite patterning in the developing brain.
An improved LSSVM based on multi-scale wavelet kernel function

This work presents a methodology for the problem of the original Least Square Support Vector Machine (LSSVM) algorithm could not reach desired precision in multi-scale regression. In this methodology, we choose Mexican hat wavelet function as the kernel function of LSSVM firstly, and then the global optimum of the multi-scale regression modeling problem can be obtained by solving a quadratic programming problem. The regression model can effectively approximate multi-scale signals. The effectiveness of the proposed algorithm is validated by computer simulation results.
Good medical practice in antipsychotic pharmacotherapy

Schizophrenia requires a comprehensive treatment programme that augments pharmacotherapy, such as antipsychotic drugs, with psychological (education) and social (rehabilitation) therapies, Antipsychotic drugs, however, are still Fundamental in the treatment of schizophrenia. When administered correctly, these drugs not only reduce psychotic symptoms but can also prevent relapse, which prevents hospitallzation and facilitates psychosocial re-integration. Unfortunately, the type of drug and dosing schedule used are often inappropriate. The antipsychotic drug prescribed should be decided on an individual patient basis according to the experiences the patient has had with previous treatments. Choosing the right drug is a key to improving compliance and treatment outcome. Additionally, antipsychotic drugs should be prescribed at an early stage, in order to increase the likelihood of a favourable treatment outcome, and for long enough to reduce the risk of relapse. The efficacy and tolerability of antipsychotic drugs have been studied extensively, and treatment guidelines have now been developed, in particular from the Bruges Consensus Conference and the American Psychiatric Association, to optimize the diagnosis and treatment of schizophrenia. The use of novel antipsychotics, which have better therapeutic and safety profiles than traditional antipsychotics, together with educational programmes should improve compliance with antipsychotic drugs and thus improve treatment outcomes for schizophrenic patients. Treatment strategies to be used at the various stages of schizophrenia have been recommended, together with preferred options for managing lack of response or side effects.
CRESCIMENTO ECONÔMICO BRASILEIRO E EMISSÃO DE CO2 BRAZILIAN ECONOMIC GROWTH AND THE EMISSION OF CO2

Resumo: O objetivo deste trabalho e verificar empiricamente a relacao entre o produto per capita e a emissao de CO2 no Brasil no periodo de 1980 a 2006. O escopo do trabalho se restringiu a este recurso natural devido ao seu papel para a atividade economica, como importante insumo no processo produtivo na matriz energetica brasileira. Dentre os principais resultados, destaca-se que existe uma relacao de longo prazo e de causalidade simultânea entre as variaveis PIB per capita e emissao de CO2. Essa evidencia, somada ao fato de que as series utilizadas nao eram estacionarias em nivel, impossibilitou estimar a Curva de Kuznets Ambiental (EKC), que e a principal base teorica utilizada nos trabalhos empiricos relacionados ao tema. Nesse sentido, um modelo VAR/VEC foi estimado e a elasticidade encontrada entre crescimento economico e emissao de CO2 foi de 7,32, ou seja, no longo prazo, podemos inferir que um aumento de 1% no PIB per capita eleva em 7,32%, as emissoes de CO2 decorrentes da utilizacao de petroleo. Palavras-chave: Curva de Kuznets Ambiental, crescimento economico e emissao.
1st Evidence-based Italian Consensus Conference on Cytoreductive Surgery and Hyperthermic Intraperitoneal Chemotherapy for Peritoneal Carcinosis from Ovarian Cancer

Ovarian cancer (OC) remains relatively rare, although it is among the top 4 causes of cancer death for women younger than 50. The aggressive nature of the disease and its often late diagnosis with peritoneal involvement have an impact on prognosis. The current scientific literature presents ambiguous or uncertain indications for management of peritoneal carcinosis (PC) from OC, both owing to the lack of sufficient scientific data and their heterogeneity or lack of consistency. Therefore, the Italian Society of Surgical Oncology (SICO), the Italian Society of Obstetrics and Gynaecology, the Italian Association of Hospital Obstetricians and Gynaecologists, and the Italian Association of Medical Oncology conducted a multidisciplinary consensus conference (CC) on management of advanced OC presenting with PC during the SICO annual meeting in Naples, Italy, on September 10-11, 2015. An expert committee developed questions on diagnosis and staging work-up, indications, and procedural aspects for peritonectomy, systemic chemotherapy, and hyperthermic intraperitoneal chemotherapy for PC from OC. These questions were provided to 6 invited speakers who answered with an evidence-based report. Each report was submitted to a jury panel, representative of Italian experts in the fields of surgical oncology, gynecology, and medical oncology. The jury panel revised the reports before and after the open discussion during the CC. This article is the final document containing the clinical evidence reports and statements, revised and approved by all the authors before submission.
Next-generation sequencing of pharmacogenes: a critical analysis focusing on schizophrenia treatment

Introduction Because of the unmet needs of current pharmacotherapy for schizophrenia, antipsychotic pharmacogenetic research is of utmost importance. However, to date, few clinically applicable antipsychotic pharmacogenomic alleles have been identified. Nonetheless, next-generation sequencing technologies are expected to aid in the identification of clinically significant variants for this complex phenotype. The aim of this study was therefore to critically examine the ability of next-generation sequencing technologies to reliably detect variation present in pharmacogenes. Materials and methods Candidate antipsychotic pharmacogenes and very important pharmacogenes were identified from the literature and the Pharmacogenomics Knowledgebase. Thereafter, the percentage sequence similarity observed between these genes and their corresponding pseudogenes and paralogues, as well as the percentage low-complexity sequence and GC content of each gene, was calculated. These sequence attributes were subsequently compared with the ‘inaccessible’ regions of these genes as described by the 1000 Genomes Project. Results It was found that the percentage ‘inaccessible genome’ correlated well with GC content (P=9.96×10−5), low-complexity sequence (P=0.0002) and the presence of pseudogenes/paralogues (P=8.02×10−7). In addition, it was found that many of the pharmacogenes were not ideally suited to next-generation sequencing because of these genomic complexities. These included the CYP and HLA genes, both of which are of importance to many fields of pharmacogenetics. Conclusion Current short read sequencing technologies are unable to comprehensively capture the variation in all pharmacogenes. Therefore, until high-throughput sequencing technologies advance further, it may be necessary to combine next-generation sequencing with other genotyping strategies.
Effect of concentration on anammox nitrogen removal rate in a moving bed biofilm reactor

Anammox biomass enriched in a moving bed biofilm reactor (MBBR) fed by actual sewage sludge reject water and synthetically added was used to study the total nitrogen (TN) removal rate of the anammox process depending on bicarbonate ( ) concentration. MBBR performance resulted in the maximum TN removal rate of 1100 g N m−3 d−1 when the optimum concentration (910 mg L−1) was used. The average reaction ratio of removal, production and removal were 1.18/0.20/1. When the concentration was increased to 1760 mg L−1 the TN removal rate diminished to 270 g N m−3 d−1. The process recovered from bicarbonate inhibition within 1 week. The batch tests performed with biomass taken from the MBBR showed that for the concentration of 615 mg L−1 the TN removal rate was 3.3 mg N L−1 h−1, whereas for both lower (120 mg L−1) and higher (5750 mg L−1) concentrations the TN removal rates were 2.3 (±0.15) and 1.6 (±0.12) mg N L−1 d−1, respectively. PCR and DGGE analyses resulted in the detection of uncultured Planctomycetales bacterium clone P4 and, surprisingly, low-oxygen-tolerant aerobic ammonia oxidizers. The ability of anammox bacteria for mixotrophy was established by diminished amounts of nitrate produced when comparing the experiments with an organic carbon source and an inorganic carbon source.
Voltage‐clamp analysis of gap junctions between embryonic muscles in Drosophila.

1. Intercellular communication between embryonic muscle fibres was examined in Drosophila melanogaster. 2. Injection of fluorescent dye revealed extensive coupling between muscle fibres which form a uniform communicating arrangement of cells without restriction at the segmental borders. 3. Dye transfer was blocked by octanol and membrane depolarization suggesting that it is mediated by gap junctions. 4. Double voltage‐clamp experiments from cell pairs in situ showed that the ionic coupling is sensitive to the voltage difference between the cytoplasm and the extracellular space (transmembrane voltage, Vi‐o) as well as between the cells (transjunctional voltage, Vj). 5. In steady‐state conditions, the gap conductance (gj) was maximal for hyperpolarized Vi‐o and decreased progressively to near zero as Vi‐o became more positive than ‐50 mV. 6. Gap conductance decreased from a maximal value as Vj increased either in the positive or negative direction (by depolarizing or hyperpolarizing, respectively, one of the cells from a holding potential of ‐60 mV). In both cases, gj asymptotically approached a non‐zero residual value which was different for negative and positive Vj (about 20% of the maximal conductance for negative transmembrane potentials and 10% for positive values). 7. Application of octanol (1 mM) resulted in an almost complete and reversible block of gj.
Let There Be Light: A tutorial on optogenetics.

The nervous system of the human brain consists of diverse types of neurons that are interconnected. The enormous number and heterogeneity of neurons and their connections has made understanding the brain a difficult task, and it has long been a dream in basic and clinical neuroscience to be able to not only read the brain? s neuronal activity but also to have control over distinct sets of neurons.
Reconstitution of the Brain Mixed Function Oxidase System: Purification of NADPH‐Cytochrome P450 Reductase and Partial Purification of Cytochrome P450 from Whole Rat Brain

Abstract: NADPH‐cytochrome P450 reductase was purified to apparent homogeneity and cytochrome P450 partially purified from whole rat brain. Purified reductase from brain was identical to liver P450 reductase by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis and western blot techniques. Kinetic studies using cerebral P450 reductase reveal Km values in close agreement with those determined with enzyme purified from rat liver. Moreover, the brain P450 reductase was able to function successfully in a reconstituted microsomal system with partially purified brain cytochrome P450 and with purified hepatic P450c (P4501A1) as measured by 7‐ethoxycoumarin and γ‐ethoxyresorufin O‐deethylation. Our results indicate that the reductase and P450 components may interact to form a competent drug metabolism system in brain tissue.
WWOX in biological control and tumorigenesis

The WW domain‐containing oxidoreductase (WWOX) gene is located at 16q23.1–16q23.2, a region that spans the second most common human fragile site, FRA16D. The WWOX protein contains two N‐terminal WW domains and a central short chain oxidoreductase‐like domain. In the last few years, considerable amount of data have shown inactivation of WWOX in a variety of human malignancies. Moreover, interacting partners have been identified biochemically that define, at least in part, the molecular mechanism of WWOX action. Recently, we demonstrated that targeted deletion of the Wwox gene in the mouse led to increased incidence of spontaneous and chemically induced tumor formation, thereby providing the first in vivo evidence that WWOX is a bona fide tumor suppressor. This review focuses on the most recent progress in understanding WWOX function as a tumor suppressor. J. Cell. Physiol. 212: 307–310, 2007. © 2007 Wiley‐Liss, Inc.
Platinum Group Metal Flows of Europe, Part 1

In this article, we analyze flows of the platinum group metals (PGMs) platinum, palladium, and rhodium and the environmental impacts associated with their supply in Europe. A model of the use of PGMs in Europe has been developed, and this is combined with a model of environmental pressures related to PGM production.
Linkage Models about Energy Consumption and Economic Growth in China

Energy sources is the headspring power and physical base of the development of social productivity.The deficiency of energy sources has became the bottle-neck restrict of durative increase of Chinese economy.Besides increasing the power to empolder energy sources and increasing consumption of energy sources,reducing expenditure of energy sources and increasing the ratio of using of energy sources are useful approaches to increase energy sources supply correspondingly.This essay designs a new econometrical model by production function of Cobb-Douglas,opens out the relationship of external inverse proportion between energy sources consumption and economy increase by time series theory and methods and bringing forward the policy suggestions that could keep the reasonable proportion and benign circle of the increase of energy sources consumption and economy increase.