gebhart/patrepeval huggingface dataset:
Serotonin G Protein-Coupled Receptor-Based Biosensing Modalities in Yeast (2022)

Serotonin is a key neurotransmitter involved in numerous physiological processes and serves as an important precursor for manufacturing bioactive indoleamines and alkaloids used in the treatment of human pathologies. In humans, serotonin sensing and signaling can occur by 12 G protein-coupled receptors (GPCRs) coupled to Gα proteins. In yeast, human serotonin GPCRs coupled to Gα proteins have previously been shown to function as whole-cell biosensors of serotonin. However, systematic characterization of serotonin biosensing modalities between variant serotonin GPCRs and application thereof for high-resolution serotonin quantification is still awaiting. To systematically assess GPCR signaling in response to serotonin, we characterized reporter gene expression at two different pHs of a 144-sized library encoding all 12 human serotonin GPCRs in combination with 12 different Gα proteins engineered in yeast. From this screen, we observed changes in the biosensor sensitivities of >4 orders of magnitude. Furthermore, adopting optimal biosensing designs and pH conditions enabled high-resolution high-performance liquid chromatography-validated sensing of serotonin produced in yeast. Lastly, we used the yeast platform to characterize 19 serotonin GPCR polymorphisms found in human populations. While major differences in signaling were observed among the individual polymorphisms when studied in yeast, a cross-comparison of selected variants in mammalian cells showed both similar and disparate results. Taken together, our study highlights serotonin biosensing modalities of relevance to both biotechnological and potential human health applications.
Letermovir Prophylaxis for Cytomegalovirus (2018)

Marty and colleagues (Dec. 21 issue)1 found that letermovir prophylaxis after hematopoietic-cell transplantation resulted in a lower risk of clinically significant cytomegalovirus (CMV) infection than placebo. This trial shows that a prophylactic agent can provide meaningful benefit after hematopoietic-cell transplantation, without considerable myelotoxic events..
Wafer fused optically-pumped semiconductor disk laser operating at 1220- nm (2009)

A novel approach based on a wafer fused optically-pumped semiconductor disk laser (SDL) operating at 1.2 mum is reported. The technique allows integrating materials with different lattice constants and provides convenient means to extend the operation wavelength of an SDL. This work demonstrates the first wafer fused optically-pumped semiconductor disk laser operating at the 1.2 m wavelength regime. The performance of the laser could be further improved by using a 920 nm pump source to achieve higher pump absorption in the active region. The active region and the distributed Bragg reflector (DBR) were grown separately with molecular beam epitaxy. The active region, grown on an InP-substrate, consists of 5 AlGalnAs quantum well pairs positioned using InP-spacer to the antinode of the standing wave created between the DBR and the semiconductor-air interface.
Effect of a Vertical Stack of Aligned Subwavelength Metal Hole Arrays on Extraordinary Transmission Spectra (2007)

We report on the effect of stacking a pair of metallic subwavelength hole arrays on the extraordinary transmission spectrum. A novel fabrication process was developed to create a self-aligned vertical stack of subwavelength metal gratings with precise control of the separation between the two metal films. For separations within the coupling region of the evanescent surface modes of the metal films, minor sharpening of the transmission filter characteristics was observed.
Phosphorylation by Casein Kinase 2 Regulates Nap1 Localization and Function (2007)

In Saccharomyces cerevisiae, the evolutionarily conserved nucleocytoplasmic shuttling protein Nap1 is a cofactor for the import of histones H2A and H2B, a chromatin assembly factor and a mitotic factor involved in regulation of bud formation. To understand the mechanism by which Nap1 function is regulated, Nap1-interacting factors were isolated and identified by mass spectrometry. We identified several kinases among these proteins, including casein kinase 2 (CK2), and a new bud neck-associated protein, Nba1. Consistent with our identification of the Nap1-interacting kinases, we showed that Nap1 is phosphorylated in vivo at 11 sites and that Nap1 is phosphorylated by CK2 at three substrate serines. Phosphorylation of these serines was not necessary for normal bud formation, but mutation of these serines to either alanine or aspartic acid resulted in cell cycle changes, including a prolonged S phase, suggesting that reversible phosphorylation by CK2 is important for cell cycle regulation. Nap1 can shuttle between the nucleus and cytoplasm, and we also showed that CK2 phosphorylation promotes the import of Nap1 into the nucleus. In conclusion, our data show that Nap1 phosphorylation by CK2 appears to regulate Nap1 localization and is required for normal progression through S phase.
Detection of Structural Magnet Defects for Permanent Magnet Synchronous Motors (2021)

This paper presents a novel method for the detection of magnet cracks or defects through back electromotive force (EMF) voltage, line current and vibration signals for radial flux permanent magnet (PM) synchronous motors. An integer slot PM motor with 12 poles is used in the study. Different types of faults including both radial and axial magnet crack defects with multiple magnet fault scenarios and multiple pole fault cases are studied in detail. In addition, the severity of magnet fault is also investigated. Random forest based magnet defect detection is utilized and a classification scheme is proposed in order to analyze the changes in the harmonics arising from single or multiple, radial or axial magnet defects. The results clearly show that the harmonics is altered in such a manner that it is possible to determine not only the magnet fault but the type of the magnet defect using motor voltage, current or vibration data.
ADAM10 Sheddase Activity is a Potential Lung-Cancer Biomarker (2018)

<b>Background</b>: Increases in expression of ADAM10 and ADAM17 genes and proteins are inconsistently found in cancer lesions, and are not validated as clinically useful biomarkers. The enzyme-specific proteolytic activities, which are solely mediated by the active mature enzymes, directly reflect enzyme cellular functions and might be superior biomarkers than the enzyme gene or protein expressions, which comprise the inactive proenzymes and active and inactivated mature enzymes. <b>Methods:</b> Using a recent modification of the proteolytic activity matrix analysis (PrAMA) measuring specific enzyme activities in cell and tissue lysates, we examined the specific sheddase activities of ADAM10 (ADAM10sa) and ADAM17 (ADAM17sa) in human non-small cell lung-carcinoma (NSCLC) cell lines, patient primary tumors and blood exosomes, and the noncancerous counterparts. <b>Results:</b> NSCLC cell lines and patient tumors and exosomes consistently showed significant increases of ADAM10sa relative to their normal, inflammatory and/or benign-tumor controls. Additionally, stage IA-IIB NSCLC primary tumors of patients who died of the disease exhibited greater increases of ADAM10sa than those of patients who survived 5 years following diagnosis and surgery. In contrast, NSCLC cell lines and patient tumors and exosomes did not display increases of ADAM17sa. <b>Conclusions:</b> This study is the first to investigate enzyme-specific proteolytic activities as potential cancer biomarkers. It provides a proof-of-concept that ADAM10sa could be a biomarker for NSCLC early detection and outcome prediction. To ascertain that ADAM10sa is a useful cancer biomarker, further robust clinical validation studies are needed.
iOptimize: A software capability for analyzing and optimizing connection-oriented data networks in real time (2005)

This paper describes a service called iOptimize that analyzes and optimizes service providers' connection-oriented data networks. In these networks, online connection routing is used to set up connections quickly, but the simple path selection scheme and the limited information available for online routing can cause network capacity to be used inefficiently. This may result in the loss or disruption of user data transmissions, leading to a degraded quality of service (QoS) in a network capable of supporting much higher throughput. The objective of iOptimize is to detect and analyze such inefficiencies and to offset them by the occasional rerouting of a selected set of connections, while causing little or no disruption of the existing data services and network operations. By helping service providers support data transport services at the QoS levels desired, iOptimize lets them make the most of their existing network resources and helps them defer capital expenditure. Moreover, by tuning their networks to perform at optimal efficiency, it improves end users' experiences, resulting in lower churn/turnover and reduced maintenance costs.
Oxygen tracer studies of ferroelectric fatigue in Pb(Zr,Ti)O3 thin films (2002)

Long-range oxygen motion has been observed in Pt/Pb(Zr,Ti)O3/Ir thin-film structures after electrical fatigue cycling at room temperature. Through an exchange anneal, isotopic O18 was incorporated as a tracer into bare Pb(Zr,Ti)O3 (PZT) films, allowing secondary ion mass spectrometry measurements of the tracer profile evolution as a function of the number of polarization reversals. Observation of O18 tracer redistribution during voltage cycling, which is presumably mediated by oxygen vacancy motion, was found to be strongly dependent upon the thermal history of the film. However, there was no strong correlation between the extent of O18 tracer redistribution and the extent of polarization suppression induced by voltage cycling. Our results suggest that oxygen vacancy motion plays, at most, a secondary role in ferroelectric fatigue of PZT thin films.
The Effect of Channelling a Polymeric Surface on Its Adhesion and Friction Characteristics (2007)

In recent years, a new approach towards enhancing tribological properties at small-scale by the fabrication of nano/micro-scale polymeric patterns using soft lithography has gained popularity. These patterned surfaces provide promising solutions to the tribological issues in small-scale devices such as micro/nano-electromechanical systems (MEMS/NEMS). In the present study, we investigate the nano-scale tribological properties of a novel topography, namely submicrometer-scale channels fabricated on thin polymeric films using a soft lithographic technique. Results show that these surfaces have superior nano-tribological properties, as they reduce adhesion and friction forces to a significant extent when compared to silicon wafer and non-patterned polymeric thin film.
Evaluation of Audio Watermark System Using Short Detection Time Frame (2009)

Assumed applications of copyright protection for music and synthesized voice are discussed. We developed a prototype audio watermark system combining the results of previous studies based on the patchwork algorithm, modifying the amplitude in the time-domain of voiced audio data, and using a reference signal. The results of experimental evaluation show that this our system can detect watermarks in a time frame as short as 2 s.
ThecycloSal-Nucleotide Delivery System (2007)

Pronucleotides represent a promising alternative to improve the biological activity of nucleoside analogs against different viral diseases and cancer chemotherapy. Moreover, pronucleotides are valuable tools for studies concerning nucleoside/nucleotide metabolism. The basic idea is to achieve nucleotide delivery into cells, bypassing limitations with intracellular formation of nucleotides from their nucleoside precursors. The cycloSaligenyl (cycloSal) concept is one of several pronucleotide systems reported so far but is the only approach in which a pronucleotide is cleaved successfully by simple but selective chemical hydrolysis. Beside others, for the nucleoside analog 2′,3′-dideoxy-2′,3′-didehydrothymidine (d4T), the application of the cycloSal approach improved antiviral potency. The basic concept, the chemistry, different structural modifications, and their effects on the antiviral potency of the cycloSal-d4T 5′-monophosphate triesters are discussed. The application of the approach to different biologically active nucleoside analogs against different targets is discussed. First results of a conceptual extension of the original cycloSal approach are summarized. Once the pronucleotides have passed the membrane, the aim is to trap the cycloSalphosphate triesters inside the cells. Therefore, enzyme-cleavable groups have been attached via a linker to the cycloSal moiety.
Table S1 from Theranostic Radiolabeled Anti-CD20 sdAb for Targeted Radionuclide Therapy of Non-Hodgkin Lymphoma (2023)

&lt;p&gt;Quantification of in vivo biodistribution of 14 anti-hCD20 sdAbs, radiolabeled with 99mTc, obtained after 1 h p.i., expressed as mean % IA/cm3 {plus minus} SD (n = 3 per sdAb).&lt;/p&gt;
ChemInform Abstract: Synthesis, Structural Characterization, and Properties of the Organothorium Alkylthiolate Complex ((CH3)5C5)2Th(SCH2CH2CH3)2. (1988)

Abstract The title complex (III) is prepared according to the scheme and characterized by X‐ray structure analysis (space group C2/c, Z=4).
On the Support of Flexible Patient Privacy Policies in Social-Medical Discovery (2012)

Many new socially flavored medical services have recently emerged, utilizing the data openness and sharing through social channels. The adoption of such services by patients is still very limited, mainly due to privacy issues. Existing social-medical discovery services support only strict patient privacy policies and are not flexible enough to accommodate a wider range of privacy policy definitions. In this paper we present the IBM Medical Information and Care System (Medics) privacy-aware social-medical discovery solution that provides a highly flexible support for both fine-grained and dynamic patient privacy policies.
Elemental fluorine : Part 16. Versatile thin-film gas–liquid multi-channel microreactors for effective scale-out (2005)

Versatile and conveniently operated microreactor devices, suitable for long term chemical synthesis for both laboratory and industrial use, are described. Direct fluorination of ethyl acetoacetate by fluorine gas is used as a model reaction to illustrate the successful application of reactors having either 9, 18 or 30 microchannels, with all channels supplied from single reagent sources, to provide significant quantities of fluorinated products. Convenient reactor maintenance, simple design, versatility and the enhanced safety features of using such modular microreactor devices, make these systems appropriate for synthesis on the large scale.
Clinical Diagnosis of Hypersensitivity Pneumonitis (2003)

The diagnosis of hypersensitivity pneumonitis (HP) is difficult and often relies on histopathology. Our objective was to identify diagnostic criteria and to develop a clinical prediction rule for this disease. Consecutive patients presenting a condition for which HP was considered in the differential diagnosis underwent a program of simple standardized diagnostic procedures. High-resolution computed tomography scan and bronchoalveolar lavage (BAL) defined the presence or absence of HP. Patients underwent surgical lung biopsy when the computed tomography scan, BAL, and other diagnostic procedures failed to yield a diagnosis. A cohort of 400 patients (116 with HP, 284 control subjects) provided data for the rule derivation. Six significant predictors of HP were identified: (1) exposure to a known offending antigen, (2) positive precipitating antibodies to the offending antigen, (3) recurrent episodes of symptoms, (4) inspiratory crackles on physical examination, (5) symptoms occurring 4 to 8 hours after exposure, (6) and weight loss. The area under the receiver operating characteristic curve was 0.93 (95% confidence interval: 0.90-0.95). The rule retained its accuracy when validated in a separate cohort of 261 patients. The diagnosis of HP can often be made or rejected with confidence, especially in areas of high or low prevalence, respectively, without BAL or biopsy.
System for Efficient Helper-Dependent Minimal Adenovirus Construction and Rescue (2001)

Helper-dependent minimal adenoviral vectors deleted for all viral coding sequences are promising vectors for gene therapy. They retain only the adenovirus cis elements for replication and packaging, can accommodate up to 36 kb of foreign DNA, and exhibit prolonged transgene expression and reduced tissue toxicity as compared with first-generation adenoviral vectors. We have developed a system consisting of a set of cosmid cloning vectors (pMV and pMVX) for simple routine construction and efficient rescue of minimal adenoviral vectors. In the cloning vectors the inverted terminal repeats (ITRs) are flanked by recognition sites for the super rare-cutting endonuclease I-SceI. This allows the release of linear minimal adenovirus genomes for rescue of minimal adenovirus regardless of the sequence of the insert DNA. pMV contains a multiple cloning site for the insertion of 26 to 36 kb of therapeutic DNA. pMVX contains a noncoding human X-chromosomal DNA fragment as a vector backbone, which provides endonuclease restriction sites that allow for complete or partial replacement of the vector backbone by 1 to 26 kb of therapeutic DNA sequences, while retaining a packageable final minimal adenovirus genome size between 27 and 37.5 kb. Both vectors exist in two forms, with or without an Escherichia coli lacZ reporter gene cassette. Several minimal adenoviral vectors with insert sizes ranging from 1.5 to 16 kb were constructed with these cloning vectors. Minimal adenoviruses were efficiently rescued and amplified to high titers, using a Cre/lox-based helper system. Vectors containing the X-chromosomal backbone were stable during amplification. This simple and efficient system facilitates the construction of minimal adenoviruses and should be useful for further improvement of these new vectors.
Ion Current Rectification, Limiting and Overlimiting Conductances in Nanopores (2015)

Previous reports on Poisson-Nernst-Planck (PNP) simulations of solid-state nanopores have focused on steady state behaviour under simplified boundary conditions. These are Neumann boundary conditions for the voltage at the pore walls, and in some cases also Donnan equilibrium boundary conditions for concentrations and voltages at both entrances of the nanopore. In this paper, we report time-dependent and steady state PNP simulations under less restrictive boundary conditions, including Neumann boundary conditions applied throughout the membrane relatively far away from the nanopore. We simulated ion currents through cylindrical and conical nanopores with several surface charge configurations, studying the spatial and temporal dependence of the currents contributed by each ion species. This revealed that, due to slow co-diffusion of oppositely charged ions, steady state is generally not reached in simulations or in practice. Furthermore, it is shown that ion concentration polarization is responsible for the observed limiting conductances and ion current rectification in nanopores with asymmetric surface charges or shapes. Hence, after more than a decade of collective research attempting to understand the nature of ion current rectification in solid-state nanopores, a relatively intuitive model is retrieved. Moreover, we measured and simulated current-voltage characteristics of rectifying silicon nitride nanopores presenting overlimiting conductances. The similarity between measurement and simulation shows that overlimiting conductances can result from the increased conductance of the electric double-layer at the membrane surface at the depletion side due to voltage-induced polarization charges. The MATLAB source code of the simulation software is available via the website http://micr.vub.ac.be.
The renin-angiotensin and adrenergic nervous system in cardiac hypertrophy in fructose-fed rats (2002)

Left ventricular hypertrophy in FFR may be less dependent on systemic elevations of BP and more dependent on the RAS and the sympathetic nervous system. Use of an AT1 receptor antagonist might be the most beneficial way to prevent progression of LVH through direct effects on tissue RAS and the sympathetic nervous system in FFR. As these changes occur in a rat model with hyperinsulinemia, insulin may have a role in promoting LVH by activating the local RAS and sympathetic nervous system activity.
CD80 in Immune Suppression by Mouse Ovarian Carcinoma–Associated Gr-1+CD11b+ Myeloid Cells (2006)

An elevated number of Gr-1+CD11b+ myeloid cells has been described in mice bearing transplantable tumors, and has been associated with immune suppression. We examined the role of such myeloid suppressor cells in mice bearing the spontaneously transformed syngeneic mouse ovarian surface epithelial cell line, 1D8. We observed high levels of CD80 expression by Gr-1+CD11b+ cells from spleen, ascites, and tumor tissue of mice bearing 1D8 ovarian carcinoma, whereas CD40 and CD86 were absent. CD80 expression was not detected on Gr-1+CD11b+ cells from naïve mice. However, the expression of CD80 by Gr-1+CD11b+ cells from naïve mice was promoted by coculture with 1D8 cells. Because irradiated 1D8 cells, but not 1D8-conditioned medium, up-regulate CD80 expression by Gr-1+CD11b+ cells, this phenomenon likely requires direct interaction. Gr-1+CD11b+ cells derived from 1D8 tumor-bearing mice provided significant suppression of antigen-specific immune responses, but Gr-1+CD11b+ cells from naïve mice did not. Both short interfering RNA-mediated knockdown and genetic knockout of CD80 expression by Gr-1+CD11b+ cells of 1D8 tumor-bearing mice alleviated the suppression of antigen-specific immune responses. Suppression via CD80 on Gr-1+CD11b+ myeloid cells was mediated by CD4+CD25+ T regulatory cells and required CD152. CD80 knockout or antibody blockade of either CD80 or CD152 retarded the growth of 1D8 tumor in mice, suggesting that expression of CD80 on Gr-1+CD11b+ myeloid cells triggered by 1D8 ovarian carcinoma suppresses antigen-specific immunity via CD152 signaling and CD4+CD25+ T regulatory cells. Thus, CD80-dependent responses to myeloid suppressor cells may contribute to tumor tolerance and the progression of ovarian carcinoma.
A novel mutation of IL1RN in the deficiency of interleukin-1 receptor antagonist syndrome: Description of two unrelated cases from Brazil (2011)

The presence of the same homozygous novel mutation in IL1RN in 2 unrelated Brazilian patients suggests that this genetic variant may be a founder mutation that has been introduced in the Brazilian population.