gebhart/patrepeval huggingface dataset:
Reactions of C‐terminal ω‐amino acid residues in liquid hydrogen fluoride (1993)

The benzyl-ester bond linking the C-terminal delta-aminovaleric acid residue of a peptide to a polymeric support was cleaved with liquid hydrogen fluoride in the presence of anisole, added as scavenger. Instead of the expected peptide with a free carboxyl group at the C-terminus, a peptide terminating in a ketone derivative was obtained. The unusual extent of this known side-reaction was attributed to the effect of the distance between the amino group and the carboxyl group in the C-terminal residue. The results of model experiments corroborated this view.
Improvement of fast responsive LC materials by bent-core dopants in optical compensated bend mode liquid crystal displays (2011)

Stabilization of bend configuration in optical compensated bend (OCB) mode cells by doping bent-core molecules was developed in this study. The values of response time (t) and threshold voltage (V th) in OCB cells were dependent not only on the concentration but also on the shape, dipole direction, and flexible chain length of the doping molecules. Experimental results showed that the total response time (t total) and threshold voltage (V th) of OCB cells could be reduced by doping bent-core molecules, and smaller t values produced by reducing flexible chain lengths. In addition, attaining smaller V th values could be achieved by reducing polarization of bent-core molecules. In general, higher concentrations of dopants normally induced shorter field-on response time (t on) and a minimum field-off response time (t off) occurred at 0.5% of doping concentration, where the fastest total response time (t total) values were achieved.
Immunophenotypic characterization of plasma cells from monoclonal gammopathy of undetermined significance patients. Implications for the differential diagnosis between MGUS and multiple myeloma. (1998)

Although the immunophenotype of plasma cells (PCs) from multiple myeloma (MM) patients has been extensively explored, information on the phenotypic characteristics of PCs in monoclonal gammopathy of undetermined significance (MGUS) patients is scanty and frequently controversial. Thus, the question of whether or not PCs are phenotypically different in the two disorders and whether this criteria could be useful for the differential diagnosis between MGUS and MM remains to be explored. In the present study, the immunophenotypic profile of bone marrow PCs (BMPCs) from a group of 76 MGUS patients has been analyzed by flow cytometry and compared with that of BMPCs present in both MM patients (n = 65) and control subjects (n = 10). For that purpose, a large panel of monoclonal antibodies against PC-related antigens was used together with a sensitive methodology in which a minimum of 10(3) PCs were studied. In all MGUS cases studied, two clearly defined and distinct PC subpopulations could be identified. One PC subpopulation, population A (33 +/- 31% of total PCs), constantly displayed a high CD38 expression with low forward light scatter (FSC)/side light scatter (SSC) and was positive for CD19 and negative for CD56 (only a small proportion of these PCs were weakly positive for CD56). The other PC subpopulation, population B (67 +/- 31% of total PCs), showed the opposite pattern; the antigen CD56 was strongly positive and CD19 was constantly negative, and it showed a lower CD38 expression and higher FSC/SSC values than population A. Clonality studies (cytoplasmic light chain restriction, DNA content studies, and polymerase chain reaction assessment) confirmed the clonal nature of PCs from population B and the polyclonal origin of PCs from population A. Moreover, the polyclonal PCs from MGUS displayed a phenotypic profile identical to that found in PCs from healthy individuals. By contrast, clonal PCs from all MGUS patients displayed a similar antigenic profile to myelomatous PCs, with clear phenotypic differences with respect to normal PCs: lower intensity of CD38 expression and a variable reactivity for markers that were not expressed in normal PCs, such as CD28, CD117, and sIg. Although the presence of residual polyclonal PCs was a constant finding in MGUS patients, it was a rare event in MM and, when present (only 22% of MM cases), its frequency was significantly lower than that observed in MGUS (0.25% versus 32.9%, respectively; P < 0.0001). Only 1.5% of patients with MM had more than 3% of normal PCs, whereas 98% of patients with MGUS had more than 3%. Moreover, as shown by multivariate analysis, the number of residual polyclonal PCs was the most powerful single parameter for the discrimination between MGUS and MM patients at diagnosis, even when only stage I MM cases were considered.
SCAnDroid (2018)

Although the Android system has been continuously hardened against side-channel attacks, there are still plenty of APIs available that can be exploited. However, most side-channel analyses in the literature consider specifically chosen APIs (or resources) in the Android framework, after a manual analysis of APIs for possible information leaks has been performed. Such a manual analysis is a tedious, time consuming, and error-prone task, meaning that information leaks tend to be overlooked.
Data Integration Models for Heterogeneous Industrial Systems: A Conceptual Analysis (2021)

In the industrial automation domain, data integration between heterogeneous systems and architectures is a challenge. Companies and factories are impatient with the selection of technical solutions that are beneficial to local requirements, therefore facing problems of data integration and incompatibility between other systems. There is a need to bridge heterogeneous industrial systems to provide data integration. This article aims to provide guidelines to industrial managers and solution designers to achieve data integration between heterogeneous industrial systems according to their requirements. For this purpose, we have explored the implementation of two data integration models that can be selected based on the state and needs of industrial systems. The first data integration model is based on event-driven architecture (EDA), where Message Queuing Telemetry Transport (MQTT) is deployed as an event broker. The second model is based on the Arrowhead Framework, which is designed by using service-oriented architecture (SOA) principles, where EventHandler provides SOA-based event-driven communication. We conceptually compare and analyze them based on selected criteria essential in an industrial environment. The qualitative analysis of these models is based on proof-of-concept implementations made available for our evaluation.
Substitute Valuations, Auctions and Equilibrium with Discrete Goods (2006)

For economies in which goods are available in several (discrete) units, this paper identifies two notions of substitutes. The weaker notion guarantees monotonicity of tˆatonnement processes and convergence of clock auctions to a pseudo-equilibrium, but only the stronger notion, which treats each unit traded as a distinct good with its own price, guarantees that every pseudo-equilibrium is a Walrasian equilibrium, the Vickrey outcome is in the core, and the “law of aggregate demand” is satisfied. The paper provides several characterizations and properties of weak and strong substitutes.
Statistical structure-to-property relationships for fuel cell materials (2013)

Development and optimization of components for fuel cells is hindered by the complex nature of the materials, a partial understanding of the reaction mechanisms and precise chemistry of active site or sites and relationship between performance and morphological properties such as size of particles, surface area, roughness, porosity, etc. XPS is one of the most widely utilized surface spectroscopic techniques for the analysis of material structure. Surface morphology is one of the most important factors affecting functional performance of fuel cell components. Correlation of structure, morphology and performance of Pt catalysts within MEA subjected to different accelerated test protocols (AST) is achieved through the application of principal component analysis (PCA) to curve-fits of high-resolution XPS spectra combined with morphological parameters extracted from SEM images and results of electrochemical measurements.
The modified osteotome technique. (2001)

Patients who have been partially edentulous in the posterior segments for many years frequently present with reduced alveolar bone and/or enlarged sinuses. The choice of treatment for these patients will depend on the volume of residual bone, morphology of the alveolar crest, and amount of space available for the prosthesis. A new, minimally invasive surgical procedure using Summers osteotomes is described for the treatment of the edentulous posterior maxilla in which the bone thickness below the sinus is limited (> or = 5 mm). This suggested modified treatment is based on the use of a combination of osteotomes, drills, and screw-type implants with a rough surface texture.
Profiling the Targets of Protective CD8+ T Cell Responses to Infection (2017)

T cells are critical effectors of host immunity that target intracellular pathogens, such as the causative agents of HIV, tuberculosis, and malaria. The development of vaccines that induce effective cell-mediated immunity against such pathogens has proved challenging; for tuberculosis and malaria, many of the antigens targeted by protective T cells are not known. Here, we report a novel approach for screening large numbers of antigens as potential targets of T cells. Malaria provides an excellent model to test this antigen discovery platform because T cells are critical mediators of protection following immunization with live sporozoite vaccines and the specific antigen targets are unknown. We generated an adenovirus array by cloning 312 highly expressed pre-erythrocytic <i>Plasmodium yoelii</i> antigens into adenovirus vectors using high-throughput methodologies. The array was screened to identify antigen-specific CD8<sup>+</sup> T cells induced by a live sporozoite vaccine regimen known to provide high levels of sterile protection mediated by CD8<sup>+</sup> T cells. We identified 69 antigens that were targeted by CD8<sup>+</sup> T cells induced by this vaccine regimen. The antigen that recalled the highest frequency of CD8<sup>+</sup> T cells, PY02605, induced protective responses in mice, demonstrating proof of principle for this approach in identifying antigens for vaccine development.
Methods of measurement of passive integrated optical waveguides (1992)

The author examines popular method of evaluating losses of integrated optical waveguides. The aim in measuring these waveguides is usually to establish the propagation loss to the optical mode, and consequently evaluating the insertion loss of a device is not sufficient. This is because the propagation loss is closely related to the properties of the material in which the waveguide is fabricated and therefore, for a given waveguide geometry, can be reduced very little without improving the quality of the materials involved or their interfaces. In evaluating the propagation loss it is sometimes difficult to distinguish between genuine propagation loss and effects related to insertion loss such as Fresnel reflection, and input coupling efficiency. For this reason these issues are also addressed briefly, by means of consideration of some example results. The parameters that affect the accuracy and convenience of each of the measurement techniques are considered. >
Vaccine-Induced CD8+ T Lymphocytes of Rhesus Monkeys Recognize Variant Forms of an HIV Epitope but Do Not Mediate Optimal Functional Activity (2011)

The sequence diversity of HIV-1 presents a challenge for the development of an effective HIV-1 vaccine, because such a vaccine must confer protection against diverse forms of the virus. The present studies were initiated to explore how vaccine-induced clonal populations of CD8(+) T lymphocytes of rhesus monkeys recognize variants of an HIV-1 envelope epitope sequence. Evaluating a subset of variants of a selected epitope peptide that retain their binding to the MHC class I molecule of rhesus monkeys that presents this epitope peptide, we show that vaccine-elicited CD8(+) T lymphocytes comparably recognize the wild-type and a number of variant epitope peptides as determined by tetramer binding assays. In fact, the same clonal populations of CD8(+) T lymphocytes recognize the wild-type and variant epitope peptides. However, functional assays show that many of these variant epitope peptides stimulate suboptimal cytokine production by the vaccine-elicited CD8(+) T lymphocytes. These findings suggest that vaccine-induced CD8(+) T lymphocyte populations may recognize diverse forms of a viral epitope, but may not function optimally to confer protection against viruses expressing many of those variant sequences.
Supplementary Figures 1-4 from Vitamin D<sub>3</sub> Metabolism in Human Glioblastoma Multiforme: Functionality of CYP27B1 Splice Variants, Metabolism of Calcidiol, and Effect of Calcitriol (2023)

Supplementary Figures 1-4 from Vitamin D&lt;sub&gt;3&lt;/sub&gt; Metabolism in Human Glioblastoma Multiforme: Functionality of CYP27B1 Splice Variants, Metabolism of Calcidiol, and Effect of Calcitriol
Role of Angiotensin II in the Renal Response to Atrial Natriuretic Peptide in Normal Subjects (1988)

Atrial natriuretic peptide (ANP) has been shown to inhibit angiotensin II (Ang II)-induced steroidogenesis and vasoconstriction. To investigate the role of Ang II in the renal response to ANP, a synthetic ANP (0.1 micron/kg/min, 60 min) was infused for 1 h in eight subjects with or without pretreatment with an inhibitor of the converting enzyme, enalapril (20 mg, p.o.), or Ang II (10 ng/kg/min). ANP infusion alone caused increases in urinary volume, urinary sodium excretion, and glomerular filtration rate (GFR). However, enalapril treatment abolished these diuretic and natriuretic effects of ANP. In this group, GFR was decreased and no tubular effects, which was estimated by urinary excretion of sodium and phosphate, were observed. The anti-natriuretic effects of exogenous Ang II were reversed by concomitant ANP infusion, which inhibited both proximal and postproximal sodium reabsorption induced by Ang II without changing the GFR. These results indicate that endogenous Ang II plays an obligatory role in the natriuretic response to ANP and also suggested that ANP inhibits Ang II-stimulated tubular reabsorption of sodium.
A Novel Series of Indole Alkaloid Derivatives Inhibit Dengue and Zika Virus Infection by Interference with the Viral Replication Complex (2021)

Here, we identified a novel class of compounds which demonstrated good antiviral activity against dengue and Zika virus infection. These derivatives constitute intermediates in the synthesis of indole (ervatamine-silicine) alkaloids and share a tetracyclic structure, with an indole and a piperidine fused to a seven-membered carbocyclic ring. Structure-activity relationship studies indicated the importance of substituent at position C-6 and especially the presence of a benzyl ester for the activity and cytotoxicity of the molecules. In addition, the stereochemistry at C-7 and C-8, as well as the presence of an oxazolidine ring, influenced the potency of the compounds. Mechanism of action studies with two analogues of this family (compounds 22 and <i>trans</i>-14) showed that this class of molecules can suppress viral infection during the later stages of the replication cycle (RNA replication/assembly). Moreover, a cell-dependent antiviral profile of the compounds against several Zika strains was observed, possibly implying the involvement of a cellular factor(s) in the activity of the molecules. Sequencing of compound-resistant Zika mutants revealed a single nonsynonymous amino acid mutation (aspartic acid to histidine) at the beginning of the predicted transmembrane domain 1 of NS4B protein, which plays a vital role in the formation of the viral replication complex. To conclude, our study provides detailed information on a new class of NS4B-associated inhibitors and strengthens the importance of identifying host-virus interactions in order to tackle flavivirus infections.
Localized vibrational modes in bars and plates (2010)

We consider the localized vibrational modes that can exist at the edge of a semi-infinite plate and at the end of a semi-infinite bar of small thickness. It is known that for certain special values of Poisson’s ratio σ these modes are perfectly localized, are uncoupled to bulk modes, and thus do not lose energy by acoustic radiation. We show that for other values of σ it is possible to modify the shape of the end of the plate or bar in a way such that a perfectly localized edge mode is formed. Finally, we discuss the effect of this localization phenomenon on the vibrational modes of plates and bars of finite length.
Synthesis of Biologically Active Amines via Rhodium−Bisphosphite-Catalyzed Hydroaminomethylation (2005)

[reaction: see text] We report the use of a highly regioselective rhodium-bisphosphite catalyst for olefin hydroaminomethylation. This catalyst system was successfully applied in the synthesis of two biologically active tertiary amines, ibutilide and aripiprazole.
Rebalancing expression of HMGB1 redox isoforms to counteract muscular dystrophy (2021)

Muscular dystrophies (MDs) are a group of genetic diseases characterized by progressive muscle wasting associated to oxidative stress and persistent inflammation. It is essential to deepen our knowledge on the mechanism connecting these two processes because current treatments for MDs have limited efficacy and/or are associated with side effects. Here, we identified the alarmin high-mobility group box 1 (HMGB1) as a functional link between oxidative stress and inflammation in MDs. The oxidation of HMGB1 cysteines switches its extracellular activities from the orchestration of tissue regeneration to the exacerbation of inflammation. Extracellular HMGB1 is present at high amount and undergoes oxidation in patients with MDs and in mouse models of Duchenne muscular dystrophy (DMD) and limb-girdle muscular dystrophy 3 (LGMDR3) compared to controls. Genetic ablation of HMGB1 in muscles of DMD mice leads to an amelioration of the dystrophic phenotype as evidenced by the reduced inflammation and muscle degeneration, indicating that HMGB1 oxidation is a detrimental process in MDs. Pharmacological treatment with an engineered nonoxidizable variant of HMGB1, called 3S, improves functional performance, muscle regeneration, and satellite cell engraftment in dystrophic mice while reducing inflammation and fibrosis. Overall, our data demonstrate that the balance between HMGB1 redox isoforms dictates whether skeletal muscle is in an inflamed or regenerating state, and that the nonoxidizable form of HMGB1 is a possible therapeutic approach to counteract the progression of the dystrophic phenotype. Rebalancing the HMGB1 redox isoforms may also be a therapeutic strategy for other disorders characterized by chronic oxidative stress and inflammation.
Butyrate modulates the expression of. beta. -adrenergic receptor subtype in 3T3-L1 cells (1986)

In mouse 3T3-L1 fibroblasts, the glucocorticoid dexamethasone (dex) affects a switch in ..beta..-adrenergic receptor (..beta..AR) subtype expression from ..beta../sub 1/AR to ..beta../sub 2/AR and increases total ..beta..AR number. They now demonstrate a similar effect by sodium butyrate (B) and find that the combined effect of these two gene-activating agents is greater than additive suggesting different mechanisms of action on the ..beta..AR. ..beta..AR are assayed in membranes prepared from 3T3-L1 cells using the radiolabeled ..beta..AR-specific antagonist (/sup 125/I)-cyanopindolol. ..beta..AR subtype is determined by competition binding of the ..beta../sub 2/AR-selective antagonist ICI 118.551 for the radioligand. B (2-10mM) causes a dose-dependent increase in total ..beta..AR number (up to 2-fold over control) and the proportion of ..beta../sub 2/AR. B (5mM) causes a time-dependent increase in total ..beta..AR number (2-fold) and the proportion of ..beta../sub 2/AR up to 24 hr. Dex maximally increases total ..beta..AR number (2-fold) when treated for 48 hr at concentrations greater than or equal to 100nM. B (2 or 5mM) together with dex (250nM) have a greater than additive effect on total ..beta..AR number at 24 hr (1.7-fold) and at 48 hr (1.4-2.4-fold, using 5 or 10mM B and dex greater than or equal to 10nM). The proportion of ..beta../submore » 2/AR is also greater when both compounds are added together. In comparison with proprionate and valerate, B increases total ..beta..AR number and the proportion of ..beta../sub 2/AR to a greater extent and at lower concentrations. To determine a functional correlate to these findings, cells were pre-treated for 48 hr with B and/or dex, intracellular ATP labeled with /sup 3/H-adenine, followed by treatment with forskolin (10..mu..M) and ..beta..AR agonists. B caused a dramatic increase in /sup 3/H-cAMP produced compared to control and dex treatments and a greater than additive effect was again achieved when B and dex were added together.« less
Improving NAND flash performance with read heat separation (2020)

The continuous growth in 3D-NAND flash storage density has primarily been enabled by 3D stacking and by increasing the number of bits stored per memory cell. Unfortunately, these desirable flash device design choices are adversely affecting reliability and latency characteristics. In particular, increasing the number of bits stored per cell results in having to apply additional voltage thresholds during each read operation, therefore increasing the read latency characteristics. While most NAND flash challenges can be mitigated through appropriate background processing, the flash read latency characteristics cannot be hidden and remains the biggest challenge, especially for the newest flash generations that store four bits per cell. In this paper, we introduce read heat separation (RHS), a new heat-aware data-placement technique that exploits the skew present in real-world workloads to place frequently read user data on low-latency flash pages. Although conceptually simple, such a technique is difficult to integrate in a flash controller, as it introduces a significant amount of complexity, requires more metadata, and is further constrained by other flash-specific peculiarities. To overcome these challenges, we propose a novel flash controller architecture supporting read heat-aware data placement. We first discuss the trade-offs that such a new design entails and analyze the key aspects that influence the efficiency of RHS. Through both, extensive simulations and an implementation we realized in a commercial enterprise-grade solid-state drive controller, we show that our architecture can indeed significantly reduce the average read latency. For certain workloads, it can reverse the system-level read latency trends when using recent multi-bit flash generations and hence outperform SSDs using previous faster flash generations.