gebhart/patrepeval huggingface dataset:
Detection of Maternal DNA in Human Cord Blood Stored for Allotransplantation by a Highly Sensitive Chemiluminescent Method (1997)

Human cord blood (CB), a rich source of hematopoietic stem and progenitor cells, is currently used for bone marrow reconstitution. However, the level of contamination of CB with maternal cells that could provoke graft-versus-host disease (GvHD) is a matter of concern. In the present study, 60 consecutive CB samples collected and stored in the Milan CB Bank, for which no maternal DNA was detected through genomic HLA typing, were examined to ascertain maternal cell contamination using polymerase chain reaction amplification of two minisatellites, apolipoprotein B gene (ApoB) and D1S80, followed by chemiluminescent detection. The sensitivity of the method employed in this study was 0.04%, comparable to that of radioactive methods. A maternal specific allele was found in 11 of the 60 CB units, at a level ranging from 1:100 to 1:2500. We could also detect the child paternal allele in 3 of the 30 mothers whose newborn was heterozygous at the loci examined. Our study indicates that maternal cells are present in 18.3% of the 60 samples examined. The clinical relevance of such a presence remains to be established. In our opinion, information on maternal cell contamination should be included within the quality control tests performed before delivering a unit.
Report of the Multisociety Task Force on GI Training (2009)

Am J Gastroenterol 2009;104:2659-2663; doi:10.1038/ajg.2009.570 Abbreviations used in this paper: AASLD, American Association for the Study of Liver Diseases; ABIM, American Board of Internal Medicine; ACG, American College of Gastroenterology; AGA, American Gastroenterological Association; ASGE, American Society for Gastrointestinal Endoscopy; IBD, inflammatory bowel disease. This article is being published jointly in 2009 in American Journal of Gastroenterology, Gastroenterology, Gastrointestinal Endoscopy, and Hepatology. © 2009 by the American Association for the Study of Liver Diseases (AASLD), the American College of Gastroenterology (ACG), the AGA Institute, and the American Society for Gastrointestinal Endoscopy (ASGE).
Acute coronary syndrome caused by coronary artery dissection mimicking acute plaque rupture. (2001)

When a middle-aged, nonpregnant female patient with no coronary risk factors presents with chest pain, what are the red flags for unusual causes? This case report provides important diagnostic clues as well as progressive therapeutic steps to solving a potentially life-threatening problem.
Orbit Design Optimization for Planetary Crosslink Radio Occultation (2021)

Crosslink radio occultation (RO) using multiple spacecraft is a promising method to observe the planetary atmosphere with higher spatial and temporal resolution than conventional RO measurements between a spacecraft and a ground station. In this paper, an optimal orbit configuration design method for crosslink RO is discussed. Orbit elements of two spacecraft are explored under two evaluation functions: values of observation and fuel costs for orbit injection. Then, generated Pareto optimal solutions are analyzed based on three categories classified by orbit characteristics, and we proposed an orbit design guideline to enhance observational value against fuel cost. The qualitative understandings for crosslink RO orbit design by this paper can contribute to future mission design.
ChemInform Abstract: Coupling Effects in Optical Metamaterials (2011)

Abstract Review: 92 refs.
High-performance continuous-time MASH sigma-delta ADCs for broadband wireless applications (2017)

This paper focuses on the design and analysis of multi-stage noise-shaping (MASH) sigma-delta modulators. Fundamentals and properties of MASH modulators are discussed. A detailed methodology on analyzing continuous-time MASH (CT-MASH) modulator based on the impulse invariant transformation is also described. Two fabricated design examples are discussed: a 130 nm CMOS CT-MASH 4-0 employing a digital pseudo-MASH compensation consumes 20mW and achieves 75 dB peak SNDR over a 15 MHz bandwidth with an active area of 1.3 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ; a 40 nm CMOS CT-MASH 2-2 architecture achieves peak SNDR of 74.4 dB within the signal bandwidth of 50.3 MHz with power consumption of 43.0 mW and active area of 0.265 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
PCSK9 (2014)

Since the discovery of proprotein convertase subtilisin kexin 9 (PCSK9) in 2003, this PC has attracted a lot of attention from the scientific community and pharmaceutical companies. Secreted into the plasma by the liver, the proteinase K-like serine protease PCSK9 binds the low-density lipoprotein (LDL) receptor at the surface of hepatocytes, thereby preventing its recycling and enhancing its degradation in endosomes/lysosomes, resulting in reduced LDL-cholesterol clearance. Surprisingly, in a nonenzymatic fashion, PCSK9 enhances the intracellular degradation of all its target proteins. Rare gain-of-function PCSK9 variants lead to higher levels of LDL-cholesterol and increased risk of cardiovascular disease; more common loss-of-function PCSK9 variants are associated with reductions in both LDL-cholesterol and risk of cardiovascular disease. It took 9 years to elaborate powerful new PCSK9-based therapeutic approaches to reduce circulating levels of LDL-cholesterol. Presently, PCSK9 monoclonal antibodies that inhibit its function on the LDL receptor are evaluated in phase III clinical trials. This review will address the biochemical, genetic, and clinical aspects associated with PCSK9's biology and pathophysiology in cells, rodent and human, with emphasis on the clinical benefits of silencing the expression/activity of PCSK9 as a new modality in the treatment of hypercholesterolemia and associated pathologies.
Synthesis of High-Performance PM Motors with Concentrated Windings (2002)

The windings concentrated around the teeth offer obvious advantages for the electrical machines with radial air-gap, because the volume of copper used in the end-windings can be reduced. The Joule losses are decreased and the efficiency is improved. These machines are still limited to applications of subfractional power and they generally present a reduced number of phases. In the three-phase machines, the concentrated winding is too often restricted to a winding with a short pitch of 120 electrical degrees, i. e., to a winding with performances reduced compared to the traditional structures. But there is a significant number of three-phase structures that can support a concentrated winding if the number of poles is increased. In this article, the authors present a synthesis of the structures of three-phase machines with concentrated windings. In the first part, the structures with a regular distribution of the slots are presented. A systematic method is proposed to determine the windings and the performances are discussed. In the second part, the authors present original structures of three-phase machines with concentrated windings that use an irregular distribution of the slots. A specific method to identify these structures is described, and a comparative analysis of the performances of the original and traditional structures is performed by using a field calculation software.
Molecular characterization and functional properties of cardiomyocytes derived from human inducible pluripotent stem cells (2009)

In view of the therapeutic potential of cardiomyocytes derived from induced pluripotent stem (iPS) cells (iPS-derived cardiomyocytes), in the present study we investigated in iPS-derived cardiomyocytes, the functional properties related to [Ca(2+) ](i) handling and contraction, the contribution of the sarcoplasmic reticulum (SR) Ca(2+) release to contraction and the b-adrenergic inotropic responsiveness. The two iPS clones investigated here were generated through infection of human foreskin fibroblasts (HFF) with retroviruses containing the four human genes: OCT4, Sox2, Klf4 and C-Myc. Our major findings showed that iPS-derived cardiomyocytes: (i) express cardiac specific RNA and proteins; (ii) exhibit negative force-frequency relations and mild (compared to adult) post-rest potentiation; (iii) respond to ryanodine and caffeine, albeit less than adult cardiomyocytes, and express the SR-Ca(2+) handling proteins ryanodine receptor and calsequestrin. Hence, this study demonstrates that in our cardiomyocytes clones differentiated from HFF-derived iPS, the functional properties related to excitation-contraction coupling, resemble in part those of adult cardiomyocytes.
Quantum cryptography with a full-fledged photonic integrated chip system (2021)

Integrated photonics can enable a wide deployment of quantum cryptography but this integration is technologically challenging. We addressed the challenges and built a complete, real-time and deployable quantum key distribution system based on integrated photonics.
Differential Growth of Francisella tularensis, Which Alters Expression of Virulence Factors, Dominant Antigens, and Surface-Carbohydrate Synthases, Governs the Apparent Virulence of Ft SchuS4 to Immunized Animals (2017)

The gram-negative bacterium <i>Francisella tularensis</i> (<i>Ft</i>) is both a potential biological weapon and a naturally occurring microbe that survives in arthropods, fresh water amoeba, and mammals with distinct phenotypes in various environments. Previously, we used a number of measurements to characterize <i>Ft</i> grown in Brain-Heart Infusion (BHI) broth as (1) more similar to infection-derived bacteria, and (2) slightly more virulent in naïve animals, compared to <i>Ft</i> grown in Mueller Hinton Broth (MHB). In these studies we observed that the free amino acids in MHB repress expression of select <i>Ft</i> virulence factors by an unknown mechanism. Here, we tested the hypotheses that <i>Ft</i> grown in BHI (BHI-<i>Ft</i>) accurately displays a full protein composition more similar to that reported for infection-derived <i>Ft</i> and that this similarity would make BHI-<i>Ft</i> more susceptible to pre-existing, vaccine-induced immunity than MHB-<i>Ft</i>. We performed comprehensive proteomic analysis of <i>Ft</i> grown in MHB, BHI, and BHI supplemented with casamino acids (BCA) and compared our findings to published "omics" data derived from <i>Ft</i> grown <i>in vivo</i>. Based on the abundance of ~1,000 proteins, the fingerprint of BHI-<i>Ft</i> is one of nutrient-deprived bacteria that-through induction of a stringent-starvation-like response-have induced the FevR regulon for expression of the bacterium's virulence factors, immuno-dominant antigens, and surface-carbohydrate synthases. To test the notion that increased abundance of dominant antigens expressed by BHI-<i>Ft</i> would render these bacteria more susceptible to pre-existing, vaccine-induced immunity, we employed a battery of LVS-vaccination and S4-challenge protocols using MHB- and BHI-grown <i>Ft</i> S4. Contrary to our hypothesis, these experiments reveal that LVS-immunization provides a barrier to infection that is significantly more effective against an MHB-S4 challenge than a BHI-S4 challenge. The differences in apparent virulence to immunized mice are profoundly greater than those observed with primary infection of naïve mice. Our findings suggest that tularemia vaccination studies should be critically evaluated in regard to the growth conditions of the challenge agent.
Change in Functional Beta Cell Capacity With Time Following Autologous Islet Transplantation (2019)

A steady drop in functional beta cell capacity was observed in the 2 years following TP and AIT. To our knowledge, to date this is the first report of the BETA-2 score applicability in the AIT setting.
Twin-S: A Digital Twin for Skull-base Surgery (2022)

Purpose: Digital twins are virtual interactive models of the real world, exhibiting identical behavior and properties. In surgical applications, computational analysis from digital twins can be used, for example, to enhance situational awareness. Methods: We present a digital twin framework for skull-base surgeries, named Twin-S, which can be integrated within various image-guided interventions seamlessly. Twin-S combines high-precision optical tracking and real-time simulation. We rely on rigorous calibration routines to ensure that the digital twin representation precisely mimics all real-world processes. Twin-S models and tracks the critical components of skull-base surgery, including the surgical tool, patient anatomy, and surgical camera. Significantly, Twin-S updates and reflects real-world drilling of the anatomical model in frame rate. Results: We extensively evaluate the accuracy of Twin-S, which achieves an average 1.39 mm error during the drilling process. We further illustrate how segmentation masks derived from the continuously updated digital twin can augment the surgical microscope view in a mixed reality setting, where bone requiring ablation is highlighted to provide surgeons additional situational awareness. Conclusion: We present Twin-S, a digital twin environment for skull-base surgery. Twin-S tracks and updates the virtual model in real-time given measurements from modern tracking technologies. Future research on complementing optical tracking with higher-precision vision-based approaches may further increase the accuracy of Twin-S.
Molecular Typing of Methicillin-Resistant <i>Staphylococcus aureus</i> by Pulsed-Field Gel Electrophoresis: Comparison of Results Obtained in a Multilaboratory Effort Using Identical Protocols and MRSA Strains (2000)

Pulsed-field gel electrophoresis (PFGE) has become the gold standard of molecular methods in epidemiological investigations. In spite of its high resolving power, use of the method has been hampered by inadequate laboratory-to-laboratory reproducibility. In the project described here we have addressed this problem by organizing a multilaboratory effort in which the same bacterial strains (subtype variants of the Iberian and Brazilian methicillin-resistant Staphylococcus aureus--MRSA--clones) were analyzed by twenty investigators in thirteen different laboratories according to an indentical protocol, which is reproduced here in detail. PFGE patterns obtained were analyzed at a central laboratory in order to identify specific technical problems that produced substandard macrorestriction patterns. The results including the specific technical problems and their most likely causes are described in this communication. Also listed are seven major epidemic clones of MRSA which have been characterized by molecular fingerprinting techniques and the prototypes of which have been deposited at the American Type Culture Collection, from where they will be available for interested investigators for the purpose of typing MRSA isolates. It is hoped that this communication will contribute to the improvement of the reproducibility and technical/aesthetic quality of PFGE analysis.
Nucleic acid detection compositions (2023)

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.
History of Monte Carlo modeling of light transport in tissues using mcml.c (2022)

The Monte Carlo simulation called mcml.c was written and shared on-line since 1992. This perspective summarizes the contributions by the people involved in the development of mcml.c, and work by others extending the code.
A Moveable Feast: An Introduction to Mobile DNA (2015)

DNA has two critical functions: to provide the cell with the information necessary for macromolecular synthesis and to transmit that information to progeny cells. Genome sequence stability is important for both these functions. Indeed, cells devote significant resources to various DNA repair processes that maintain genome structure and repair alterations that can arise from DNA synthesis errors and assaults from both endogenous and exogenous sources. DNA sequence variation, however, provides the substrate for adaptation, selection, and evolution.
Luminescent Copper(I) Halides for Optoelectronic Applications (2021)

Lead‐free copper(I) halides have been demonstrated to exhibit high photoluminescence quantum yields with high air and light stability, making them one of the most promising semiconductors for next‐generation light‐emitting diode devices. The low‐dimensional structures and soft lattices of Cu(I) halides induce the formation of self‐trapped excitons (STEs) to achieve broadband emissions with high quantum yields. Herein, the recent studies on the electronic and optical properties of Cu(I) halides (i.e., Cs 3 Cu 2 X 5 , CsCu 2 X 3 , and A 2 CuX 3 , where A = K + or Rb + , X = Cl − , Br − , or I − ) are reviewed and particular emphasis is placed on the role of the dimensionality and the halide in governing the electronic and optical properties (e.g., emission color and photoluminescence efficiency) via STEs. Several optoelectronic applications of Cu(I) halides are also discussed. In the last section, perspectives and challenges for the future development of Cu(I) halides in both optoelectronic and photocatalytic applications are outlined.
Risk stratification and prognostic value of multi-modal MRI-based radiomics for extranodal nasal-type NK/T-cell lymphoma (2022)

Abstract Background: Magnetic resonance imaging (MRI) performs well in the locoregional assessment of extranodal nasal-type NK/T-cell lymphoma (ENKTCL). It’s important to assess the value of multi-modal MRI-based radiomics for estimating overall survival (OS) in patients with ENKTCL. Methods: Patients with ENKTCL in a prospectively cohort were systemically reviewed and all the pretreatment MRI were acquisitioned. An unsupervised spectral clustering method was used to identify risk groups of patients and radiomic features. A nomogram-revised risk index (NRI) plus MRI radiomics signature (NRI-M) was developed, and compared with the NRI. Results: The 2 distinct type I and II groups of the MRI radiomics signatures were identified. The 5-year OS rates between the type I and type II groups were 87.2% versus 67.3% (P = 0.002) in all patients, and 88.8% versus 69.2% (P = 0.003) in early-stage patients. The discrimination and calibration of the NRI-M for OS prediction demonstrated a better performance than that of either MRI radiomics or NRI, with a mean area under curve (AUC) of 0.748 and 0.717 for predicting the 5-year OS in all-stages and early-stage patients. Conclusions: The NRI-M model has good performance for predicting the prognosis of ENKTCL and may help design clinical trials and improve clinical decision making.
Improved Routing and Sorting on Multibutterflies. (1996)

This paper shows that an N -node AKS network (as described by Paterson) can be embedded in a (3N /2)-node twinbutterfly network (i.e., a multibutterfly constructed by superimposing two butterfly networks) with load 1, congestion 1, and dilation 2. The result has several implications, including the first deterministic algorithms for sorting and finding the median of n log n items on an n-input multibutterfly in O(log n) time, a work-efficient deterministic algorithm for finding the median of n log 2 n log log n items on an n-input multibutterfly in O(log n log log n) time, and a three-dimensional VLSI layout for the n-input AKS network with volume O(n 3/2 ).While these algorithms are not practical, they provide further evidence of the robustness of multibutterfly networks.We also present a separate, and more practical, deterministic algorithm for routing h-relations on an n-input multibutterfly in O(h + log n) time.Previously, only algorithms for solving h one-to-one routing problems were known.Finally, we show that a twinbutterfly, whose individual splitters do not exhibit expansion, can emulate a bounded-degree multibutterfly with (α, β)-expansion, for any α • β < 1 4 .
Using molded chalcogenide glass technology to reduce cost in a compact wide-angle thermal imaging lens (2006)

This paper presents the design, analysis, and fabrication of a telecentric f/1.3 thermal imaging lens. The 14.8 mm wideangle lens provides a 62° diagonal field-of-view, and was designed to operate over the 8-14 &#956;m infrared spectral band. Focus can be manually adjusted from 0.5 m to infinity, maintaining constant image quality over the entire range. A compact air-spaced doublet design limits the overall length to 34 mm and the maximum diameter to 28 mm. Lens materials were chosen to minimize chromatic aberrations, reduce cost, and fit within the molded chalcogenide glass manufacturing capabilities. Combining a molded aspheric chalcogenide lens with a polished spherical Germanium lens eliminated the need for a diffractive surface to correct chromatic aberrations, and reduced the fabrication cost. Vignetting was purposely introduced at the extreme fields to compensate for the effects of aberrations on the relative illumination variation across the field-of-view. Athermalization of the lens was achieved mechanically over the entire operating temperature range (- 40 to + 80°C).
Potencial de la biorremediación de suelo y agua impactadospor petróleo en el trópico mexicano (1999)

Resumen es: En este articulo se evalua la tecnologia de biorremediacion para el tratamiento de sitios contaminados con petroleo en el tropico mexicano. Se describ...
Molecular Crowding Enhanced ATPase Activity of the RNA Helicase eIF4A Correlates with Compaction of Its Quaternary Structure and Association with eIF4G (2013)

Enzymatic reactions occur in a crowded and confined environment in vivo, containing proteins, RNA and DNA. Previous reports have shown that interactions between macromolecules, and reactions rates differ significantly between crowded environments and dilute buffers. However, the direct effect of crowding on the level of high-resolution structures of macromolecules has not been extensively analyzed and is not well understood. Here we analyze the effect of macromolecular crowding on structure and function of the human translation initiation factors eIF4A, a two-domain DEAD-Box helicase, the HEAT-1 domain of eIF4G, and their complex. We find that crowding enhances the ATPase activity of eIF4A, which correlates with a shift to a more compact structure as revealed with small-angle X-ray scattering. However, the individual domains of eIF4A, or the eIF4G-HEAT-1 domain alone show little structural changes due to crowding except for flexible regions. Thus, the effect of macromolecular crowding on activity and structure need to be taken into account when evaluating enzyme activities and structures of multidomain proteins, proteins with flexible regions, or protein complexes obtained by X-ray crystallography, NMR, or other structural methods.