gebhart/patrepeval huggingface dataset:
RFLP Analysis of Soybean Breeding Populations: I. Genetic Structure Differences due to Inbreeding Methods (1994)

Segregating soybean [ Glycine max (L.) Merr.] breeding populations are frequently inbred by either single‐seed descent or by bulking progeny at each generation. During inbreeding, repetitive sampling of individual genotypes, or natural selection, may decrease the potential for genetic gain in a population. This is most likely to occur in populations that are inbred by the bulk method. This study examines the genetic structure of two soybean populations, each containing 261 segregating lines. One population was derived from a cross of two elite lines and was inbred by a multiple‐seed descent (MSD) strategy that is frequently employed by soybean breeders. A second population was derived from an elite × unadapted genotype cross that was inbred by single‐seed descent (SSD). The genetic composition of each line and the genetic distances among lines were estimated using 100 RFLP markers. The genetic contribution of each parent to each population was equivalent regardless of the inbreeding procedure. No individual in either population obtained greater than 75% of its genes from a particular parent. Close genetic relationships among lines were not observed in the SSD population, but were common in the MSD population. Cluster analysis of individual lines within the MSD population indicated that about 18% of the lines were due to repetitive sampling and, therefore, did not represent independent lineages. The repetitive sampling appeared to be caused by stochastic processes, as opposed to systematic factors such as differential fecundity among genotypes. Genetic marker analysis of population structure provides a method for directly assessing the effectiveness of inbreeding strategies.
Tracking a 3D maneuvering target with passive sensors (1991)

A novel application of the interacting multiple models (IMM) algorithm in which passive infrared sensors are fused for tracking a target maneuvering in three dimensions is discussed. More accurate models of target motion are proposed to improve performance. When the general models are used to describe the maneuvering periods, it is shown that the IMM behaviour is not satisfactory, in that the innovations associated with the different models do not discriminate between the corresponding target maneuvering regimes. The turning of the Markov chain transition matrix, i.e., a priori information, is then crucial to obtaining the correct ordering of the a posteriori regime probabilities. On the contrary, a more satisfactory behavior of the IMM algorithm is obtained by carefully selecting the target motion models in the different regimes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Telomerase promotes formation of a telomere protective complex in cancer cells (2019)

Telomerase is a ribonucleoprotein complex that catalyzes addition of telomeric DNA repeats to maintain telomeres in replicating cells. Here, we demonstrate that the telomerase protein hTERT performs an additional role at telomeres that is independent of telomerase catalytic activity yet essential for telomere integrity and cell proliferation. Short-term depletion of endogenous hTERT reduced the levels of heat shock protein 70 (Hsp70-1) and the telomere protective protein Apollo at telomeres, and induced telomere deprotection and cell cycle arrest, in the absence of telomere shortening. Short-term expression of hTERT promoted colocalization of Hsp70-1 with telomeres and Apollo and reduced numbers of deprotected telomeres, in a manner independent of telomerase catalytic activity. These data reveal a previously unidentified noncanonical function of hTERT that promotes formation of a telomere protective complex containing Hsp70-1 and Apollo and is essential for sustained proliferation of telomerase-positive cancer cells, likely contributing to the known cancer-promoting effects of both hTERT and Hsp70-1.
Contribution of enhanced engagement of antigen presentation machinery to the clinical immunogenicity of a human interleukin (IL)-21 receptor-blocking therapeutic antibody (2015)

Reliable risk assessment for biotherapeutics requires accurate evaluation of risk factors associated with immunogenicity. Immunogenicity risk assessment tools were developed and applied to investigate the immunogenicity of a fully human therapeutic monoclonal antibody, ATR-107 [anti-interleukin (IL)-21 receptor] that elicited anti-drug antibodies (ADA) in 76% of healthy subjects in a Phase 1 study. Because the ATR-107 target is expressed on dendritic cells (DCs), the immunogenicity risk related to engagement with DC and antigen presentation pathways was studied. Despite the presence of IL-21R on DCs, ATR-107 did not bind to the DCs more extensively than the control therapeutic antibody (PF-1) that had elicited low clinical ADA incidence. However, ATR-107, but not the control therapeutic antibody, was translocated to the DC late endosomes, co-localized with intracellular antigen-D related (HLA-DR) molecules and presented a dominant T cell epitope overlapping the complementarity determining region 2 (CDR2) of the light chain. ATR-107 induced increased DC activation exemplified by up-regulation of DC surface expression of CD86, CD274 (PD-L1) and CD40, increased expansion of activated DC populations expressing CD86(hi), CD40(hi), CD83(hi), programmed death ligand 1 (PD-L1)(hi), HLA-DR(hi) or CCR7(hi), as well as elevated secretion of tumour necrosis factor (TNF)-α by DCs. DCs exposed to ATR-107 stimulated an autologous T cell proliferative response in human donor cells, in concert with the detection of immunoglobulin (Ig)G-type anti-ATR-107 antibody response in clinical samples. Collectively, the enhanced engagement of antigen presentation machinery by ATR-107 was suggested. The approaches and findings described in this study may be relevant to identifying lower immunogenicity risk targets and therapeutic molecules.
Mutational Analysis of the Ethylene Receptor ETR1. Role of the Histidine Kinase Domain in Dominant Ethylene Insensitivity (2002)

The ethylene receptor family of Arabidopsis consists of five members, one of these being ETR1. The N-terminal half of ETR1 contains a hydrophobic domain responsible for ethylene binding and membrane localization. The C-terminal half of the polypeptide contains domains with homology to histidine (His) kinases and response regulators, signaling motifs originally identified in bacteria. The role of the His kinase domain in ethylene signaling was examined in planta. For this purpose, site-directed mutations were introduced into the full-length wild-type ETR1 gene and into etr1-1, a mutant allele that confers dominant ethylene insensitivity on plants. The mutant forms of the receptor were expressed in Arabidopsis and the transgenic plants characterized for their ethylene responses. A mutation that eliminated His kinase activity did not affect the ability of etr1-1 to confer ethylene insensitivity. A truncated version of etr1-1 that lacks the His kinase domain also conferred ethylene insensitivity. Possible mechanisms by which a truncated version of etr1-1 could exert dominance are discussed.
Cellular uptake and efflux of peplomycin in sensitive and bleomycin-resistant subline of mouse lymphoblastoma L5178Y cells. (1988)

Bleomycin (BLM) is clinically useful in the treatment of humansquamouscell carcinomas, testicular carcinoma, and malignant lymphoma.
Towards a unified theory of parameter adaptive control. I. Tunability (2003)

A conceptual framework is proposed in which a parameter adaptive control system is taken to be a particular interconnection of a process, a parameterized controller, and a tuner. Emphasis is placed on the importance of a tuning error in the adaptation process. The concept of tunability is defined, characterized, and shown to be necessary for adaptive stabilization. Tunability also proves to be sufficient for adaptive stabilization for systems using tuning algorithms with certain typical capabilities.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
LIN28 expression and prognostic value in hepatocellular carcinoma patients who meet the Milan criteria and undergo hepatectomy (2012)

Stem cell marker LIN28, related closely with SOX2 and OCT4, has been studied as a biomarker for the maintainance of pluripotent cells in several malignancies. Our previous study showed that SOX2 and OCT4 were negative predictors for hepatocellular carcinoma (HCC). However, the predictive value of LIN28 in HCC outcome is still undetermined. We hypothesized that LIN28 may also play a role as a biomarker for HCC. To test this hypothesis, we examined the expression of LIN28 in 129 radically resected HCC tissues using reverse transcription-polymerase chain reaction and analyzed the association of LIN28 expression with clinicopathologic features and prognosis. Our study showed that LIN28 was expressed at a higher frequency in tumor tissues than in non-HCC tissues (45.0% vs. 21.7%, P = 0.020). Moreover, LIN28 expression was significantly increased in cases with large tumor size (P = 0.010). Univariate analysis did not reveal a significant correlation between LIN28 expression and overall survival or recurrence-free survival. For HCC patients who met the Milan criteria, stratified analysis revealed shorter overall survival (P = 0.007) and recurrence-free survival (P < 0.001) in those with detectable LIN28 expression compared to those with no detectable LIN28 expression. Furthermore, multivariate analysis revealed that LIN28 was a negative independent predictor for both overall survival (hazard ratio= 7.093, P = 0.017) and recurrence-free survival (hazard ratio=5.518, P = 0.004) in patients who met the Milan criteria. Taken together, our results suggest that LIN28 identifies low-risk and high-risk subsets of HCC patients meeting the Milan criteria who undergo hepatectomy.
A monopole/loop dual-tuned RF coil for ultrahigh field MRI. (2014)

Proton and heteronuclear MRI/MRS using dual-tuned (DT) coils could provide both anatomical and metabolic images without repositioning the subject. However, it is technologically challenging to attain sufficiently electromagnetic (EM) decoupling between the heteronuclear channel and proton channel, and keep the imaging areas and profiles of two nuclear channels highly matched. In this study, a hybrid monopole/loop technique was proposed for DT coil design and this technique was validated by implementing and testing a DT (1)H/(23)Na coil for MR imaging at 7T. The RF fields of the monopole ((1)H channel) and regular L/C loop ((23)Na channel) were orthogonal and intrinsically EM decoupled. Bench measurement results demonstrated the isolation between the two nuclear channels was better than -28 dB at both nuclear frequencies. Compared with the conventional DT coil using trap circuits, the monopole/loop DT coil had higher MR sensitivity for sodium imaging. The experimental results indicated that the monopole/loop technique might be a simple and efficient design for multinuclear imaging at ultrahigh fields. Additionally, the proposed DT coils based on the monopole/loop technique can be used as building blocks in designing multichannel DT coil arrays.
Protein Kinase Cβ Selective Inhibitor LY333531 Attenuates Diabetic Hyperalgesia Through Ameliorating cGMP Level of Dorsal Root Ganglion Neurons (2003)

Streptozocin (STZ)-induced diabetic rats show hyperalgesia that is partially attributed to altered protein kinase C (PKC) activity. Both attenuated neuronal nitric oxide synthase (nNOS)-cGMP system and tetrodotoxin-resistant (TTX-R) Na channels in dorsal root ganglion neurons may be involved in diabetic hyperalgesia. We examined whether PKCbeta inhibition ameliorates diabetic hyperalgesia and, if so, whether the effect is obtained through action on neurons by testing nociceptive threshold in normal and STZ-induced diabetic rats treated with or without PKCbeta-selective inhibitor LY333531 (LY) and by assessing the implication of LY in either nNOS-cGMP system or TTX-R Na channels of isolated dorsal root ganglion neurons. The decreased nociceptive threshold in diabetic rats was improved either after 4 weeks of LY treatment or with a single intradermal injection into the footpads. The treatment of LY for 6 weeks significantly decreased p-PKCbeta and ameliorated a decrease in cGMP content in dorsal root ganglia of diabetic rats. The latter effect was confirmed in ex vivo condition. The treatment with NO donor for 4 weeks also normalized both diabetic hyperalgesia and decreased cGMP content in dorsal root ganglions. The expressions of nNOS and TTX-R Na channels were not changed with LY treatment. These results suggest that LY is effective for treating diabetic hyperalgesia through ameliorating the decrease in the nNOS-cGMP system.
Microwave Induced Transparency in Ruby (1997)

We report experimental observations of field-induced transparency in a solid medium. Absorption reduction of 20% was observed in ruby using a magnetic field for the creation of closely spaced lower levels and a microwave field for the coupling of these states.
Statistical en-route filtering of injected false data in sensor networks (2005)

In a large-scale sensor network individual sensors are subject to security compromises. A compromised node can inject into the network large quantities of bogus sensing reports which, if undetected, would be forwarded to the data collection point (i.e. the sink). Such attacks by compromised sensors can cause not only false alarms but also the depletion of the finite amount of energy in a battery powered network. We present a statistical en-route filtering (SEF) mechanism that can detect and drop such false reports. SEF requires that each sensing report be validated by multiple keyed message authentication codes (MACs), each generated by a node that detects the same event. As the report is forwarded, each node along the way verifies the correctness of the MACs probabilistically and drops those with invalid MACs at earliest points. The sink further filters out remaining false reports that escape the en-route filtering. SEF exploits the network scale to determine the truthfulness of each report through collective decision-making by multiple detecting nodes and collective false-report-detection by multiple forwarding nodes. Our analysis and simulations show that, with an overhead of 14 bytes per report, SEF is able to drop 80/spl sim/90% injected false reports by a compromised node within 10 forwarding hops, and reduce energy consumption by 50% or more in many cases.
Resilient Dynamic Data Driven Application Systems (rDDDAS) (2013)

There is a growing interest in Cloud Computing for delivering computing as a utility. Security in Cloud Computing is a challenging research problem because it involves many interdependent tasks including vulnerability scanning, application layer firewalls, configuration management, alert monitoring and analysis, source code analysis, and user identity management. It is widely accepted that we cannot build software and computing systems that are free from vulnerabilities and cannot be penetrated or attacked. Consequently, there is a strong interest in resilience approach because of its potential to address the cybersecurity challenges. Our is based on using the Dynamic Data Driven Application System (DDDAS) and Moving Target Defence (MTD) strategies to develop resilient DDDAS. The Resilient Applications utilize the following capabilities: Software Behaviour Encryption (SBE), Replication, Diversity, Automated Checkpointing and Recovery. Software Behaviour Encryption employs spatiotemporal behaviour encryption and a moving target defence to make active software components change their implementations and their resources randomly and consequently evade attackers. Diversity and random execution is achieved by “hot” shuffling multiple functionally- equivalent, behaviourally-different software versions at runtime (This encryption of the execution environment will make it extremely difficult for an attack to disrupt the normal operations of a cloud application. Also, the dynamic change in the execution environment will hide the software flaws that would otherwise be exploited by a cyberattacker. Checkpointing is used to save the current state of the task to a reliable storage and thus enabling rollback recovery if it is required to tolerate cyberattacks and mitigate their impacts. We use the Compiler for Portable Checkpointing (CPPC), a tool for automatically inserting portable checkpoints into the code. We also evaluate the performance and overhead of running three applications in our rDDDAS environment. Our experimental results show that the rDDDAS environment can be used to develop resilient cloud applications are resilient against attacks with around 7% in execution time overhead.
Evaluating Protocols for Embryonic Stem Cell Differentiation into Insulin-Secreting β-Cells Using Insulin II-GFP as a Specific and Noninvasive Reporter (2009)

Stable and full differentiation of pluripotent stem cells into functional beta-cells offers the potential to treat type I diabetes with a theoretically inexhaustible source of replacement cells. In addition to the difficulties in directed differentiation, progress toward an optimized and reliable protocol has been hampered by the complication that cultured cells will concentrate insulin from the media, thus making it difficult to tell which, if any, cells are producing insulin. To address this, we utilized a novel murine embryonic stem cell (mESC) research model, in which the green fluorescent protein (GFP) has been inserted within the C-peptide of the mouse insulinII gene (InsulinII-GFP). Using this method, cells producing insulin are easily identified. We then compared four published protocols for differentiating mESCs into beta-cells to evaluate their relative efficiency by assaying intrinsic insulin production. Cells differentiated using each protocol were easily distinguished based on culture conditions and morphology. This comparison is strengthened because all testing is performed within the same laboratory by the same researchers, thereby removing interlaboratory variability in culture, cells, or analysis. Differentiated cells were analyzed and sorted based on GFP fluorescence as compared to wild type cells. Each differentiation protocol increased GFP fluorescence but only modestly. None of these protocols yielded more than 3% of cells capable of insulin biosynthesis indicating the relative inefficiency of all analyzed protocols. Therefore, improved beta-cells differentiation protocols are needed, and these insulin II GFP cells may prove to be an important tool to accelerate this process.
Remote sensing of liquid characteristics using time domain reflectometry (2002)

Time domain reflectometry (TDR) instrumentation is widely used in hydrology and soil science for accurate and flexible soil water content measurements. The most attractive advantages concerning the considered TDR measurement system are: good precision and accuracy, high reliability of the measuring head, an unique approach of pulsing a long coaxial probe and analysing the reflected voltage signature caused by changes in impedance, capability of multiplexing several probes, possibility of remotely acceding, controlling and electronically retrieving and transmitting data through existing telecommunications. A time domain reflectometer transmits the incident signal, an ultra short rise time (200 ps), step voltage pulse, along the transmission line and records the travel time and magnitude of all reflected signals (echo) returning from the controlled system. Changes in capacitance, impedance, inductance and resistance causing electromagnetic discontinuities that reflect voltage can be located, particularly, for liquid level and soil dielectric properties monitoring purposes, discontinuities result from impedance changes produced by changes in the dielectric constant. Moreover, different systems are currently used to measure liquid levels in stocking tanks or vessels. The time domain reflectometry method used in this research has the purpose to monitor the behavior of the different liquid interfaces, detecting their levels. One of the the goals of present paper is to enhance field measurement capabilities; miniature pulsing and sampling cards have been used to create a smaller and more rugged time domain reflectometer, associated to the special steel probes working like a closed circuit radar, detecting any mismatch along the measuring lines. Measurements can be performed in a wide range of environmental conditions, independently from the nature or properties of the involved substances, giving information about their characteristics, such as volumetric content, dielectric constant, emulsions, dispersions, etc. Agreements with current TDR research data have been found. Furthermore, by characterizing several complex systems, the main objective of the present work is to develop an interpretation method based on the changes in the reflected TDR signal caused by the presence of hydrocarbons and their concentration in a soil.
Visual constraint diagrams: runtime conformance checking of UML object models versus implementations (2004)

This paper presents visual constraint diagrams (VCD), an extension to UML (Unified Modeling Language) object diagrams for expressing constraints over object models. VCD allows designers to express well-formedness constraints that cannot be expressed using class diagrams alone; an example of such a constraint is that a linked list data structure cannot have any loops. VCD offers two advances over existing techniques: (1) they allow constraints to be expressed within the visual notation of UML, without resorting to complex textual notations such as OCL; and (2) VCD can be checked at runtime, increasing the value of design documents to developers. An editor and a checker for VCD have been implemented as part of the Rosetta software design tool.
Mn(II,III) oxidation and MnO <sub>2</sub> mineralization by an expressed bacterial multicopper oxidase (2013)

Reactive Mn(IV) oxide minerals are ubiquitous in the environment and control the bioavailability and distribution of many toxic and essential elements and organic compounds. Their formation is thought to be dependent on microbial enzymes, because spontaneous Mn(II) to Mn(IV) oxidation is slow. Several species of marine Bacillus spores oxidize Mn(II) on their exosporium, the outermost layer of the spore, encrusting them with Mn(IV) oxides. Molecular studies have identified the mnx (Mn oxidation) genes, including mnxG, encoding a putative multicopper oxidase (MCO), as responsible for this two-electron oxidation, a surprising finding because MCOs only catalyze single-electron transfer reactions. Characterization of the enzymatic mechanism has been hindered by the lack of purified protein. By purifying active protein from the mnxDEFG expression construct, we found that the resulting enzyme is a blue (absorption maximum 590 nm) complex containing MnxE, MnxF, and MnxG proteins. Further, by analyzing the Mn(II)- and (III)-oxidizing activity in the presence of a Mn(III) chelator, pyrophosphate, we found that the complex facilitates both electron transfers from Mn(II) to Mn(III) and from Mn(III) to Mn(IV). X-ray absorption spectroscopy of the Mn mineral product confirmed its similarity to Mn(IV) oxides generated by whole spores. Our results demonstrate that Mn oxidation from soluble Mn(II) to Mn(IV) oxides is a two-step reaction catalyzed by an MCO-containing complex. With the purification of active Mn oxidase, we will be able to uncover its mechanism, broadening our understanding of Mn mineral formation and the bioinorganic capabilities of MCOs.