gebhart/patrepeval huggingface dataset:
Detection of Antilymphocyte Antibody with Two-Color Method in Systemic Lupus Erythematosus and Its Heterogeneous Specificities against Human T-Cell Subsets (1979)

The two-color method originally described by Van Rood et al. (Van Rood, J. J., A. Van Leeuwen, and J. S. Ploen. 1976. Simultaneous detection of two cell populations by two-color fluorescence and application to the recognition of B-cell determinants. Nature (Lond.). 262: 795-797) for the typing of homologous leukocytic antibodies, D-region was used for the detection of antilymphocyte antibody (ALA) in systemic lupus erythematosus. In this method, surface immunoglobulin-bearing cells were identified with fluorescein isothiocyanate-labeled anti-immunoglobulin and nuclei of killed cells were stained with ethidium bromide. Therefore, cell type (T or B) of the target cells can be identified without fractionating them. ALA was detected in 87% of lupus sera and had a preferential reactivity with T cells. Its major immunoglobulin class was shown to be immunoglobulin (Ig)M. The subspecificity of ALA was further analyzed using fractionated T-cell subsets as target cells. When T lymphocytes were separated into Fc receptor-bearing (Tgamma) and lacking (Tgamma[-]) cells, 64% of ALA showed preferential reactivity with Tgamma cells and 14% with Tgamma(-) cells. The remainder had no selective reactivity against Tgamma or Tgamma(-) cells. Tgamma cells were shown to have suppressor activity, whereas Tgamma(-) cells were indicated to contain helper cells. The above finding was in agreement with the observation that treatment of T cells with ALA that preferentially react with Tgamma cells considerably enhanced immunoglobulin synthesis in vitro, whereas treatment of T cells with ALA reactive with Tgamma(-) cells clearly suppressed the formation of immunoglobulins. Treatment of ALA with no selective reactivity showed variable effects on in vitro immunoglobulin synthesis. These results indicate that ALA in lupus have heterogeneous specificities against human T-cell subsets.
Power scaling, passive Q-switching and intracavity frequency doubling of blue-diode-pumped Pr3+:YLF laser (2018)

We demonstrate a continuous-wave Pr3+:YLF laser pumped by blue laser diodes, and obtain the output power of 6.7 and 3.7 W at 640 and 607 nm, respectively. The Pr3+:YLF laser is extended to passive Q-switching by utilizing a Co2+:MgAl2O4 spinel saturable absorber and its intracavity second harmonic generation at DUV.
Mechanism of Tripeptide Trimming by γ-Secretase (2021)

Abstract The membrane-embedded γ-secretase complex processively cleaves within the transmembrane domain of amyloid precursor protein (APP) to produce 37-to-43-residue amyloid β-peptides (Aβ) of Alzheimer’s disease (AD). Despite its importance in pathogenesis, the mechanism of processive proteolysis by γ-secretase remains poorly understood. Here, mass spectrometry and western blotting were used to quantify the efficiency of the first tripeptide trimming step (Aβ49→Aβ46) of wildtype (WT) and familial AD (FAD) mutant APP substrate. In comparison to WT APP, the efficiency of this first trimming step was similar for the I45F, A42T and V46F APP FAD mutants, but substantially diminished for the I45T and T48P mutants. In parallel with biochemical experiments, all-atom simulations using a novel Peptide Gaussian accelerated molecular dynamics (Pep-GaMD) method were applied to investigate tripeptide trimming of Aβ49 by γ-secretase. The starting structure was active γ-secretase bound to Aβ49 and APP intracellular domain (AICD), as generated from our previous study that captured activation of γ-secretase for the initial endoproteolytic cleavage of APP (Bhattarai et al ., ACS Cent Sci , 2020, 6:969-983). Pep-GaMD simulations captured remarkable structural rearrangements of both the enzyme and substrate, in which hydrogen-bonded catalytic aspartates and water became poised for tripeptide trimming of Aβ49 to Aβ46. These structural changes required a positively charged N-terminus of endoproteolytic coproduct AICD, which could dissociate during conformational rearrangements of the protease and Aβ49. The simulation findings were highly consistent with biochemical experimental data. Taken together, our complementary biochemical experiments and Pep-GaMD simulations have enabled elucidation of the mechanism of tripeptide trimming by γ-secretase. Significance statement Production of amyloid β-peptide (Aβ) of Alzheimer’s disease (AD) from its precursor protein requires a series of proteolytic events carried out by the membrane-embedded γ-secretase complex. Mutations in the substrate and enzyme that produce Aβ cause hereditary AD and these mutations affect tripeptide trimming of initially formed long Aβ peptides by γ-secretase. Little is known about the structural mechanism of this trimming process. Here, we have developed a molecular dynamic model for the first step of trimming (Aβ49 to Aβ46) by γ-secretase. Conformational changes in the enzyme-substrate complex to set up this trimming step require the presence of N-terminally charged endoproteolytic cleavage co-product. Computational effects of AD-causing mutations in Aβ49 on the trimming process were validated through biochemical experiments.
Comparison of Electron Spin Resonance Probe and Dielectric Relaxation in Physically and Chemically Crosslinked Polymers (1996)

Dielectric relaxation spectroscopy in the frequency range from 10−2 Hz to 106 Hz and electron spin resonance (ESR) experiments are employed to study the dynamics in chemically and physically crosslinked networks. As examples for physically crosslinked networks ortho- and para-cresol novolacs were investigated. Dielectrically these materials show low-temperature β- and high-temperature α-relaxation. Both relaxation regions differ for both types of novolacs. This is also reflected by the ESR measurements and is discussed in terms of different hydrogen bonds found to be stronger in para-cresol novolac. For the chemically crosslinked poly(triallyl isocyanurate) only a β-peak is found by the dielectric measurements. Also in the ESR experiment the slow motion regime is characterized up to high temperatures. This means that the segmental motion is strongly suppressed by chemical crosslinking. Nevertheless the obtained change in the formal T50G value can be used to characterize the glass transition in highly crosslinked systems by the ESR method.
Slow Light Enhanced Accelerometry (2022)

We show how to realize a slow-light enhanced accelerometer using a Mach-Zehnder Interferometer. A proof-of-principle experiment carried out with Rb vapor is found to produce results in close agreement with the theoretical model.
The Gazayerli Endoscopic Retractor Model 1 (1991)

A simple yet effective abdominal wall retractor for use in endoscopic surgery is described. It has been used in laparoscopic herniorrhaphy, laparoscopic cholecystectomy in the morbidly obese, and lysis of abdominal wall adhesions, and to control abdominal wall bleeding.
THE CONTEXT IN ENGINEERING EDUCATION (2008)

Context is the cultural framework, or environment, in which technical knowledge and skills are learned.The culture of education, the skills we teach, and the attitudes we convey should all indicate that C-D-I-O is the role of engineers in their service to society.It is important to note that we believe that the product, process, or system lifecycle should be the context, not the content, of engineering education.In this paper, we highlight models that, while different from CDIO, serve as the context for engineering education in disciplines that do not necessarily build products.One example is the Measure-Model-Manipulate-Make approach in biological engineering.This approach simulates the processes that biological engineers follow in their work.In other words, it is what engineers do.The rationale for teaching engineering in context is clear and compelling.It is based on theories and best practices of contextual learning as applied in engineering and higher education.Finally, the paper concludes with a discussion of the broader societal need for adopting an appropriate context, and more effectively training engineers.The case of development of engineering education in China is highlighted, and parallels are drawn to educational needs in Sweden and in the United States.
A randomized, phase II study of ATN-224 in patients with biochemically relapsed, hormone-naive prostate cancer: A DOD/PCF Prostate Cancer Clinical Trials Consortium trial (2009)

5135 Background: ATN-224 (choline tetrathiomolybdate) is an orally active, small molecule that has antiangiogenic and antitumor effects in prostate cancer (PCa) models. ATN-224 targets Cu 2+ /Zn 2+ superoxide dismutase 1 (SOD1) and suppress the generation of H 2 O 2 leading to activation of a number of phosphatases, a group of negative growth regulatory enzymes. We hypothesized that ATN-224 may induce antitumor effect as an antiangiogenic (at 30 mg dose level) and possesses direct antitumor activity at higher dose (300 mg/day). Methods: PCa pts with PSA doubling time (PSADT) of &lt; 12 months, no radiographic evidence of metastasis, no hormonal therapy within 6 months were enrolled. All pts had testosterone &gt; 150 ng/dL at baseline. ATN-224 was administered at 2 dose levels. PSA progression was defined as at least a 50% increase in PSA and &gt;5 ng/mL increase from baseline or post-treatment nadir and confirmed. Endpoints included the proportion of pts who did not have PSA progression for 24 weeks, change in PSA slope/PSADT, and assessment of safety and tolerability. The study was not powered to detect difference between the two groups. Results: 52 pts were enrolled at 6 centers. Fourteen of 27 (52%) in the low dose and 6/25 (24%) in the high dose cohort were PSA progression free for 24 weeks. One patient in high dose cohort showed PSA &gt;50% decrease of 40 days duration. Pre- and on-treatment PSA kinetics are shown below. Median duration on study was 134 days in both groups. ATN-224 was well tolerated with a few reversible Grade 3/4 neutropenia and Grade 3 skin rash (both 4%). Conclusions: ATN-224 may have biologic activity in men with androgen-dependent PCa at low doses, as demonstrated by &gt; 50% of pts being PSA progression free at 6 month and a significant decrease in mean PSA slope. The implication of this study is not clear without a comparative design and ceruloplasmin correlation which is still pending. [Table: see text] [Table: see text]
Design of Inhibitors of the Intrinsically Disordered Protein NUPR1: Balance between Drug Affinity and Target Function (2021)

Intrinsically disordered proteins (IDPs) are emerging as attractive drug targets by virtue of their physiological ubiquity and their prevalence in various diseases, including cancer. NUPR1 is an IDP that localizes throughout the whole cell, and is involved in the development and progression of several tumors. We have previously repurposed trifluoperazine (TFP) as a drug targeting NUPR1 and, by using a ligand-based approach, designed the drug ZZW-115 starting from the TFP scaffold. Such derivative compound hinders the development of pancreatic ductal adenocarcinoma (PDAC) in mice, by hampering nuclear translocation of NUPR1. Aiming to further improve the activity of ZZW-115, here we have used an indirect drug design approach to modify its chemical features, by changing the substituent attached to the piperazine ring. As a result, we have synthesized a series of compounds based on the same chemical scaffold. Isothermal titration calorimetry (ITC) showed that, with the exception of the compound preserving the same chemical moiety at the end of the alkyl chain as ZZW-115, an increase of the length by a single methylene group (i.e., ethyl to propyl) significantly decreased the affinity towards NUPR1 measured in vitro, whereas maintaining the same length of the alkyl chain and adding heterocycles favored the binding affinity. However, small improvements of the compound affinity towards NUPR1, as measured by ITC, did not result in a corresponding improvement in their inhibitory properties and in cellulo functions, as proved by measuring three different biological effects: hindrance of the nuclear translocation of the protein, sensitization of cells against DNA damage mediated by NUPR1, and prevention of cancer cell growth. Our findings suggest that a delicate compromise between favoring ligand affinity and controlling protein function may be required to successfully design drugs against NUPR1, and likely other IDPs.
Correlation between microbial diversity and geochemistry of representative elements in the surface environment of the antimony mining area in Xikuangshan, China (2023)

Abstract Microbes are key mediators in maintaining environmental stability and the migration of geological elements. Although the effect of environmental factors on the geochemical distribution of elements and microbes in Xikuangshan have been studied, the connection between the above two remains to be clarified. In this study, the distribution of elemental forms, especially heavy metals, various geochemical conditions, and the microbial community compositions of the soil, sediment and water samples collected from different sites of Xikuangshan were investigated to study the correlation between representative elemental geochemistry and microbial diversity. The results show that the pH values of the soil samples were significantly lower than those of the sediment and water samples, and the soil had the highest microbial biomass. The contents of As and Sb in the samples are higher than those of other heavy metal elements, and the most abundant occurrence form of heavy metals is reducible. The most abundant type of the microorganisms is bacteria, followed by fungi and archaea. The correlation analyses between environmental factors and microbial diversities indicated that the microbial community structure composition of Xikuangshan was strictly correlated with the content and speciation of elements. The main factors impacting microbial diversity are pH and redox potential, as well as the content and occurrence forms of Sb, As and Fe. This study is of value for revealing the geochemical characteristics of heavy metal occurrence forms associated with microbial diversity in the Xikuangshan mine and for pollution control of Sb mines.
Triticale forrajero y de doble aptitud (2014)

The techniques that underpin modern molecular biology have been rapidly adopted by those interested in the major parasitic infections of humans. The parasitological literature is full of reports of genes and their amino acid sequences, of molecules, of cell membrane receptors and channels, and of the fine details of the immunological responses mounted by the host to combat infection. Much less enthusiasm has been shown for the mathematical techniques that facilitate the analysis and interpretation of dynamical processes such as transmission, evolution, and the interplay between parasite population growth and immunological responses within the host. Molecular techniques provide enormous opportunities for description, but ultimately, understanding biological systems with the precision that physicists and engineers aspire to in their own fields will require quantitative description of the many rate processes that dictate both an observed pattern and the dynamics of its change.
Shallow water flow prediction using prestack waveform inversion of conventional 3D seismic data and rock modeling (2002)

Shallow water flow (SWF) layers are frequently encountered in deepwater areas when drilling into poorly consolidated geopressured sands (Figure 1). These sands, when flowing, can cause extensive damage to a borehole. More than $200 million has been lost to date for remediation and prevention of SWF problems in the Gulf of Mexico. Lately, this problem has also been a concern in many other deepwater clastic basins in the world.
Synthesis of isosorbide bis(methyl carbonate) by transesterification of isosorbide with dimethyl carbonate, and evidence of its usefulness as a monomer for manufacturing polycarbonates (2016)

Isosorbide bis(methyl carbonate) (IBMC) is a barely explored isosorbide derivative potentially useful as a monomer for synthesizing biobased polymers. In this paper, its synthesis by transesterification of isosorbide (IS) with dimethyl carbonate (DMC) at reflux temperature using potassium and cesium carbonates as catalysts is reported. Using a semicontinuous operation mode, a 97% yield was obtained with cesium carbonate as catalyst at a concentration of 0.2 mol% vs. IS, and a DMC/IS molar ratio of 30. Oligomerization by reaction between IS, the intermediate isosorbide mono(methyl carbonate) and IBMC is a severe competitive reaction. Oligomers formation is strongly suppressed at high molar ratios and low catalyst concentrations. Cesium carbonate leads to a lower oligomer formation than potassium carbonate which is explained by the “cesium effect”. Evidence of the usefulness of IBMC as a biobased monomer for polymer synthesis through its polycondensation with 1,4-butanediol (1,4-BDO) is provided. A poly(isosorbide-1,4-BDO carbonate) with a weight average molar mass of 1800 g/mol and a polydispersity of 1.43 is obtained in 63.4% yield using 3 mol% DBU vs. IBMC as a catalyst with an IBMC/1,4-BDO molar ratio of 1 at 130 °C. Keywords: Isosorbide, Isosorbide bis(methyl carbonate), Biobased monomers, Transesterification, Biobased polymers, Cesium carbonate effect
Control oriented system identification: a worst-case/deterministic approach in H/sub infinity / (1991)

The authors formulate and solve two related control-oriented system identification problems for stable linear shift-invariant distributed parameter plants. In each of these problems the assumed a priori information is minimal, consisting only of a lower bound on the relative stability of the plant, an upper bound on a certain gain associated with the plant, and an upper bound on the noise level. The first of these problems involves identification of a point sample of the plant frequency response from a noisy, finite, output time series obtained in response to an applied sinusoidal input with frequency corresponding to the frequency point of interest. This problem leads naturally to the second problem, which involves identification of the plant transfer function in H/sub infinity / from a finite number of noisy point samples of the plant frequency response. Concrete plans for identification algorithms are provided for each of these two problems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Frequency tuning and doubling in Yb-doped fiber lasers (2007)

A compact Yb-doped fiber laser (YDFL) based on a tunable fiber Bragg grating (FBG) with ∼6 W output power and ∼45 nm tuning around 1080 nm has been developed. The laser output power and its spectral width (∼0.15 nm) do not change significantly at the tuning, while the FBG reflection coefficient increases with an increase in FBG compression. It has been shown that this increase is due to stress-induced changes in the FBG’s refractive-index modulation amplitude. Intracavity frequency doubling in the YDFL has also been performed. About 0.4 W of green radiation with tuning in the range 540–548 nm has been achieved with a KTP nonlinear crystal.
Table S6 from Chemotherapy Induces Senescence-Like Resilient Cells Capable of Initiating AML Recurrence (2023)

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Homophobia: An Impulsive Attraction to the Same Sex? Evidence From Eye-Tracking Data in a Picture-Viewing Task (2016)

These findings confirm the importance of considering the variability in impulsive processes to understand why some (but not all) men high in homophobia have homosexual interest. These findings reinforce the theoretical basis for elaborating a dual-process model for behaviors in the sexual context.
ChemInform Abstract: Catalytic Hydrogenation of Olefins in Biphasic Water‐Liquid System. (1987)

Abstract Olefins such as (I), (III), and (V) are hydrogenated in a biphasic aqueous solution in the presence of a catalyst system obtained from RhCl 3 and a triphenylphosphine trisulfonate.
Enhanced lipid isomer separation in human plasma using reversed-phase UPLC with ion-mobility/high-resolution MS detection (2014)

An ultraperformance LC (UPLC) method for the separation of different lipid molecular species and lipid isomers using a stationary phase incorporating charged surface hybrid (CSH) technology is described. The resulting enhanced separation possibilities of the method are demonstrated using standards and human plasma extracts. Lipids were extracted from human plasma samples with the Bligh and Dyer method. Separation of lipids was achieved on a 100 × 2.1 mm inner diameter CSH C18 column using gradient elution with aqueous-acetonitrile-isopropanol mobile phases containing 10 mM ammonium formate/0.1% formic acid buffers at a flow rate of 0.4 ml/min. A UPLC run time of 20 min was routinely used, and a shorter method with a 10 min run time is also described. The method shows extremely stable retention times when human plasma extracts and a variety of biofluids or tissues are analyzed [intra-assay relative standard deviation (RSD) <0.385% and <0.451% for 20 and 10 min gradients, respectively (n = 5); interassay RSD <0.673% and <0.763% for 20 and 10 min gradients, respectively (n = 30)]. The UPLC system was coupled to a hybrid quadrupole orthogonal acceleration time-of-flight mass spectrometer, equipped with a traveling wave ion-mobility cell. Besides demonstrating the separation for different lipids using the chromatographic method, we demonstrate the use of the ion-mobility MS platform for the structural elucidation of lipids. The method can now be used to elucidate structures of a wide variety of lipids in biological samples of different matrices.
Communication Delay Co-Design in $\mathcal{ H}_{2}$-Distributed Control Using Atomic Norm Minimization (2015)

When designing distributed controllers for large-scale systems, the actuation, sensing, and communication architectures of the controller can no longer be taken as given. In particular, controllers implemented using dense architectures typically outperform controllers implemented using simpler ones - however, it is also desirable to minimize the cost of building the architecture used to implement a controller. The recently introduced Regularization for Design framework poses the controller architecture/control law co-design problem as one of jointly optimizing the competing metrics of controller architecture cost and closed-loop performance, and shows that this task can be accomplished by augmenting the variational solution to an optimal control problem with a suitable atomic norm penalty. Although explicit constructions for atomic norms useful for the design of actuation, sensing and joint actuation/sensing architectures are introduced, no such construction is given for atomic norms used to design communication architectures. This paper describes an atomic norm that can be used to design communication architectures for which the resulting distributed optimal controller is specified by the solution to a convex program. Using this atomic norm, we then show that in the context of H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> -distributed optimal control, the communication architecture/control law co-design task can be performed through the use of finite-dimensional second-order cone programming.