gebhart/patrepeval huggingface dataset:
QBB rapid transformation into COVID-19 Biorepository: A showcase (2021)

Background: The SARS-CoV-2 virus and the outbreak of COVID-19 disease has been one of the most important global crises on public health. Qatar Biobank (QBB) had to convert and respond to this crisis by providing its services for the collection, processing and storage of high-quality data and specimens for the better understanding and the response to the therapy and survival of COVID-19 disease. In this study we will highlight the challenges, risks and opportunities of QBB during this transformation period. Methods: QBB is CAP accredited and holds ISO certification for Quality Management Systems 9001:2105 and Information Security Management Systems 27001: 2013. These standards helped QBB management to rabidly adapt by following rigorous processes to effectively convert its operations and facilitate the COVID-19 National project. Results: Within 5 weeks QBB transformed to accommodate a disease/virus-based biorepository. Multi-adjustments had to be implemented at operational level such as: i) QBB IT department developed a highly secured electronic system for the data collection and specimen traceability ii) Clinically trained staff (n = 17) were transferred to different healthcare facilities in order to recruit COVID-19 positive patients;iii) QBB Laboratory designed special collection kit, iv) QBB Medical Review Office (n = 4) and Scientific and Education (n = 2) departments managed the recruitment process, set up the study and provided training to the staff;v) the Communications and Participants Recruitment Department (n = 7) transformed its operations to fit the needs of the COVID-19 initiative. The Research Access Office (n = 6) designed the COVID-19 access portal and supported the project from the purchasing of PPE and other administrative works needed. Conclusion: It is now time to consider lessons learned, as many countries have been affected by COVID-19 outbreak, and to understand that biobanks are an asset for a country and integrate them into a new standard with their sustainability in mind. Qatar Biobank and its network with academic, research and governmental entities is a good showcase.
Determination of Partial Discharge Propagation and Location in Transformer Windings Using a Hybrid Transformer Model (2007)

Abstract Experimental experiences prove that partial discharge (PD) is a major source of inner insulation system failure in power transformers. If the deterioration of the insulation system caused by PD activity can be detected at an early stage, preventive maintenance measures may be taken. Due to the complex structure of the transformer, accurate determination of PD location is one of the major challenges in front of power utilities. This problem comes to be vital in open access systems. A hybrid transformer model and its application for locating partial discharge and studying its propagation along the transformer windings are proposed in this article. It is based on the structural data of the transformer for equivalent model parameters determination. The lumped parameter equivalent model for winding sections is constructed satisfying the quasi-static condition. Then an algorithm is developed to use the constructed matrices for PD propagation and location studies by application of the multi-conductor transmission line equivalent model. The results of the study are presented for a 66 kV/25 MVA transformer with fully interleaved winding.
Genotype-phenotype correlation in a family with Arg135Leu rhodopsin retinitis pigmentosa (2004)

An Arg135Leu change in rhodopsin results in a severe form of RP that evolves through various fundus appearances that include white dots early in life and classic appearing RP later. This transmembrane change in rhodopsin proves to be more severe than in a family with an intradiscal change and a family with a cytoplasmic change.
Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential (2022)

Influenza is one of the leading causes of disease-related mortalities worldwide. Several strategies have been implemented during the past decades to hinder the replication cycle of influenza viruses, all of which have resulted in the emergence of resistant virus strains. The most recent example is baloxavir marboxil, where a single mutation in the active site of the target endonuclease domain of the RNA-dependent-RNA polymerase renders the recent FDA approved compound ∼1000-fold less effective. Raltegravir is a first-in-class HIV inhibitor that shows modest activity to the endonuclease. Here, we have used structure-guided approaches to create rationally designed derivative molecules that efficiently engage the endonuclease active site. The design strategy was driven by our previously published structures of endonuclease-substrate complexes, which allowed us to target functionally conserved residues and reduce the likelihood of resistance mutations. We succeeded in developing low nanomolar equipotent inhibitors of both wild-type and baloxavir-resistant endonuclease. We also developed macrocyclic versions of these inhibitors that engage the active site in the same manner as their 'open' counterparts but with reduced affinity. Structural analyses provide clear avenues for how to increase the affinity of these cyclic compounds.
Stain Resistance Method Development for Consumer Digital Ink Jet and Thermal Imaging Systems. Part I (2008)

Methods for determining overall print permanence or image stability for digital ink jet and thermal photographic prints have been well defined and are used to represent typical "long-term, home storage conditions" for consumer prints. What these methods do not take into consideration are instances where a consumer might accidentally spill substances onto unprotected prints, resulting in unwanted staining. Typical substances can range from high staining materials such as coffee to lower staining materials such as milk. In these instances, damage caused by unwanted staining could certainly impact the long-term preservation of consumer prints. To date, the only existing international standards for this type of image degradation include an ASTM procedure for stain resistance and an ISO procedure for water resistance. This article will discuss the importance of considering stain resistance as part of long-term image permanence criteria for digital consumer color prints and shortcomings associated with the current international standards. Emphasis will be placed on the rationale and development of a more robust procedure for stain resistance and a final method proposal will be made. In addition, application of the proposed method will be discussed and the results from this for several digital ink jet and thermal imaging systems will be summarized.
Reverse engineering camouflaged sequential circuits without scan access (2017)

Integrated circuit (IC) camouflaging is a promising technique to protect the design of a chip from reverse engineering. However, recent work has shown that even camouflaged ICs can be reverse engineered from the observed input/output behaviour of a chip using SAT solvers. However, these so-called SAT attacks have so far targeted only camouflaged combinational circuits. For camouflaged sequential circuits, the SAT attack requires that the internal state of the circuit is controllable and observable via the scan chain. It has been implicitly assumed that restricting scan chain access increases the security of camouflaged ICs from reverse engineering attacks. In this paper, we develop a new attack methodology to decamouflage sequential circuits without scan access. Our attack uses a model checker (a more powerful reasoning tool than a SAT solver) to find a discriminating set of input sequences, i.e., one that is sufficient to determine the functionality of camouflaged gates. We propose several refinements, including the use of a bounded model checker, and sufficient conditions for determining when a set of input sequences is discriminating to improve the run-time and scalabilty of our attack. Our attack is able to decamouflage a large sequential benchmark circuit that implements a subset of the VIPER processor.
Crystal structures of highly simplified BPTIs provide insights into hydration-driven increase of unfolding enthalpy (2017)

We report a thermodynamic and structural analysis of six extensively simplified bovine pancreatic trypsin inhibitor (BPTI) variants containing 19-24 alanines out of 58 residues. Differential scanning calorimetry indicated a two-state thermal unfolding, typical of a native protein with densely packed interior. Surprisingly, increasing the number of alanines induced enthalpy stabilization, which was however over-compensated by entropy destabilization. X-ray crystallography indicated that the alanine substitutions caused the recruitment of novel water molecules facilitating the formation of protein-water hydrogen bonds and improving the hydration shells around the alanine's methyl groups, both of which presumably contributed to enthalpy stabilization. There was a strong correlation between the number of water molecules and the thermodynamic parameters. Overall, our results demonstrate that, in contrast to our initial expectation, a protein sequence in which over 40% of the residues are alanines can retain a densely packed structure and undergo thermal denaturation with a large enthalpy change, mainly contributed by hydration.
Using IIO Structure to enable additional workflows (2017)

Serialization is an important VDP (variable data printing) application. Incremental Information Objects (IIOs) allow us to keep track of steps in a workflow by modifying their serialized information at each step. Usually the IIO progression is defined by specific rules that change the visual properties of the IIO. We herein propose an additional constraint that defines a specific structure to the underlying bit string defining the IIO. We can then use the structure to either identify the workflow stage without access to the main ID database; modify the current workflow stage due to additional factors (user authentication, location, etc.); or use the information in the IIO as additional security information
Polyadenylation releases mRNA from RNA polymerase II in a process that is licensed by splicing (2009)

When transcription is coupled to pre-mRNA processing in HeLa nuclear extracts nascent transcripts become attached to RNA polymerase II during assembly of the cleavage/polyadenylation apparatus (CPA), and are not released even after cleavage at the poly(A) site. Here we show that these cleaved transcripts are anchored to the polymerase at their 3' ends by the CPA or, when introns are present, by the larger 3'-terminal exon definition complex (EDC), which consists of splicing factors complexed with the CPA. Poly(A) addition releases the RNA from the polymerase when the RNA is anchored only by the CPA. When anchored by the EDC, poly(A) addition remains a requirement, but it triggers release only after being licensed by splicing. The process by which RNA must first be attached to the polymerase by the EDC, and then can only be released following dual inputs from splicing and polyadenylation, provides an obvious opportunity for surveillance as the RNA enters the transport pathway.
Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures (2019)

Specialized immune cell subsets are involved in autoimmune disease, cancer immunity, and infectious disease through a diverse range of functions mediated by overlapping pathways and signals. However, subset-specific responses may not be detectable in analyses of whole blood samples, and no efficient approach for profiling cell subsets at high throughput from small samples is available. We present a low-input microfluidic system for sorting immune cells into subsets and profiling their gene expression. We validate the system's technical performance against standard subset isolation and library construction protocols and demonstrate the importance of subset-specific profiling through in vitro stimulation experiments. We show the ability of this integrated platform to identify subset-specific disease signatures by profiling four immune cell subsets in blood from patients with systemic lupus erythematosus (SLE) and matched control subjects. The platform has the potential to make multiplexed subset-specific analysis routine in many research laboratories and clinical settings.
Geroprotection by Glycerol (2006)

Chaperones, particularly the heat-shock proteins, are considered as key players in the maintenance of protein homeostasis and are associated with longevity and cellular immortalization. In this study, we investigated the geroprotective activity of the chemical chaperone glycerol. Glycerol showed significant chaperoning activity in refolding heat-denatured luciferase in vivo and in protecting cells from heat stress-induced cytotoxicity. This was accompanied by decrease in p53, an upregulation of a stress chaperone mortalin/mtHsp70, and an increase in proteasome activity in the presence of oxidative stress.
Humanized c-Myc Mouse (2012)

The newly established hc-Myc mouse strain provides a model system to study in detail the adverse effects of therapies that target the human c-MYC protein. To mimic the clinical situation, hc-Myc mice may be cross-bred to mice that develop tumors due to overexpression of human c-MYC. With these double transgenic mice it will be possible to study simultaneously the therapeutic efficiency and adverse side effects of MYC-specific therapies in the same mouse.
Real-Time Image Distortion Correction: Analysis and Evaluation of FPGA-Compatible Algorithms (2016)

Image distortion correction is a critical pre-processing step for a variety of computer vision and image processing algorithms. Standard real-time software implementations are generally not suited for direct hardware porting, so appropriated versions need to be designed in order to obtain implementations deployable on FPGAs. In this paper, hardware-compatible techniques for image distortion correction are introduced and analyzed in details. The considered solutions are compared in terms of output quality by using a geometrical-error-based approach, with particular emphasis on robustness with respect to increasing lens distortion. The required amount of hardware resources is also estimated for each considered approach.
Overview of 3‐D Shell Implementations (2020)

Motivated by the proven performance of macro-scale Hemispherical Resonator Gyroscopes, there has been a growing interest in 3-D micro-electromechanical system micro-shell resonators for use in timing and inertial sensing applications. This chapter reviews the recent advances in 3-D shell micro-technology. Starting with a brief history of macro-scale shell resonator gyroscopes, it reports novel fabrication processes and architectures for implementation of whole-angle gyroscopes at micro-scale. Majority of the focus is directed toward development of a surface tension and pressure driven micro-glassblowing paradigm, which is envisioned to serve as an enabling mechanism for wafer-scale fabrication of 3-D micro-wineglass gyroscopes. Surface-micro-machined micro-shells are almost exclusively fabricated by depositing a thin film onto a predefined mold with a sacrificial layer to create the resonator element. In order to achieve functional resonators based on micro-shell structures, efficient methods for transduction are required.
Transport Controlled Pattern Photopolymerization in a Single-Component System (2004)

The purpose of the present paper is to extend the concept of pattern photopolymerization-induced phase separation of a binary blend to a single-component system containing pure photoreactive monomers with a minute level of photoinitiators. The patterning formation process was simulated in the framework of Cahn−Hilliard equation coupled with the photoreaction kinetic equation. Unlike binary systems undergoing photopolymerization-induced phase separation driven by thermodynamic force, the mechanism of pattern formation in the single-component system is essentially a photoreaction-induced transport phenomenon. Of particular interest is the observation of polymer concentration profiles evolving from a sinusoidal wave to various truncated ones. On the basis of two-wave interference optics, the microchannel layers have been fabricated. Resultant morphology was characterized using optical and atomic force microscopes. A two-dimensional light scattering device was utilized to study the diffraction patterns from the fabricated microchannel layers. The observed concentration profiles were compared with the theoretical predictions, and good agreement was found.
Calculation Technique for Externally Unbonded CFRP Strips in Structural Concrete Retrofitting (2016)

This paper presents a calculation procedure for externally unbonded carbon fiber–reinforced polymer (CFRP) strips anchored at their ends in flexural strengthening of existing reinforced concrete structures. Due to strain incompatibility between the composite strip and the neighboring concrete surface, the well-known conventional cross-section analysis (CSA) employed for bonded reinforcements cannot be implemented. An iterative force equilibrium and strip strain adaptation with previously defined constitutive materials laws together with an optimization procedure in a numerical computing environment are used to overcome the computational complexities. For validation purposes, two static loading tests on reinforced concrete beams with an externally prestressed CFRP strip without bond except in the anchorage zones are compared to the numerical predictions. Prior to the final evaluation, a model for the anchorage resistance is implemented in the algorithm in order to capture the ultimate load due to anchorage failure. An excellent agreement in terms of structural behavior as well as of ultimate load-carrying capacity is observed. Eventually, the differences in the structural response between bonded and unbonded strips are pointed out.
Study of Combined Heat and Mass Transfer From Fins Using Non-Dimensional Finite Element Formulation (2013)

The use of dimensional analysis and dimensionless parameters is very common in the field of heat transfer. The paper presents a non-dimensional finite element capable of modeling combined heat and mass transfer from fins. The aim of the formulation is to get solution of the fin problems that do not have a closed form solution. The performance of a fin is described through its efficiency and numerous closed form solutions for fin efficiency under combined heat and mass transfer are available in the literature. Deriving a closed form solution for geometric or material complexities is somewhat a difficult task. An example is variable profile composite fin. A composite fin is composed of base material or substrate with a coating layer. Finite element approach can handle such complexity with relatively ease, Therefore the main objective is to developed formulation for mass transfer problems. The formulation is derived in dimensionless form to extend the applicability of finite element results to a class of problems with same governing dimensionless parameters. The derived formulation is then applied to study the combined heat and mass transfer for variable profile composite fins under fully wet condition.
1673: Ureteral Stents: Analysis of Properties (2004)

You have accessJournal of UrologyTuesday, May 11, 2004, 1:00 - 3:00 pm1 Apr 20041673: Ureteral Stents: Analysis of Properties Carlos Uribe, Matthew Clayman, Louis Eichel, Zach Gordon, Corollas Abdelshehid, Elspeth M. McDougall, and Ralph V. Clayman Carlos UribeCarlos Uribe More articles by this author , Matthew ClaymanMatthew Clayman More articles by this author , Louis EichelLouis Eichel More articles by this author , Zach GordonZach Gordon More articles by this author , Corollas AbdelshehidCorollas Abdelshehid More articles by this author , Elspeth M. McDougallElspeth M. McDougall More articles by this author , and Ralph V. ClaymanRalph V. Clayman More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)38881-5AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "1673: Ureteral Stents: Analysis of Properties." The Journal of Urology, 171(4S), pp. 442–443 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 171Issue 4SApril 2004Page: 442-443 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Carlos Uribe More articles by this author Matthew Clayman More articles by this author Louis Eichel More articles by this author Zach Gordon More articles by this author Corollas Abdelshehid More articles by this author Elspeth M. McDougall More articles by this author Ralph V. Clayman More articles by this author Expand All Advertisement PDF DownloadLoading ...
Synthetic Studies on Bioactive Natural Products Utilizing the Elimination Reaction of 1, 2-Dibromides Possessing Oxygen-Functional Groups at Adjacent Positions (2008)

2-Bromo-1-alkenes have been recognized as one of useful functional groups for preparation of vinyl lithiums and vinyl Grignard reagents, for coupling partners in a wide range of transition metal-mediated coupling reactions, substrates of radical reactions, and precursors of a-haloke-tones. Selective elimination reaction of 1, 2-dibromoalkanes possessing aryloxy or acyloxy groups at the C 3 position into 2-bromo-1-alkenes under mild basic conditions was developed. Alkyne units are also one of the important functional groups for substrates of C-C coupling reactions. During our extensive investigation, the acidity enhancement of hydrogen at the C 1 position by oxygen-functional groups at the C 3 position was also observed. This observation indicated a new prospective synthesis of propargyl ethers from 1, 2-dibromoalkanes using DBU as a base. As application of these elimination reactions, total synthesis of biologically active natural products was accomplished.
Bone Marrow-Derived c-kit+Cells Attenuate Neonatal Hyperoxia-Induced Lung Injury (2013)

Recent studies suggest that bone marrow (BM)-derived stem cells have therapeutic efficacy in neonatal hyperoxia-induced lung injury (HILI). c-kit, a tyrosine kinase receptor that regulates angiogenesis, is expressed on several populations of BM-derived cells. Preterm infants exposed to hyperoxia have decreased lung angiogenesis. Here we tested the hypothesis that administration of BM-derived c-kit(+) cells would improve angiogenesis in neonatal rats with HILI. To determine whether intratracheal (IT) administration of BM-derived c-kit(+) cells attenuates neonatal HILI, rat pups exposed to either normobaric normoxia (21% O2) or hyperoxia (90% O2) from postnatal day (P) 2 to P15 were randomly assigned to receive either IT BM-derived green fluorescent protein (GFP)(+) c-kit(-) cells (PL) or BM-derived GFP(+) c-kit(+) cells on P8. The effect of cell therapy on lung angiogenesis, alveolarization, pulmonary hypertension, vascular remodeling, cell proliferation, and apoptosis was determined at P15. Cell engraftment was determined by GFP immunostaining. Compared to PL, the IT administration of BM-derived c-kit(+) cells to neonatal rodents with HILI improved alveolarization as evidenced by increased lung septation and decreased mean linear intercept. This was accompanied by an increase in lung vascular density, a decrease in lung apoptosis, and an increase in the secretion of proangiogenic factors. There was no difference in pulmonary vascular remodeling or the degree of pulmonary hypertension. Confocal microscopy demonstrated that 1% of total lung cells were GFP(+) cells. IT administration of BM-derived c-kit(+) cells improves lung alveolarization and angiogenesis in neonatal HILI, and this may be secondary to an improvement in the lung angiogenic milieu.