gebhart/patrepeval huggingface dataset:
Pka, Ras and RGS Protein Interactions Regulate Activity of AflR, a Zn(II)2Cys6 Transcription Factor in Aspergillus nidulans (2003)

Abstract Sterigmatocystin (ST) is a carcinogenic polyketide produced by several filamentous fungi including Aspergillus nidulans. Expression of ST biosynthetic genes (stc genes) requires activity of a Zn(II)2Cys6 transcription factor, AflR. aflR is transcriptionally and post-transcriptionally regulated by a G-protein/cAMP/protein kinase A (PkaA) signaling pathway involving FlbA, an RGS (regulator of G-protein signaling) protein. Prior genetic data showed that FlbA transcriptional regulation of aflR was PkaA dependent. Here we show that mutation of three PkaA phosphorylation sites in AflR allows resumption of stc expression in an overexpression pkaA background but does not remediate stc expression in a ΔflbA background. This demonstrates negative regulation of AflR activity by phosphorylation and shows that FlbA post-transcriptional regulation of aflR is PkaA independent. AflR nucleocytoplasmic location further supports PkaA-independent regulation of AflR by FlbA. GFP-tagged AflR is localized to the cytoplasm when pkaA is overexpressed but nuclearly located in a ΔflbA background. aflR is also transcriptionally and post-transcriptionally regulated by RasA. RasA transcriptional control of aflR is PkaA independent but RasA post-transcriptional control of AflR is partially mediated by PkaA.
A new restriction fragment length polymorphism from Cryptosporidium parvum identifies genetically heterogeneous parasite populations and genotypic changes following transmission from bovine to human hosts (1997)

Length and restriction site polymorphism within a 2.8-kb threonine-rich open reading frame from Cryptosporidium parvum was identified and used to determine the genotypes of isolates from calves and humans. In agreement with observations of other genetic loci, all calf isolates were identical at this locus. In contrast, human isolates showed two profiles, one found exclusively in humans and one a superposition of both profiles, which were indicative of heterogeneous parasite populations. PCR fingerprints were consistent with a change in the genetic profile of C. parvum isolates following transmission from bovine to human hosts.
Disseminated Calcitonin-Poor Medullary Thyroid Carcinoma in a Patient With Calcitonin-Rich Primary Tumor (1986)

A multiple endocrine neoplasia type Ia patient who initially had a calcitonin-rich medullary thyroid carcinoma followed an indolent clinical course for 7 years after surgical resection. Sudden rapid dissemination of tumor led to death 2 years later. At autopsy, calcitonin immunostaining of tumor was diffusely negative, with slight positivity in less than 5% of cells. The loss of a marker of differentiation in association with the marked change in the clinical course suggests the development within the well-differentiated tumor of a poorly differentiated, biologically aggressive population of tumor cells.
Phase Variation Mapping, a Dynamic Laser Stimulation Technique with Picosecond Timing Resolution (2007)

Timing issues in modern CMOS technology can be very difficult to localize, especially when circuits are sensitive to timing variation in the picosecond range. Very powerful time resolved emission (TRE) tools are limited to bandwidths of sim;52 ps and can be SNR limited. Dynamic laser stimulation (DLS) identifies circuit's marginal regions by slightly perturbing local timing. It has the unique ability to induce timing perturbations proportional to the laser beam power. Therefore, timing perturbation can be made sufficiently small (i.e. in the picosecond range or less) not to modify the overall device behavior. Laser induced timing perturbation can speed-up or slow down transitions either from 1 to 0 (VDD to VSS) or from 0 to 1 (VSS to VDD). Knowledge of the physics behind those effects will help the designer or failure analyst to resolve timing issues. Unfortunately, timing perturbation measurements are often difficult to perform with suitable accuracy. This paper presents a new technique, phase variation mapping (PVM), which overcomes measurement accuracy issues. The measurement is based on a phase sensitive detector which provides an analog output representation of the laser induced timing variation. PVM belongs to a broader class of variation mappings techniques (which we refer to as `xVM') aimed at solving a variety of marginality-related IC issues
Comparison of bulk and thin film structures of the liquid crystal 28OBC: measurements and simulations (1998)

Freely-suspended liquid crystalline films of ethyl 4'-n-octyloxybiphenyl-4-carboxylate (28OBC) were prepared and transferred onto different substrates which enable detailed structural characterization. The structures of these thin film assemblies, which are only accessible in this way, were determined and compared with the crystal and molecular structure of 28OBC as formed by crystallization from toluene solution. The compound crystallizes in the monoclinic space group P21/c, a = 11.168(1) A, b = 7.595(2) A, c = 49.106(1) A, beta = 94.01(1) degree, Z = 8. The two symmetrically independent molecules of the asymmetric unit have been used as starting geometries for semi-empirical MO calculations. The difference between the experimentally observed and the optimized molecular structures is interpreted as the influence of the crystal field. The structures of the crystalline and E film phases have been investigated by SAXR and TED and the former has been found to be different from the bulk structure. The structural relationships between the different phases are discussed and a suggestion for the crystalline film structure is given as deduced from simulations of electron diffraction patterns.
Supplementary Figures 1 - 5 from Genetically Defined Subsets of Human Pancreatic Cancer Show Unique <i>In Vitro</i> Chemosensitivity (2023)

&lt;p&gt;PDF file, 1588K, S1: Correlations of drug response to DPC4 genotype; S2: Correlations of drug response to P16 genotype; S3: Reponses of isogenic cancer cell lines to anticancer drugs; S4: Gene expression profiles correlated with chemotherapeutic response; S5: Gene expression profiles correlated with DPC4/SMAD4.md, TP53.md and P16/CDKN2A.md.&lt;/p&gt;
Anemia falciforme: desafios e avanços na busca de novos fármacos (2012)

ADVANCES IN DRUG DISCOVERY. Sickle Cell Disease (SCD) is a disease characterized by a punctual mutation (GTG -GAG) in the sixth codon of the gamma globin gene leading to a substitution of glutamic acid by a valine in the chain of hemoglobin. Despite the huge progress on the molecular knowledge of the disease in recent years, few therapeutic resources were developed. Currently, the treatment is mainly done with the anticancer agent hydroxyurea. This review summarizes current knowledge about possible targets and new approaches to the discovery new compounds to treat the symptoms of SCD.
ChemInform Abstract: Reactions of a New Type of Intermediate Formed by Triflate Rearrangement. (1988)

Abstract Treatment of the pyranoside (VIIa), prepared from (I) as outlined in the reaction scheme, with triflic anhydride (VIII) produces the triflate (VIIb).
Comparative performance of ex situ artificial solid electrolyte interphases for Li metal batteries with liquid electrolytes (2021)

The design of artificial solid electrolyte interphases (ASEIs) that overcome the traditional instability of Li metal anodes can accelerate the deployment of high-energy Li metal batteries (LMBs). By building the ASEI <i>ex situ</i>, its structure and composition is finely tuned to obtain a coating layer that regulates Li electrodeposition, while containing morphology and volumetric changes at the electrode. This review analyzes the structure-performance relationship of several organic, inorganic, and hybrid materials used as ASEIs in academic and industrial research. The electrochemical performance of ASEI-coated electrodes in symmetric and full cells was compared to identify the ASEI and cell designs that enabled to approach practical targets for high-energy LMBs. The comparative performance and the examined relation between ASEI thickness and cell-level specific energy emphasize the necessity of employing testing conditions aligned with practical battery systems.
Fluorescence Spectroscopy and Multivariate Spectral Descriptor Analysis for High-Throughput Multiparameter Optimization of Polymerization Conditions of Combinatorial 96-Microreactor Arrays (2002)

Selection of optimum process conditions in combinatorial microreactors is essential if the combinatorial synthesis process is to be correlated with the synthesis process on a more conventional scale and the materials are to have the desired chemical properties. We have developed a new methodology for the high-throughput multiparameter optimization of polymerization reaction conditions in arrays of microreactors. Our strategy is based on the application of nondestructive spectroscopic techniques to measure chemical properties of polymers directly in individual microreactors followed by the multivariate spectral descriptor analysis for rapid determination of the optimal process conditions. We have demonstrated our strategy in the high-throughput multiparameter optimization of process conditions in thin-film melt polymerization reactions performed in 96-microreactor arrays for combinatorial screening of new polymerization catalysts. The combinatorial polymerization system was optimized for the best processing parameters using a set of input variables that included reactant parameters (relative amounts of starting components and catalyst loading) and processing variables (reaction time, reaction temperature, and inert gas flow rate). The measured output parameters were the chemical properties of materials and reproducibility of the material formation in replicate polymerizations in microreactors. Spatially resolved nondestructive evaluation of polymer formation was performed directly in individual microreactors and provided information about the spatial homogeneity of polymers in microreactors. It showed to be another powerful indicator of the reproducible polymerization process on the combinatorial scale. Although the methodology described here was implemented for high-throughput optimization of polymerization conditions, it is more general and can be further implemented for a variety of applications in which optimization of process parameters can be studied in situ or off-line using spectroscopic and other tools.
Nucleotide sequence upstream of a glucose-repressible Drosophila gene (1987)

Journal Article Nucleotide sequence upstream of a glucose-repressible Drosophila gene Get access Donal A. Hickey, Donal A. Hickey Department of Biology, University of Ottawa30 Somerset East, Ottawa, Ontario K1N 6N5, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Yves Genest, Yves Genest Department of Biology, University of Ottawa30 Somerset East, Ottawa, Ontario K1N 6N5, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Bernhard F. Benkel Bernhard F. Benkel Department of Biology, University of Ottawa30 Somerset East, Ottawa, Ontario K1N 6N5, Canada Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 15, Issue 17, 11 September 1987, Page 7184, https://doi.org/10.1093/nar/15.17.7184 Published: 11 September 1987 Article history Received: 04 August 1987 Published: 11 September 1987
OpenCAPI Memory Interface Simulation and Test for Differential DIMM Channel with SNIA SFF-TA-1002 Connector (2020)

DDR5 Differential DIMM (DDIMM) is being defined in JEDEC and uses OMI as a host interface with the data transfer rate per data differential pair being specified at 25.6Gb/s minimum at present and at 51.2Gb/s maximum in the future. This is a significant data rate increase for DRAM modules over conventional single-ended data transferring DIMMs. For example, the DDR5 LRDIMM data transfer rate per pin is 3.2Gbps. This study utilizes the DDIMM early engineering samples with DDR4 to evaluate the OMI channel running at 25.6Gb/s.Validating the DDIMM PCB wiring for the high-speed differential memory bus requires accurate high-speed link simulations. These simulations require accurate models representing differential wiring in the DDIMM PCB stack up. The models must be built using not only representative physical dimensions but also accurate frequency dependent material properties obtained through PCB characterization. The simulation results of the initial study in 2018-19 concluded that the typical Copper Clad Laminate (CCL) and prepreg material used in the industry standard R/LR DIMM leads to signal integrity degradation relative to a better reference material at 25.6Gb/s OMI bus data rate[l]. This paper is based on 2019-20 DDIMM test results and the full channel time domain eye diagram analysis with BER at 10-15 assuming an improved DDIMM PCB stack up with hybrid structure to satisfy signal integrity while minimize the material cost premium.DDIMM will be paired with the Storage Networking Industry Association (SNIA) SFF-TA-1002 high speed connector which differs significantly from the JEDEC RDIMM connector for improved electrical signaling characteristics. The connector to PCB interface design has been studied as it is of utmost importance for achieving good signal integrity[l]. The DDIMM test samples for this study include the high speed connector to PCB interface attributes such as Plated Through Hole (PTH) in ground contact pad, ground plane void under OMI signal pad and tie bar removal.The challenges of DDIMM PCB mechanical interaction with SFF-TA-1002 connector have been highlighted in the initial study[l]. This study uses early engineer samples to evaluate the insertion/extraction performance. Future work will use test vehicle of PCB/connector pairs to characterize the high speed electrical performance and evaluate the contact reliability.In summary, this paper presented the full channel simulation result assuming an improved DDIMM PCB material/stack-up at 25.6Gbps for comparison with the performance that baselined in the initial work with the industry standard PCB material. Physical characterization of the engineering samples has been conducted to baseline the DDIMM PCB to connector contact interface. Electrical test is performed with early engineering samples in IBM high speed system to verify the simulation result.
Large-Scale Analysis of the Prevalence and Geographic Distribution of HIV-1 Non-B Variants in the United States (2013)

The genetic diversity of human immunodeficiency virus type 1 (HIV-1) has significant implications for diagnosis, vaccine development, and clinical management of patients. Although HIV-1 subtype B is predominant in the United States, factors such as global travel, immigration, and military deployment have the potential to increase the proportion of non-subtype B infections. Limited data are available on the prevalence and distribution of non-B HIV-1 strains in the United States. We sought to retrospectively examine the prevalence, geographic distribution, diversity, and temporal trends of HIV-1 non-B infections in samples obtained by ARUP Laboratories, a national reference laboratory, from all regions of the United States. HIV-1 pol sequences from 24,386 specimens collected from 46 states between 2004 and September 2011 for drug resistance genotyping were analyzed using the REGA HIV-1 Subtyping Tool, version 2.0. Sequences refractory to subtype determination or reported as non-subtype B by this tool were analyzed by PHYLIP version 3.5 and Simplot version 3.5.1. Non-subtype B strains accounted for 3.27% (798/24,386) of specimens. The 798 non-B specimens were received from 37 states and included 5 subtypes, 23 different circulating recombinant forms (CRFs), and 39 unique recombinant forms (URFs). The non-subtype B prevalence varied from 0% in 2004 (0/54) to 4.12% in 2011 (201/4,884). This large-scale analysis reveals that the diversity of HIV-1 in the United States is high, with multiple subtypes, CRFs, and URFs circulating. Moreover, the geographic distribution of non-B variants is widespread. Data from HIV-1 drug resistance testing have the potential to significantly enhance the surveillance of HIV-1 variants in the United States.
Ultra-Broadband, Low-Power, 2×2 Electro-Optic Switch using Sub-Micron Silicon Waveguides (2010)

We present a broadband Mach-Zehnder electro-optic switch capable of simultaneously routing multiple channels within 110-nm optical bandwidth with only 3.1-mW power consumption and a 4-ns switching time. Switching bandwidth is maintained over 30°C temperature variation.
Real-time modal control implementation for adaptive optics (1998)

The electronics, computing hardware, and computing used to provide real-time modal control for a laser guide-star adaptive optics system are presented. This approach offers advantages in the control of unobserved modes, the elimination of unwanted modes (e.g., tip and tilt), and automatic handling of the case of low-resolution lens arrays. In our two-step modal implementation, the input vector of gradients is first decomposed into a Zernike polynomial mode by a least-squares estimate. The number of modes is assumed to be less than or equal to the number of actuators. The mode coefficients are then available for collection and analysis or for the application of modal weights. Thus the modal weights may be changed quickly without recalculating the full matrix. The control-loop integrators are at this point in the algorithm. To calculate the deformable-mirror drive signals, the mode coefficients are converted to the zonal signals by a matrix multiply. When the number of gradients measured is less than the number of actuators, the integration in the control loop will be done on the lower-resolution grid to avoid growth of unobserved modes. These low-resolution data will then be effectively interpolated to yield the deformable-mirror drive signals.
Artificial olfactory system based on nanomaterials-based sensors for early detection of tuberculosis via breath test (2013)

Background: Commonly used tools for the diagnosis of tuberculosis (TB) have suboptimal accuracy, remain inaccessible as they are not point-of-care, and require a sputum sample, which is often unavailable in HIV-infected persons. Aim: To evaluate the feasibility and accuracy of nanomaterials-based electro-chemical sensor array, with odor detection ability, to diagnose TB infection, via exhaled breath analysis. Methods: A case control study (n= 198) was conducted using 64 patients with culture-proven TB and 134 controls (67 were symptomatic patients who presented to a TB clinic but were culture negative on follow-up and not started on anti-TB treatment, and 67 were healthy volunteers). Exhaled breath was sampled and analyzed using an array of chemically modified, nanomaterial-based and odor detecting sensors. While using 138 randomly selected samples as a derivation set, the remaining 60 samples as the blinded validation set. The impact of HIV status, smoking, and treatment effect was also evaluated. Results: Sensitivity, specificity, Positive and Negative Predictive Values (PPV and NPV), when using a ROC-derived most accurate cutoff point, in the derivation set were, 85%,89%,78% and 92%, respectively, moreover, in validation, blind set experiment, the relevant values were 90%,92%,86% and 95% respectively. These results were un-affected by smoking habits, HIV status, and/or prior TB treatment of several days. Conclusion: These preliminary proof-of-concept data indicate that a nanomaterial-based sensors may be a non-invasive, simple and useful for the accurate diagnosis of TB, used as mobile point-of-care screening tool.
A characterization of indoor space and frequency diversity by ray-tracing modeling (1996)

The performance of space and frequency diversity techniques at 1800 MHz in an indoor environment are investigated. Three linear signal combining techniques are considered: signal selection (SEL), maximal ratio combining (MRC), and equal gain combining (EGC). The computations of received fading envelopes are performed by means of an analytical model, based on a three-dimensional ray-tracing (RT)/uniform theory of diffraction (UTD) technique; the reliability of the adopted approach is confirmed by comparison with some test measurements. The electromagnetic field components are adequately processed to obtain the single branch and combined signal envelope. The results show the very significant benefits that can be achieved both in terms of diversity gain and diversity advantage for both diversity techniques. Antenna spacings of about 0.75-1/spl lambda/ are nearly sufficient for achieving optimum performance, whereas frequency separation on the order of 10 MHz is needed for sufficiently decorrelated transmission on the two carriers.
Sensitive and Quantitative Detection of MHC-I Displayed Neoepitopes Using a Semiautomated Workflow and TOMAHAQ Mass Spectrometry (2021)

Advances in several key technologies, including MHC peptidomics, have helped fuel our understanding of basic immune regulatory mechanisms and the identification of T cell receptor targets for the development of immunotherapeutics. Isolating and accurately quantifying MHC-bound peptides from cells and tissues enables characterization of dynamic changes in the ligandome due to cellular perturbations. However, the current multistep analytical process is challenging, and improvements in throughput and reproducibility would enable rapid characterization of multiple conditions in parallel. Here, we describe a robust and quantitative method whereby peptides derived from MHC-I complexes from a variety of cell lines, including challenging adherent lines such as MC38, can be enriched in a semiautomated fashion on reusable, dry-storage, customized antibody cartridges. Using this method, a researcher, with very little hands-on time and in a single day, can perform up to 96 simultaneous enrichments at a similar level of quality as a manual workflow. TOMAHAQ (Triggered by Offset, Multiplexed, Accurate-mass, High-resolution, and Absolute Quantification), a targeted mass spectrometry technique that combines sample multiplexing and high sensitivity, was employed to characterize neoepitopes displayed on MHC-I by tumor cells and to quantitatively assess the influence of neoantigen expression and induced degradation on neoepitope presentation. This unique combination of robust semiautomated MHC-I peptide isolation and high-throughput multiplexed targeted quantitation allows for both the routine analysis of >4000 unique MHC-I peptides from 250 million cells using nontargeted methods, as well as quantitative sensitivity down to the low amol/μl level using TOMAHAQ targeted MS.
Ortho- and Paramyxoviruses from Migrating Feral Ducks: Characterization of a New Group of Influenza A Viruses (1976)

SUMMARY Ortho- and parainfluenza viruses isolated from the cloacas of migrating feral ducks shot on the Mississippi flyway included three strains of influenza A virus (Hav6 Nav1, Hav6 Nl, Hav7 Neq2) as well as Newcastle disease virus. One influenza virus, A/duck/Memphis/546/74, possessed Hav3 haemagglutinin, but the neuraminidase was not inhibited by any of the known influenza reference antisera. The neuraminidase on this virus was related to the neuraminidases on A/duck/GDR/72 (H2 N?), A/turkey/Ontario/7732/66 (Hav 5 N?), A/duck/Ukraine/1/60 (Hav3 N?) and A/turkey/Wisconsin/68. We therefore propose that the neuraminidase on this group of influenza viruses be designated Nav6. The A/duck/Memphis/546/74 influenza virus caused an ocular discharge in 1 of 5 ducks and was shed in faeces for 10 days; it was stable in faecal samples for up to 3 days at 20 °C. These results suggest that ecological studies on influenza in avian species should include attempts to isolate virus from faeces. Faecal-oral transmission is an attractive explanation for the spread of influenza virus from feral birds to other animals.