nils-herrmann/clean_scirepeval huggingface dataset:
PD L1 is upregulated by EBV driven LMP1 through NF kB pathway and correlates with poor prognosis in natural killer/T cell lymphoma
Venue: Journal of Hematology Oncology

BackgroundNatural killer/T cell lymphoma (NKTCL) is an Epstein Barr virus (EBV) associated, highly aggressive lymphoma. Treatment outcome remains sub optimal, especially for advanced stage or relapsed diseases. Programmed cell death receptor 1 (PD 1) and PD ligand 1 (PD L1) have become promising therapeutic targets for various malignancies, but their role in the pathogenesis and their interactions with EBV in NKTCL remains to be investigated.MethodsExpression of PD L1 was measured in NK 92 (EBV negative) and SNK 6 (EBV positive) cells by western blot, quantitative real time PCR and enzyme linked immunosorbent assay, and flow cytometry, respectively. Latent membrane protein 1 (LMP1) harboring lentiviral vectors were transfected into NK 92 cells to examine the correlation between LMP1 and PD L1 expression. Proteins in the downstream pathways of LMP1 signaling were measured in NK 92 cells transfected with LMP1 harboring or negative control vectors as well as in SNK 6 cells. PD L1 expression on tumor specimens and serum concentration of soluble PD L1 were collected in a retrospective cohort of patients with Ann Arbor stage I~II NKTCL, and their prognostic significance were analyzed.ResultsExpression of PD L1 was significantly higher in SNK 6 cells than in NK 92 cells, at both protein and mRNA levels. Expression of PD L1 was remarkably upregulated in NK 92 cells transfected with LMP1 harboring lentiviral vectors compared with those transfected with negative control vectors. Proteins in the MAPK/NF kB pathway were upregulated in LMP1 expressing NK 92 cells compared with the negative control. Selective inhibitors of those proteins induced significant downregulation of PD L1 expression in LMP1 expressing NK 92 cells as well as in SNK 6 cells. Patients with a high concentration of serum soluble PD L1 =3.4 ng/ml) or with a high percentage of PD L1 expression in tumor specimens =38 exhibited significantly lower response rate to treatment and remarkably worse survival, compared with their counterparts. A high concentration of serum soluble PD L1 and a high percentage of PD L1 expression in tumor specimens were independent adverse prognostic factors among patients with stage I~II NKTCL.ConclusionsPD L1 expression positively correlated LMP1 expression in NKTCL, which was probably mediated by the MAPK/NF kB pathway. PD L1 expression in serum and tumor tissues has significant prognostic value for early stage NKTCL.
Pediatric type nodal follicular lymphoma: a biologically distinct lymphoma with frequent MAPK pathway mutations.
Venue: Blood

Pediatric type nodal follicular lymphoma (PTNFL) is a variant of follicular lymphoma (FL) characterized by limited stage presentation and invariably benign behavior despite often high grade histological appearance. It is important to distinguish PTNFL from typical FL in order to avoid unnecessary treatment; however, this distinction relies solely on clinical and pathological criteria, which may be variably applied. To define the genetic landscape of PTNFL, we performed copy number analysis and exome and/or targeted sequencing of 26 PTNFLs (16 pediatric and 10 adult) The most commonly mutated gene in PTNFL was MAP2K1, encoding MEK1, with a mutation frequency of 43% All MAP2K1 mutations were activating missense mutations localized to exons 2 and 3, which encode negative regulatory and catalytic domains, respectively. Missense mutations in MAPK1 (2/22) and RRAS (1/22) were identified in cases that lacked MAP2K1 mutations. The second most commonly mutated gene in PTNFL was TNFRSF14, with a mutation frequency of 29% similar to that seen in limited stage typical FL (P .35) PTNFL was otherwise genomically bland and specifically lacked recurrent mutations in epigenetic modifiers (eg, CREBBP, KMT2D) Copy number aberrations affected a mean of only 0.5% of PTNFL genomes, compared with 10% of limited stage typical FL genomes (P .02) Importantly, the mutational profiles of PTNFLs in children and adults were highly similar. Together, these findings define PTNFL as a biologically and clinically distinct indolent lymphoma of children and adults characterized by a high prevalence of MAPK pathway mutations and a near absence of mutations in epigenetic modifiers.
The role of HGF/c MET signaling pathway in lymphoma
Venue: Journal of Hematology Oncology

Inappropriate activation of c mesenchymal epithelial transition (MET) the receptor tyrosine kinase (RTK) for hepatocyte growth factor (HGF) has been implicated in tumorigenesis and represented a promising therapeutic target for developing anticancer agents. In contrast to other solid tumors, there are limited data describing the functional role of HGF/c MET signaling pathway in lymphoma. In the current review, we summarize recent findings about the expression, cellular mechanisms/functions, and therapeutic application of HGF/c MET in different types of lymphoma, especially B cell lymphoma, T and NK cell lymphoma, and Hodgkin lymphoma. We also discuss the existing problems and future directions about studying the HGF/c MET pathway in lymphoma cells.
Rationales for a Multi Epitope Approach in an Autologous Renal Cell Cancer Tumor Vaccine

We report about a study according to a detailed characterization of an autologous tumor vaccine already used successfully in the immune therapy of renal cell carcinoma (RCC) The original paper was published in Onco Targets Therapy in 2016. This short communication summarizes the contents of the respective publication as well as shows new results of additional investigations by FACS analysis.  A total of 133 tumor cell lysates (TCL) were investigated by ELISA, Western blots, topological proteomics and FACS analysis.  A total of 36 tumor associated antigens (TAA) and cellular marker proteins were considered for analysis, whereof none was detectable in each tumor lysate. Moreover, the coincidental presence of potential danger signals was shown for HSP 60 and 70.  In conclusion the verified tumor heterogeneity indicates the need for a multi epitope approach for the successful immunotherapy in renal cell carcinoma.
An adenoviral cancer vaccine co encoding a tumor associated antigen together with secreted 4 1BBL leads to delayed tumor progression.
Venue: Vaccine

Previous studies have shown promising results when using an agonistic anti 4 1BB antibody treatment against established tumors. While this is promising, this type of treatment can induce severe side effects. Therefore, we decided to incorporate the membrane form of 4 1BB ligand (4 1BBL) in a replicative deficient adenovirus vaccine expressing the invariant chain (Ii) adjuvant fused to a tumor associated antigen (TAA) The Ii adjuvant increases and prolongs TAA specific CD8+ T cells as previously shown and local expression of 4 1BBL was chosen to avoid the toxicity associated with systemic antibody administration. Furthermore, adenovirus encoded 4 1BBL expression has previously been successfully used to enhance responses toward Plasmodium falciparum and Influenza A antigens. We showed that the incorporation of 4 1BBL in the adenovirus vector led to surface expression of 4 1BBL on antigen presenting cells, but it did not enhance T cell responses in mice towards the Ii linked antigen. In tumor bearing mice, our vaccine was found to decrease the frequency of TAA specific CD8+ T cells, but this difference did not alter the therapeutic efficacy. In order to reconcile our findings with the previous reports of increased anti cancer efficacy using systemically delivered 4 1BB agonists, we incorporated a secreted version of 4 1BBL (Fc 4 1BBL) in our vaccine and co expressed it with the Ii linked to TAA. In tumor bearing mice, this vaccine initially delayed tumor growth and slightly increased survival compared to the vaccine expressing the membrane form of 4 1BBL. Accordingly, secreted 4 1BBL co encoded with the Ii linked antigen may offer a simplification compared to administration of drug and vaccine separately.
Making the Most Beautiful Experiment: Reconstructing Gassiot's Cascade

Iwan Rhys Morus investigates the electrical performances of Charles Gassiot, who demonstrated his electrical coil, and especially its most famous instantiation as the cascade, to numerous public audiences through the 1850s. Morus considers the extensive knowledge both technical and scientific that was required to stage the cascade demonstrations and reveals the numerous networks of production that contributed to it. In doing this, and in revealing the complex skills required to make such performances work, Morus also shows how these popular demonstrations fed back into the skills needed for scientific experimentation and claims that without them late Victorian physics would have lacked the expertise it needed to investigate.
Short term distribution system state forecast based on optimal synchrophasor sensor placement and extreme learning machine
Venue: 2016 IEEE Power and Energy Society General Meeting (PESGM)

This paper proposes an approach for distribution system state forecasting, which aims to provide an accurate and high speed state forecasting with an optimal synchrophasor sensor placement (OSSP) based state estimator and an extreme learning machine (ELM) based forecaster. Specifically, considering the sensor installation cost and measurement error, an OSSP algorithm is proposed to reduce the number of synchrophasor sensor and keep the whole distribution system numerically and topologically observable. Then, the weighted least square (WLS) based system state estimator is used to produce the training data for the proposed forecaster. Traditionally, the artificial neural network (ANN) and support vector regression (SVR) are widely used in forecasting due to their nonlinear modeling capabilities. However, the ANN contains heavy computation load and the best parameters for SVR are difficult to obtain. In this paper, the ELM, which overcomes these drawbacks, is used to forecast the future system states with the historical system states. The proposed approach is effective and accurate based on the testing results.
Growth and yield of summer groundnut (Arachis hypogaea L. as influenced by foliar application of water soluble fertilizer

The field experiment was undertaken at the District Seed Farm, Kalyani at Bidhan Chandra Krishi Viswavidyalaya, Nadia, West Bengal during summer season of 2012 and 2013 to study the growth and yield of summer groundnut as influenced by application of water soluble foliar grade fertilizer. Application of liquid grade fertilizerat early growth stage up to 45 DAE did not influence the plant height and dry matter production significantly, but towards maturity varied significantly (P a%0$ 0.05) Crop growth rate was faster at early part of the crop age and gradually slows at later part towards maturity. Foliar application of water soluble fertilizer along with RDF 85% had the significant (P a%0$ 0.05) influence to increase the number of pods per plant, but shelling percentage and hundred kernel weight did not vary significantly. Liquid grade fertilizer either starter dose or booster dose or in both had the positive response to increased the groundnut pod yield up to 4 6 over RDF only. The crop was equally responsive in increasing the pod yield, when RDF was reduced by 15% along with foliar application of liquid grade fertilizer. The foliar application of water soluble fertilizer was not the substitute to soil applied inorganic fertilizer. Instead, foliar supplementation of nutrients showed positive response to increase the pod yield, in addition to the fertilizers added to soil. Gross return decreased with reduction in amount of RDF applied for the crop, but gross return increased, when water soluble foliar grade inorganic fertilizer was supplemented with RDF. The maximum gross return of `150399 was obtained. The results obtained from correlation analysis carried out to examine the linear relationship between pod yields with different plant characters. Data obtained in case of dry matter of the plant was 0.995 and 0.997 in the respective years at 1% level of significance. Thus, it was concluded that dry matter content of plant is solely responsible over the yield increase in groundnut and foliar application of inorganic fertilizers in addition to that in soil has helped in better adsorption of nutrients in adequate amount by the crop.
Oral candida infection among HIV patients at Kilimanjaro Christian Medical Centre in northern, Tanzania

Oral candidiasis has been a global health challenge especially in immunocompromised patients particularly with HIV infection. Though the incidence and prevalence of opportunistic infections have been reduced due to the use of anti retroviral therapy (ART) oral candidiasis remains the most frequently HIV associated oral lesion in Tanzania. This study aimed at determining the prevalence of oral candida infection in HIV positive patients and investigate the relationship between oral manifestations and the level of immunosuppression.  This study was carried out at Kilimanjaro Christian Medical Centre in Moshi, Tanzania. The study included 314 HIV patients with complete clinical results records who were diagnosed with HIV and who were on ARV and attending the hospital for care and treatment.  Prevalence of oral candida was 42.0% (132/314) Age group 6 27 years accounted for half of the infections (49/98) A significantly higher prevalence of candida infection (66.7% 24/36) was obseved among patients with 500 cells/ul (Chi square kh 2 =14.9, p =0.001) The mean CD4+T cell counts in HIV patients infected with oral candida was lower (523+ 35) than patients without oral candida infection (645+ 31 cells/ul) (ANOVA, p 0.009) The mean CD4+ T cell count among HIV patients on ART and those not on ART was not statistically different.  The prevalence of oral candida infection was significantly higher in patients with CD4+ cell counts less than 200 cells/ul.
Tuning of Extended Kalman Filter using Self adaptive Differential Evolution Algorithm for Sensorless Permanent Magnet Synchronous Motor Drive

In this paper, a novel method based on a combination of Extended Kalman Filter (EKF) with Self adaptive Differential Evolution (SaDE) algorithm to estimate rotor position, speed and machine states for a Permanent Magnet Synchronous Motor (PMSM) is proposed. In the proposed method, as a first step SaDE algorithm is used to tune the noise covariance matrices of state noise and measurement noise in off line. In the second step, the optimized values of above covariance matrices are injected into EKF in order to estimate the rotor speed on line. The estimated speed is fed back to the PI controller and to minimize the speed error, parameters of PI controller are tuned again using SaDE algorithm. The simulation results show that the tuned covariance matrices Q and R improve convergence of estimation process, quality of estimated states and PI controller improves the settling time and stability of the system.
A Single Patch Antenna With Broadside and Conical Radiation Patterns for 3G/4G Pattern Diversity
Venue: IEEE Antennas and Wireless Propagation Letters

A single square patch antenna for pattern diversity is investigated. The proposed antenna consists of a double feed square patch antenna with a rat race network. By switching the feeding ports, the different radiation patterns for two modes TM10 mode and the capacitive loaded monopole radiating mode) operating over an overlapped frequency band from 1.88 to 2.34 GHz are achieved. TM10 mode reveals good broadside radiation patterns, and the capacitive loaded monopole radiating mode shows conical radiation patterns. The antenna is fabricated and tested. The measured gains across the common frequency band are 8.9 9.9 and 2.8 3.8 dBi for TM10 mode and the capacitive loaded monopole radiating mode, respectively. Moreover, the measured bandwidths of 10 dB reflection coefficient are 750 MHz (1.59 2.34 GHz, 38.2% for TM10 mode and 880 MHz (1.88 2.76 GHz, 37.9% for the capacitive loaded monopole radiating mode. High isolation 20 dB between the two feeding ports for the common impedance matching band is achieved. These results make the single dual port patch antenna an attractive solution for 3G/4G pattern diversity applications such as in gym scenarios.
An electronically switchable wideband pattern diversity antenna
Venue: 2016 Asia Pacific Microwave Conference (APMC)

A wideband pattern diversity antenna operating at 5.5 GHz is proposed. The antenna is a monopole radiating element with two orthogonal feeds. The antenna has a bandwidth of 90% over which the radiation patterns are consistent. A broadband phase shifting network is integrated with the antenna. Single pole double throw (SPDT) switches are used with the phase shifting network to electronically control radiation pattern of the antenna. Consistent diversity performance is achieved in terms of the radiation pattern by the integrated system over the entire bandwidth as that of the antenna.
A Note on the Schnute Growth Model

Mathematical models of growth have been developed a long period of time. Estimating the lag time in the growth process is a practically important problem. Any sigmoidal function can be good illustration for the concept of lag time. The Schnute growth model is described by free parameters, each contributing to the characteristics of the curve: an initial lag or period of slow growth; a period of rapid exponential growth; a period of reduced growth rate. In this note we provide estimates for the one sided Hausdorff approximation of the step function by sigmoidal Schnute function lag new t Numerical examples, illustrating our results are given, too.
On Some Growth Curve Modeling: Approximation Theory And Applications

Mathematical models of growth have been developed a long period of time. Estimating the lag time in the growth process is a practically important problem. Any sigmoidal function can be good illustration for the concept of lag time. The Stannard growth model is described by 4 free parameters, each contributing to the characteristics of the curve: an initial lag or period of slow growth; a period of rapid exponential growth; a period of reduced growth rate. In this note we provide more precise estimates for the one sided Hausdorff approximation of the Heaviside step function by sigmoidal Stannard function new lag t Numerical examples, illustrating our results are given, too. Keywords sigmoidal Stannard function; interval step function; Hausdorff distance; upper and lower bounds; lag time.
First description of clinical presentation of piscine orthoreovirus (PRV) infections in salmonid aquaculture in Chile and identification of a second genotype (Genotype II) of PRV
Venue: Virology Journal

BackgroundHeart and skeletal muscle inflammation (HSMI) is an emerging disease of marine farmed Atlantic salmon Salmo salar, first recognized in 1999 in Norway, and recently associated with piscine orthoreovirus (PRV) infection. To date, HSMI lesions with presence of PRV have only been described in marine farmed Atlantic salmon in Norway. A new HSMI like disease in rainbow trout Oncorhynchus mykiss associated with a PRV related virus has also been reported in Norway.MethodsSampling of Atlantic salmon and coho salmon was done during potential disease outbreaks, targeting lethargic/moribund fish. Fish were necropsied and tissues were taken for histopathologic analysis and testing for PRV by RT qPCR assay for segment L1 and conventional RT PCR for PRV segment S1. The PCR products were sequenced and their relationship to PRV strains in GenBank was determined using phylogenetic analysis and nucleotide and amino acid homology comparisons.ResultsThe Atlantic salmon manifested the classical presentation of HSMI with high PRV virus loads (low Ct values) as described in Norway. The coho salmon with low Ct values had myocarditis but only in the spongy layer, the myositis of red muscle in general was mild, and the hepatic necrosis was severe. Upon phylogenetic analysis of PRV segment S1 sequences, all the Chilean PRV strains from Atlantic salmon grouped as sub genotype Ib, whereas the Chilean PRV strains from coho salmon were more diversified, grouping in both sub genotypes Ia and Ib and others forming a distinct new phylogenetic cluster, designated Genotype II that included the Norwegian PRV related virus.ConclusionsTo our knowledge the present work constitutes the first published report of HSMI lesions with presence of PRV in farmed Atlantic salmon outside of Europe, and the first report of HSMI like lesions with presence of PRV in coho salmon in Chile. The Chilean PRV strains from coho salmon are more genetically diversified than those from Atlantic salmon, and some form a distinct new phylogenetic cluster, designated Genotype II.
Differences in gene expression in Atlantic salmon parr and smolt after challenge with Piscine orthoreovirus (PRV)
Venue: Molecular immunology

Heart and skeletal muscle inflammation (HSMI) are a disease of farmed Atlantic salmon (Salmo salar) associated with Piscine orthoreovirus (PRV) The disease appears mainly during the marine production phase. This study examined if smoltification and transfer to seawater could compromise immune responses to PRV. Parr and smolts of the same origin were challenged by cohabitation with intraperitoneally injected salmon. Peak levels of PRV in spleen of cohabitants were reached after 8 weeks, but at a lower level in parr compared to smolts. Thereafter the virus levels declined, but remained significantly lower in parr than in smolts. Both groups developed typical HSMI histopathological heart lesions, which were most prominent after 10 weeks. Microarray and qPCR analyses revealed slightly lower expression of immune genes in spleen and head kidney of smolts before challenge. Infected parr showed earlier induction of genes involved in innate antiviral immunity, as well as for genes related to B and T cell responses. Gene expression profiles also indicated stimulation of heme and iron metabolism and erythropoiesis in smolts, which may indicate replacement of PRV infected erythrocytes.
Detection of Matrilysin Activity Using Polypeptide Functionalized Reduced Graphene Oxide Field Effect Transistor Sensor.
Venue: Analytical chemistry

A novel approach for rapid and sensitive detection of matrilysin (MMP 7, a biomarker involved in the degradation of various macromolecules) based on a polypeptide (JR2EC) functionalized reduced graphene oxide (rGO) field effect transistor (FET) is reported. MMP 7 specifically digests negatively charged JR2EC immobilized on rGO, thereby modulating the conductance of rGO FET. The proposed assay enabled detection of MMP 7 at clinically relevant concentrations with a limit of detection (LOD) of 10 ng/mL (400 pM) attributed to the significant reduction of the net charge of JR2EC upon digestion by MMP 7. Quantitative detection of MMP 7 in human plasma was further demonstrated with a LOD of 40 ng/mL, illustrating the potential for the proposed methodology for tumor detection and carcinoma diagnostic (e.g. lung cancer and salivary gland cancer) Additionally, excellent specificity of the proposed assay was demonstrated using matrix metallopeptidase 1 (MMP 1) a protease of the same family. With appropriate selection and modification of polypeptides, the proposed assay could be extended for detection of other enzymes with polypeptide digestion capability.