gebhart/patrepeval huggingface dataset:
A deletion mutation at the <i>ep</i> locus causes low seed coat peroxidase activity in soybean (1997)

The Ep locus severely affects the amount of peroxidase enzyme in soybean seed coats. Plants containing the dominant Ep allele accumulate large amounts of peroxidase in the hourglass cells of the sub-epidermis. Homozygous recessive epep genotypes do not accumulate peroxidase in the hourglass cells and are much reduced in total seed coat peroxidase activity. To isolate the gene encoding the seed coat peroxidase and to determine whether it corresponds to the Ep locus, a cDNA library was constructed from developing seed coats and an abundant 1.3 kb peroxidase transcript was cloned. The corresponding structural gene was also isolated from a genomic library. Sequence analysis shows that the seed coat peroxidase is translated as a 352 amino acid precursor protein of 38 kDa. Processing of a putative 26 amino acid signal sequence results in a mature protein of 326 residues with a calculated mass of 35 kDa and a pl of 4.4. Using probes derived from the cDNA, genomic DNA blot hybridization and polymerase chain reaction analysis detected polymorphisms that distinguished EpEp and epep genotypes. Co-segregation of the polymorphisms in an F2 population from a cross of EpEp and epep plants shows that the Ep locus encodes the seed coat peroxidase protein. Comparison of Ep and ep alleles indicates that the recessive gene lacks 87 bp of sequence encompassing the translation start codon. Analysis by RNA blot hybridization shows that epep plants have drastically reduced amounts of peroxidase transcript compared with EpEp plants. The peroxidase mRNA is abundant in seed coat tissues of EpEp plants during the late stages of seed maturation, and could also be detected in root tissues, but not in the flower, embryo, pod or leaf. The results indicate that the lack of peroxidase accumulation in seed coats of homozygous recessive epep plants is due to a mutation of the structural gene that reduces transcript abundance.
A flexible architecture for systematic implementation of SoC security policies (2015)

Modern SoC designs incorporate several security policies to protect sensitive assets from unauthorized access. The policies affect multiple design blocks, and may involve subtle interactions between hardware, firmware, and software. This makes it difficult for SoC designers to implement these policies, and system validators to ensure adherence. Associated problems include complexity in upgrading these policies, IP reuse for systems targeted for markets with differing security requirement, and consequent increase in design time and time-to-market. In this paper, we address this important problem by developing a generic, flexible architectural framework for implementing arbitrary security policies in SoC designs. Our architecture has several distinctive features: (1) it relies on a dedicated, centralized, firmware-upgradable plug-and-play IP block that can implement diverse security policies; (2) it interfaces with individual IP blocks through their “security wrapper”, which exploits and extends test/debug wrappers; (3) it implements a security policy as firmware code following existing security policy languages; (4) it can implement any security policy as long as relevant observable and controllable signals from the constituent IPs are accessible through the security wrappers; and (5) it realizes a low-overhead communication link between security wrappers of IP blocks and the centralized, dedicated controller. The approach builds on and extends the recent work on developing a centralized infrastructure IP for SoC security, referred to as IIPS, that interface with IP blocks using their boundary scan based wrappers. While this architecture is generic and independent of security policy types, we provide case studies with several common policies to show the flexibility and extendibility of the architecture. We also evaluate its viability in terms of overhead in area and power.
Detection of equine antibody to Babesia equi merozoite proteins by a monoclonal antibody-based competitive inhibition enzyme-linked immunosorbent assay (1991)

A competitive inhibition enzyme-linked immunosorbent assay (CI ELISA) was developed to detect antibody to Babesia equi. One hundred fifty-four equine serum samples from 19 countries were tested for antibody to B. equi by the complement fixation test and by CI ELISA. The CI ELISA and complement fixation test results agreed in 94% (144) of the serum samples tested. The 10 discrepant serum samples were retested and analyzed for ability to immunoprecipitate in vitro translation products from B. equi merozoite mRNA. Five discrepant results were clearly resolved in favor of the CI ELISA, and the remaining five discrepancies were not definitively resolved.
Comparison of Line Scan Luminescence Imaging Techniques for Defect Characterisation in Crystalline Silicon Solar Modules (2018)

Luminescence inspection of modules is currently being adopted as a standard practice in the photovoltaic industry. This paper presents a comparison of electroluminescence and photoluminescence imaging on industrial crystalline silicon modules, employed with a line scan system. We find that specific defects appear differently in the two techniques due to the difference in excitation method. Line scan photoluminescence images enable differentiation of series resistance defects from recombination defects and can identify the presence of encapsulant discolouration. Line scan electroluminescence images allow defects that prevent majority carrier transport to be evaluated. The use of both techniques enables robust defect characterisation.
Compact CMOS constant-gm rail-to-rail input stages with gm-control by an electronic zener diode (1995)

A family of compact rail-to-rail input stages are presented. To obtain a constant-gm over the common-mode input range, an electronic zener diode is inserted between the tails of the complementary input pairs. The zener keeps the sum of the gate-source voltage of the input pairs, and therefore the gm of the input stage, constant. Two possible implementations of the zener have been realized. The input stages have been inserted in a two stage compact amplifier. Both amplifiers have been realized in a 1 ?m BiCMOS process. The unity-gain frequency is 2-MHz, for a load of 20 pF
CD38 Expression Identifies an Active Subset of Proliferating Cells within the Clonal Population in Chronic Lymphocytic Leukemia Patients (In Vitro Analysis). (2006)

The prognostic relevance of CD38 expression by clonal B cells from chronic lymphocytic leukemia (B-CLL) cases has been extensively reported. Expression of CD38 by a B cell indicates both its activation status and differentiation stage and remains fairly constant over time in most B-CLL cases although it has been reported to change with time in some cases and this change is associated with change in clinical behavior of the patient. Due to these reasons it has achieved a prominent place among other prognostic indicators such as Ig V gene mutation and ZAP-70 expression in assessment of B-CLL patients. To assess which aspects of the immunobiology of B-CLL cells are impacted by their expression of CD38 by clonal members “within” a B-CLL case we flow-sorted B-CLL cells from peripheral blood of 16 patients (% CD38 expression pre-sort, ranging from 1–90%), into CD38− and CD38+ subsets and quantified telomere lengths as a measure of their replicative history. As a measure of cellular activation we studied telomerase activity in these flow-sorted cells. In addition, expression of CD69 and CD62L (activation-associated), ZAP-70 (signaling-associated) and Ki-67 (cell cycle-associated) were studied on CD38− and CD38+ cell subsets by immunofluorecence and multi-color flow cytometry in 35 cases (including those used for cell sorting experiments). Telomerase activity was markedly higher in the CD38+ subset compared to the CD38− subset in each case (p< 0.01), although telomere lengths of the subsets did not differ significantly within individual cases. Simultaneously, the percentages of cells expressing CD69 and ZAP-70 were significantly higher (p<0.01) and those expressing CD62L (lost after cell activation) were significantly lower (p<0.05) in the CD38+ subset compared to those in the CD38−− subset. Not only did cells from the CD38+ subset exhibit greater percentages of cells with features of “activated cells”, they also identified cells that had recently exited the G0/G1 phase as indicated by differences in Ki-67 expression (p<0.001). Unlike other hematological neoplasms, cell division, noticeable in the peripheral blood, is not a feature of B-CLL. The current findings suggest that the CD38+ fraction of the clone is more “active” than the CD38− fraction, regardless of the initial percentage of CD38+ cells in the clone. Therefore, a detailed phenotypic analysis of CD38-based subpopulations within a B-CLL case could identify even the low level turnover of clonal cells and provide important supplementary information for prediction of prognosis.
Human Mesenchymal Stem Cell–Educated Macrophages Are a Distinct High IL-6–Producing Subset that Confer Protection in Graft-versus-Host-Disease and Radiation Injury Models (2017)

Mesenchymal stem cells (MSCs) have immunosuppressive and tissue repair properties, but clinical trials using MSCs to prevent or treat graft-versus-host disease (GVHD) have shown mixed results. Macrophages (MØs) are important regulators of immunity and can promote tissue regeneration and remodeling. We have previously shown that MSCs can educate MØs toward a unique anti-inflammatory immunophenotype (MSC-educated MØs [MEMs]); however, their implications for in vivo models of inflammation have not been studied yet. We now show that in comparison with MØs, MEMs have increased expression of the inhibitory molecules PD-L1, PD-L2, in addition to markers of alternatively activated MØs: CD206 and CD163. RNA-Seq analysis of MEMs, as compared with MØs, show a distinct gene expression profile that positively correlates with multiple pathways important in tissue repair. MEMs also show increased expression of IL-6, transforming growth factor-β, arginase-1, CD73, and decreased expression of IL-12 and tumor necrosis factor-α. We show that IL-6 secretion is controlled in part by the cyclo-oxygenase-2, arginase, and JAK1/STAT1 pathway. When tested in vivo, we show that human MEMs significantly enhance survival from lethal GVHD and improve survival of mice from radiation injury. We show these effects could be mediated in part through suppression of human T cell proliferation and may have attenuated host tissue injury in part by enhancing murine fibroblast proliferation. MEMs are a unique MØ subset with therapeutic potential for the management of GVHD and/or protection from radiation-induced injury.
A distributed algorithm for equitable bandwidth allocation for content distribution in a tree network (2011)

We present a distributed algorithm for bandwidth allocation for content distribution in tree networks, where the intensive computations are executed independently at the nodes while some information is exchanged among the nodes. The root node has a server that stores and broadcasts multiple programs requested at the nodes through links with limited capacity. The bandwidth allocated for a specific program can be decreased from one link to the next in a path from the root node to an end-node, but it cannot be increased. The objective is to determine equitable bandwidth allocations among all programs across all links, which leads to a formulation of a lexicographic maximin optimization model. The performance function at each of the nodes for a specific program represents customers’ satisfaction as a function of the incoming bandwidth into the node. The distributed algorithm that determines the equitable bandwidth allocations extends the algorithm described in Luss (2010).
Asymmetric Hydrogenation of Ketones with H<sub>2</sub> and Ruthenium Catalysts Containing Chiral Tetradentate S<sub>2</sub>N<sub>2</sub> Ligands (2013)

Getting more for less: In the presence of H2 and a base, air- and moisture-tolerant RuII complexes catalyze the hydrogenation of ketones and aldehydes with excellent activity and chemoselectivity, and with enantioselectivity of up to 95 % under mild conditions. The ratio of substrate to catalyst can be lowered to 106:1. The reactions tolerate scale-up and can be carried out with almost no solvent. A base-free method is available for base-sensitive substrates. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Motion-Compensated Transform Coding (1979)

Interframe hybrid transform/dpcm coders encode television signals by taking a spatial transform of a block of picture elements in a frame and predictively coding the resulting coefficients using the corresponding coefficients of the spatial block at the same location in the previous frame. These coders can be made more efficient for scenes containing objects in translational motion by first estimating the translational displacement of objects and then using coefficients of a spatially displaced block in the previous frame for prediction. This paper presents simulation results for such motion-compensated transform coders using two algorithms for estimating displacements. The first algorithm, which is developed in a companion paper, recursively estimates the displacements from the previously transmitted transform coefficients, thereby eliminating the need to transmit the displacement estimates. The second algorithm, due to Limb and Murphy, estimates displacements by taking ratios of accummulated frame difference and spatial difference signals in a block. In this scheme, the displacement estimates are transmitted to the receiver. Computer simulations on two typical real-life sequences of frames show that motion-compensated coefficient prediction results in coder bit rates that are 20 to 40 percent tower than conventional interframe transform coders using “frame difference of coefficients.” Comparisons of bit rates for approximately the same picture quality show that the two methods of displacement estimation are quite similar in performance with a slight preference for the scheme with recursive displacement estimation.
Green hydroelectrical energy source based on water dissociation by nanoporous ferrite (2016)

Dissociation of water molecule occurs on octahedrally coordinated unsaturated suface cations and oxygen vacancies created by lithium substitution in magnesium ferrite. Lower synthesis temperature of ferrite has generated nanopores in microstructure. Dissociated hydronium and hydroxyl ions are transported through surface and capillary diffusion in porous ferrite network towards attached Zn and Ag electrodes. Water molecule dissociation ability of nanoporous ferrite has been exploited to develop a green electrical energy cell, which is a combination of material science and electrode chemistry. The innovated cell has been nomenclatured as hydroelectric cell (HEC). When HEC is partially dipped in deionized water, spontaneously hydroxide and hydronium ions are produced by water molecule dissociation. Hydronium ions trapped in nanopores develop enough electric field that further dissociates physisorbed water molecules. Thereby, the process of water molecule dissociation is accelerated in a bigger way to increase ionic current in the cell. Oxidation of Zn electrode by hydroxide ion and reduction of H3O+ at Ag electrode develop voltage and electric current in the cell. The HEC cell of a 17 cm2 area is able to generate a short circuit current of 82 mA and 920 mV emf with a maximum output power of 74 mW, which is three order higher than reported output power 1.4 μW/cm2 produced by water in cement matrix. Hydroelectric cell performance is repetitive, stable and possesses potential to replace traditional ways of generating renewable energy in terms of cost and safety. Copyright © 2016 John Wiley & Sons, Ltd.
RNAi therapeutics for the treatment of chronic hepatitis B virus infection (2012)

Background: Chronic infection with Hepatitis B virus (HBV) is a global health problem, with over 350 million carriers worldwide and up to 1,000,000 deaths annually from HBV-associated cirrhosis or hepatocellular carcinoma. There is significant unmet medical need for new treatments yielding a clinical cure or disease suppression with limited dosing and limited adverse effects. RNA interference (RNAi) is a promising modality for the treatment of viral disease. RNAi trigger molecules, such as small interfering RNAs (siRNAs), can be readily designed to possess the specificity, potency, and flexibility to target any viral gene with high efficacy and without the side effects observed with existing anti-viral drugs. The challenge in using anti-HBV siRNAs as drugs is to safely and effectively deliver them to hepatocytes. To this end, we developed an siRNA delivery vehicle named Dynamic PolyConjugates (DPCs). Methods: 145 anti-HBV siRNAs designed to target conserved sequences in HBV serotypes A-D were synthesized and then screened in cultured cells to identify those with highest potency. To determine efficacy in vivo, lead siRNAs were formulated in DPCs and intravenously injected in mouse models of HBV infection. Studies to assess toxicity were conducted in rats and non-human primates (NHPs). Results: Four biweekly injections of anti-HBV siRNA DPCs in mice carrying a hepatocyte-specific reporter gene fused to HBV sequences resulted in a 3-4 log reduction in gene expression over 2 months without changes in cytokines or clinical chemistries. Single dose injections in a replication-competent, transient transgenic HBV mouse model resulted in greatly reduced serum HBsAg levels (> 2 logs) and serum levels of HBV DNA. Single dose studies using transgenic HBV mice revealed dramatic reductions in HBeAg levels in serum, and in viral RNAs and viral replication intermediates in the liver. Safety and tolerability studies using rats and NHPs revealed that DPCs have a wide safety margin. Conclusion: Formulation of potent anti-HBV siRNAs in DPCs allowed highly effective reduction of viral protein production and viral load in mouse models of HBV infection. Combined with the favorable results observed in toxicological studies, we anticipate that anti-HBV siRNA DPCs will become a viable therapeutic for patients with chronic HBV infection.
Human sodium–iodide symporter (hNIS) gene expression is inhibited by a trans-active transcriptional repressor, NIS-repressor, containing PARP-1 in thyroid cancer cells (2010)

Radioiodine remains the only tumoricidal therapy for disseminated thyroid carcinomas; however, dedifferentiated tumors lose the expression of human sodium-iodide symporter (hNIS) gene, and cannot respond to this treatment. Previous studies suggested that a trans-active protein factor (NIS-repressor) represses endogenous hNIS transcription, likely contributing to the loss of radioiodine uptake, and defined the NIS-repressor binding site (NRBS) in the proximal hNIS promoter. Using electrophoretic mobility shift assay (EMSA), we found evidence of NIS-repressor in the nuclear extract from KAK-1 cells, and confirmed this result using nuclear extracts prepared from multiple verified thyroid cell lines. Luciferase reporter assays of hNIS promoter constructs and EMSA were used to define two core sequences, NRBS-P and NRBS-D, in the hNIS promoter as the binding sites for NIS-repressor. Electrophoretic analysis of KAK-1 nuclear extract proteins cross-linked with NRBS-P suggests that NIS-repressor is a protein complex. Analysis of KAK-1 nuclear extract proteins bound to NRBS-P, via liquid chromatography coupled with tandem mass spectroscopy, demonstrated poly(ADP-ribose) polymerase-1 (PARP-1) as a NIS-repressor component. Pharmacological inhibition of PARP-1 enzymatic activity using PJ34 stimulated both the luciferase reporter activity driven by hNIS promoter and the endogenous hNIS mRNA level. Supershift studies suggest that thyroid transcription factor 2 (TTF-2) is also associated with the NIS-repressor complex. NIS-repressor, including its PARP-1 component, presents a potential therapeutic target to restore radioiodine uptake in dedifferentiated thyroid carcinomas.
1-Aryl-4-[(5-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl)alkyl]piperazines and Their Analogues:  Influence of the Stereochemistry of the Tetrahydronaphthalen-1-yl Nucleus on 5-HT<sub>1A</sub> Receptor Affinity and Selectivity versus α<sub>1</sub> and D<sub>2</sub> Receptors. 5 (1999)

Some 1-aryl-4-[(5-methoxy-1,2,3, 4-tetrahydronaphthalen-1-yl)-n-propyl]piperazines and their alkylamino and alkylamido analogues, previously studied as 5-HT1A ligands, were prepared in enantiomerically pure form, and their absolute configuration was determined by chemical correlation or by chiroptical properties. They were evaluated for in vitro 5-HT1A, D2, and alpha1 receptor affinity by radioligand binding assays, to study the influence of the chiral carbon atom of the tetrahydronaphthalene nucleus on the 5-HT1A affinity and selectivity. Results indicated that, as regarding the 5-HT1A receptor affinity, there was no difference in affinity between (-)- and (+)-enantiomers as well as the racemate of each compound. The stereochemistry, instead, influenced the selectivity: all (-)-enantiomers displayed affinity values higher than those of (+)-isomers at D2 receptors, and conversely, all (+)-enantiomers displayed affinity values higher than those of (-)-isomers at alpha1 receptors. As a result of this trend, it is not possible to predict the isomer with a better selectivity profile. However, compounds (S)-(+)-2, (S)-(+)-4, and (R)-(+)-6 displayed high affinity for the 5-HT1A receptor (IC50 values ranging between 7.0 and 2.3 nM) and good selectivity (>/=250-fold) versus both D2 and alpha1 receptors. Furthermore, compounds (S)-(+)-4 and (R)-(-)-4 were submitted to the [35S]GTPgammaS binding assay for a preliminary evaluation of their intrinsic activity on the 5-HT1A receptor.
A New Result on Distributed Input and State Estimation for Heterogeneous Sensor Networks (2017)

An important research area in sensor networks is the design and analysis of distributed estimation algorithms for dynamic information fusion in the presence of heterogeneity resulting from (i) nonidentical information roles of nodes and (ii) nonidentical modalities of nodes. In particular, (i) implies that both active (i.e., subject to observations of a process of interest) and passive (i.e., subject to no observations) nodes can be present in the sensor network. Furthermore, (ii) implies that active nodes can observe different measurements from a process (e.g., a subset of active nodes can observe position measurements and the rest can observe velocity measurements for a target tracking problem). In this paper, we focus on heterogeneous sensor networks, sensor networks with (i) and (ii), and present a new distributed input and state estimation approach. In addition to the presented theoretical contribution including the stability and performance of the proposed estimation approach, an illustrative numerical example is also given to demonstrate its efficacy.
Electrochromic passive-matrix displays (2003)

Historically, the realization of passive-matrix addressing was a crit. issue in the development of electrochromic displays. The authors report on electrochromic passive-matrix displays based on viologen-derivatized films of TiO2 nanoparticles. High and uniform contrast was obtained for lab. devices with few pixels.