gebhart/patrepeval huggingface dataset:
Coupling Isotachophoresis with Affinity Chromatography for Rapid and Selective Purification with High Column Utilization, Part 2: Experimental Study (2014)

We present an experimental study of coupling of isotachophoresis (ITP) and affinity chromatography (AC) to effect rapid, selective purification with high column utilization and high resolution. We provide a detailed protocol for performing ITP-AC and describe the design of a buffer system to perform sequence specific separation of nucleic acids. We describe the synthesis and functionalization of our affinity substrate, poly(glycidyl methacrylate-co-ethylene dimethacrylate) porous polymer monolith (GMA-EDMA PPM). This substrate allows easy immobilization of affinity probes, is nonsieving (even to macromolecules), and exhibits negligible nonspecific binding. We demonstrate ITP-AC with 25 nt, Cy5 labeled DNA target and a DNA probe and study the spatiotemporal dynamics using epifluorescence imaging. We make qualitative and quantitative comparisons between these data and the model presented in the first part of this two-paper series. We vary the target concentration from 1 pg μL(-1) to 100 pg μL(-1) and ITP velocity over the range of 10-50 μm s(-1), and thereby explore over 4 orders of magnitude of scaled target amount. We observe very good agreement between predictions and experimental data for the spatiotemporal behavior of the coupled ITP and affinity process, and for key figures of merit, including scaled capture length and maximum capture efficiency. Lastly, we demonstrate that the resolution of ITP-AC increases linearly with time and purify 25 nt target DNA from 10,000-fold higher abundance background (contaminating) genomic fish sperm DNA. We perform this capture from 200 μL of sample in under 1 mm column length and within <10 min.
Aortobifemoral surgery induces complement activation and release of interleukin-6 but not tumour necrosis factor-alpha (1996)

The aim of the present study was to determine the inflammatory response by an extended analysis of complement in 16 patients undergoing aortobifemoral bypass surgery. The patients were randomized to receive either a bifurcated expanded polytetrafluoroethylene graft (n = 8; group I) or a collagen-impregnated knitted Dacron graft (n = 8; group II) to determine whether differences in graft surface properties might influence the inflammatory response during and after the procedure. The following components of complement: C1q, C4, C3, C3d, C5a and terminal complement complexes were all analysed. C-reactive protein and interleukin-6 were also determined to assess the acute phase response. The complement data were corrected for haemodilution, which was assessed from alpha 2-macroglobulin concentrations. A significant decrease of C1q (P < 0.0001) and an increase in C5a (P < 0.0005) was observed in both groups. C4 and C3 levels showed slight fluctuations in group I, whereas in group II these proteins increased significantly (P < 0.05, P < 0.005, respectively) between 2 and 7 days after surgery. Terminal complement complexes remained unchanged in both groups. Interleukin-6 levels peaked at 12-24 h and the C-reactive protein at 24-72 h. Higher interleukin-6 levels (P < 0.05) were found in group II 6 h after surgery compared with group I; no release of tumour necrosis factor-alpha was identified. An early inflammatory response was found in all patients. The patterns of the complement proteins varied with a C1q depletion and a C5a increase, interpreted as complement activation. Whether the variations between the two graft groups represent any differences in graft surface properties has to be further elucidated.
Supplementary Figure Legends from Chronic Myelogenous Leukemia– Initiating Cells Require Polycomb Group Protein EZH2 (2023)

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Current Status of Implant-Based Breast Reconstruction in Patients Receiving Postmastectomy Radiation Therapy (2012)

Although the majority of patients who undergo implant-based reconstruction and irradiation ultimately keep the implant reconstruction, patient surveys show that irradiation has a significantly negative effect on patient satisfaction.
Recommending source code examples via API call usages and documentation (2010)

Online source code repositories contain software projects that already implement certain requirements that developers must fulfill. Programmers can reuse code from these existing projects if they can find relevant code without significant effort. We propose a new method to recommend source code examples to developers by querying against Application Programming Interface (API) calls and their documentations that are fused with structural information about the code. We conducted an empirical evaluation that suggests that our approach is lightweight and accurate.
Hemodynamics in Coronary Arterial Tree of Serial Stenoses (2016)

Serial segmental narrowing frequently occurs in humans, which alters coronary hemodynamics and further affects atherosclerotic progression and plaque formation. The objective of this study was to understand the distribution of hemodynamic parameters in the epicardial left main coronary arterial (LMCA) tree with serial stenoses reconstructed from patient computer tomography angiography (CTA) images. A finite volume method was used in conjunction with the inlet pressure wave and outlet flow resistance. The time-averaged wall shear stress (TAWSS) and oscillatory shear index (OSI) were determined from the flow field. A stenosis at a mother vessel mainly deteriorated the hemodynamics near the bifurcation while a stenosis at a daughter vessel affected the remote downstream bifurcation. In comparison with a single stenosis, serial stenoses increased the peak pressure gradient along the main trunk of the epicardial left anterior descending arterial tree by > 50%. An increased distance between serial stenoses further increased the peak pressure gradient. These findings have important implications on the diagnosis and treatment of serial coronary stenoses.
The TWEAK/Fn14 pathway is required for calcineurin inhibitor toxicity of the kidneys (2017)

Calcineurin inhibitor toxicity (CNT) is a frequent occurrence in transplanted renal grafts and autochthone kidneys from patients undergoing long-term treatment with calcineurin inhibitors, notably cyclosporin A (CsA) and tacrolimus. Here, we show an indispensable role of the tumor necrosis factor superfamily (TNFS) molecule TNF-related weak inducer of apoptosis (TWEAK) (TNFSF12) in the pathogenesis of acute CNT lesions in mice. A deficiency in TWEAK resulted in limited tubulotoxicity after CsA exposure, which correlated with diminished expression of inflammatory cytokines and reduced intraparenchymal infiltration with immune cells. We further identified tubular epithelial cells of the kidney as major targets of CsA activity and found that Fn14 (tumor necrosis factor receptor superfamily 12A), the receptor for TWEAK, is a highly CsA-inducible gene in these cells. Correlating with this, CsA pretreatment sensitized tubular epithelial cells specifically to the pro-inflammatory activities of recombinant TWEAK in vitro. Moreover, injection of rTWEAK alone into mice induced moderate disease similar to CsA, and rTWEAK combined with CsA resulted in synergistic nephrotoxicity. These findings support the importance of tubular epithelial cells as cellular targets of CsA toxicity and introduce TWEAK as a critical contributor to CNT pathogenesis.
Dynamics of concerted bubble cluster collapse in shock wave lithotripsy (2003)

Cavitation bubble cluster collapse at the surface of artificial kidney stones during shock wave lithotripsy was investigated in vitro by means of multiframe high-speed photography, passive cavitation detection (PCD), and pressure waveform measurements using a fiber-optic probe hydrophone (FOPH). It was observed that after the passage of the lithotripter shock pulse the stone was covered by numerous individual bubbles. During their growth phase the bubbles coalesced into bubble clusters, with the biggest cluster at the proximal face of the stone. High-speed camera images suggested that cluster collapse started at the periphery and ended with a violent collapse in a small region in the center of the surface of the stone. Shadowgraphy resolved numerous secondary shock waves emitted during this focused collapse. Shock wave emission during cluster collapse was confirmed by PCD. Measurement with the FOPH showed that these shock waves were typically of short duration (0.2 μs). The majority of the shock waves emanating from cluster collapse were low amplitude but some shock waves registered amplitudes on the order of the incident shock pulse (tens of MPa). [Work supported by NIH DK43881, DK55674.]
A 100 year sedimentary record of heavy metal pollution in a shallow eutrophic lake, Lake Chaohu, China (2011)

This study has worked on the evaluation of the temporal and spatial evolution of heavy metal contamination in sediment taken from a shallow eutrophic lake, Lake Chaohu, China, over the last 100 years, and thereby used (137)Cs and (210)Pb dating, a PIRLA procedure, statistical analysis, geochemical normalization and a enrichment factor calculation (EF). Concentrations of 5174, 29 325, 10.7, 36.4, 20.4, 386.0, 21.1 and 38.4 mg kg(-1) for Ti, Fe, Co, Cr, Cu, Mn, Pb and Zn, respectively, are proposed as natural background values for the Lake Chaohu based on a PIRLA procedure. The contamination history from the last 100 years can be divided into two periods. Before the 1960s, heavy metal contamination did not occur and there was no spatial difference for heavy metal distribution. Since the 1960s, heavy metal enrichment and contamination has occurred, and the west half of the lake region showed a higher degree of contamination than the east half to various intensified anthropogenic activities. In the east half of the lake region, the anthropogenic source of heavy metals mainly originated from agricultural intensification, whereas in the west half of the lake it originated from city runoff and industry as well as agriculture. In all anthropogenic heavy metals, Co is only from industry.
Thomson scattering measurements on an atmospheric Ar dc discharge lamp (2004)

Thomson scattering (TS) experiments have been performed in the region near the electrodes of a dc powered model lamp filled with 1-2 bar argon gas. In order to suppress the false stray light and Rayleigh scattered photons, a triple grating spectrograph was used. In this way the electron density and electron temperature could be measured in the near-electrode region for different arc currents. In order to get the electron density and electron temperature out of the TS spectrum, both collective and non-collective TS fitting procedures were used for the data processing. It was found that the radial profile of the electron temperature is more or less flat in the anode region with a value of about 1 eV. The electron density increases with arc current and is of the order of 10/sup 21/ m/sup -3/. From the result, we can see that the plasma regions investigated are not in local thermal equilibrium in the sense that, locally, the rate of ionization is much larger than that of recombination
Trends in Reservoir Simulation: Big Models, Scalable Models? Will you Please Make up Your Mind? (2001)

Abstract Over the past 20–30 years, reservoir simulation technology has gone through various stages of acceptance and utilization. This paper will discuss the most common workflows as well as several of the emerging trends in reservoir simulation technology, particularly: 1) building ever larger increasingly complex simulation models, 2) building smaller models, which can be evaluated quickly, and 3) building scalable or "fit for purpose" models. This paper will discuss these trends in more detail, reconcile these approaches and discuss the appropriateness of each method. Potential conflicts with respect to the user profile and the differing demands imposed on development and usage of a reservoir simulation system will also be discussed relative to each of these workflows.
Wireless Power Transmission Using Acoustic-to-Inductive Relayed Transfer (2022)

This paper presents, for the first time, a wireless power transfer technology that uses acoustic power transfer to transfer through/along a metal structure, then relays to conventional inductive power transfer to charge receivers not in contact with the metal structure. Acoustic waves have the unique ability to transfer directly through/along metal structures without experiencing electromagnetic shielding, which is useful for powering wireless sensors for infrastructure monitoring (e.g., within metal pipelines). For powering receivers detached from the metal structure, acoustic and inductive can be combined, and in this work, we demonstrate 28% power efficiency at 28 kHz by transferring through a metal tube. Higher efficiencies can be achieved by improving the inductive coil coupling.
Translating OWL and Semantic Web Rules into Prolog: Moving Toward Description Logic Programs (2007)

To appear in Theory and Practice of Logic Programming (TPLP), 2008. We are researching the interaction between the rule and the ontology layers of the Semantic Web, by comparing two options: 1) using OWL and its rule extension SWRL to develop an integrated ontology/rule language, and 2) layering rules on top of an ontology with RuleML and OWL. Toward this end, we are developing the SWORIER system, which enables efficient automated reasoning on ontologies and rules, by translating all of them into Prolog and adding a set of general rules that properly capture the semantics of OWL. We have also enabled the user to make dynamic changes on the fly, at run time. This work addresses several of the concerns expressed in previous work, such as negation, complementary classes, disjunctive heads, and cardinality, and it discusses alternative approaches for dealing with inconsistencies in the knowledge base. In addition, for efficiency, we implemented techniques called extensionalization, avoiding reanalysis, and code minimization.
Enhanced Power and Signal Integrity Through Layout Optimization of High-Speed Memory Systems (2019)

In this paper, a high-speed memory bus with non-ideal power/ground reference was analyzed. Noise from power planes and vias would couple to the double-data-rate (DDR) signals and impact signal quality. Several design parameters of the system structure were considered to improve the DDR signal quality. Parameters such as location of the signals, location of noise source and placement of decoupling capacitor are considered to reduce the noise coupling. With optimized parameters, the transfer impedance between the victim signal and noise source could be suppressed and the noise coupling can be reduced accordingly. Time domain eye-diagram plots of the DDR signal are also used to depict the signal quality.
Superconductivity in the Filled Cage CompoundsBa6Ge25andBa4Na2Ge25 (2001)

The clathrate compound Ba 6Ge25 and its relatives consist of a rigid germanium skeleton, into which barium or other metal atoms are coordinated. These guest atoms can "rattle" freely at high temperatures, but in Ba 6Ge25 some of them lock randomly into split positions below T(S) approximately 200 K. The resulting bad metal undergoes a BCS-like superconducting transition at T(c) approximately 0.24 K. T(c) increases more than 16-fold, as T(S) is suppressed by hydrostatic pressure p, but changes only slightly with p from T(c) approximately 0.84 K in the undistorted sister compound Ba 4Na2Ge25. The large enhancement of T(c) in Ba 6Ge25 may be attributed mainly to the pressure tuning of strong disorder caused by the random displacement of Ba atoms at T(S).
CCDC 699147: Experimental Crystal Structure Determination (2010)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
ChemInform Abstract: Efficient Synthesis of Heterocyclic Neurotensin Receptor Ligands by Microwave‐Assisted Aminocarbonylation. (2014)

Abstract Conversion of functionalized aryl bromides (I) to the corresponding amides (V) including the potent neurotensin NTS1 receptor SR142948A (IVd) is developed using aminocarbonylation with Mo(CO) 6 as the CO source.
Non-Convex Phase Retrieval From STFT Measurements (2017)

The problem of recovering a one-dimensional signal from its Fourier transform magnitude, called Fourier phase retrieval, is ill-posed in most cases. We consider the closely-related problem of recovering a signal from its phaseless short-time Fourier transform (STFT) measurements. This problem arises naturally in several applications, such as ultra-short laser pulse characterization and ptychography. The redundancy offered by the STFT enables unique recovery under mild conditions. We show that in some cases the unique solution can be obtained by the principal eigenvector of a matrix, constructed as the solution of a simple least-squares problem. When these conditions are not met, we suggest using the principal eigenvector of this matrix to initialize non-convex local optimization algorithms and propose two such methods. The first is based on minimizing the empirical risk loss function, while the second maximizes a quadratic function on the manifold of phases. We prove that under appropriate conditions, the proposed initialization is close to the underlying signal. We then analyze the geometry of the empirical risk loss function and show numerically that both gradient algorithms converge to the underlying signal even with small redundancy in the measurements. In addition, the algorithms are robust to noise.
Low-frequency ripple-shaping controller for operation of non-inverting buck-boost converters near step-up step-down boundary (2018)

This paper introduces a practical controller for low power noninverting dc-dc buck-boost converters that minimizes the step-up step-down mode transition problem, while also significantly improving power processing efficiency compared to existing state-of-the-art solutions. Near the step-down step-up boundary, the controller enters a low-frequency ripple shaping mode of operation that allows lower operation frequency than in conventional buck or boost modes without paying a penalty of increased ripple, i.e. RMS, current. As a result, both switching and conduction losses are reduced. Furthermore, since the ripple shaping mode can cover both buck and boost modes of operation, mode toggling problems are practically eliminated. The effectiveness of the controller is demonstrated with a 1.8 V to 5 V input, 3.3 V/10W output experimental prototype where stable operation, smooth mode transitions, and power processing efficiency improvements of up to 6% are demonstrated.
High efficiency intramuscular plasmid electrotransfer: application for sustained plasmatic secretion of cytokines (2001)

There is increasing interest in adeno-associated virus (AAV) vectors for a wide variety of gene therapy applications. AAV is a nonpathogenic human parvovirus that can mediate long-term transduction of a number of cell types without provoking a significant immune response. These properties make AAV especially attractive for use in gene therapy of rheumatoid arthritis (RA), a chronic inflammatory disease. To investigate the potential of AAV in gene therapy of arthritis, the ability of AAV to infect synovium in vitro and in vivo was tested. Three human RA synovial fibroblast cell lines and two murine (one DBA/1J and one DBA1JC3H F1) synovial fibroblast cell lines were used to test AAV transduction in vitro. The cell lines (2 10 5 cells) were infected with 10 4 particles/cell of a murine IL-10-encoding vector (AAV-mIL-10) alone or with the addition of a low titer (100 particles/cell) of an E1-, E3-deleted recombinant adenovirus to provide E4orf6 activity to enhance second-strand synthesis. The supernatants were harvested from the wells at various time points and assayed for mIL-10 expression by ELISA. Both human synovial cell lines infected with AAV alone demonstrated low-level transgene expression throughout the course of the study. However, by day 10, all human cultures coinfected with adenovirus showed a 16-to 56-fold increase in mIL-10 compared to cultures infected with AAV-mIL10 alone. By day 30, a 31-to 135-fold increase was observed. No such increase was observed in any of the mouse cell lines. To determine the AAV transduction efficiency for synovium in vivo, human RA synovial tissues obtained from patients undergoing joint-replacement surgery were implanted subcutaneously on the backs of NOD.CB17-Prkdc SCID mice. After allowing a 2-week period for engraftment, tissues were injected with 3.4 10 11 particles of AAV-luciferase alone or in combination with 1.0 10 11 particles of adenovirus. Two weeks following AAV administration, the tissues were homogenized and assayed for expression of luciferase. Only the tissues coinfected with adenovirus had luciferase levels above background. A similar experiment with AAV-LacZ demonstrated X-gal staining only of synovial tissues coinfected with adenovirus. These findings demonstrate a preferential ability of AAV to transduce human, compared to mouse, synovial tissue and suggest that second strand synthesis may be a limiting factor in gene transduction. Further studies to elucidate the mechanisms limiting gene transduction in human synovium may allow optimization of this vector for the treatment of arthritis.
The Role of Complement in Transplantation (2006)

Organ transplantation is an established therapy for patients with end-stage organ disease. In the past years, a growing understanding of physiology and pathophysiology, refinement of tissue typing, better surgical techniques and more effective immunosuppressive strategies has progressively favoured prolonged graft survival. However, still a significant proportion of grafts fail within the first months and years after transplantation because of a progressive and irreversible immune response of the recipient. The pathogenesis of graft rejection comprises complex immunological and non-immunological mechanisms. Humoral as well as cell-mediated immune reactions have been implicated in graft rejection. Although primarily driven by T-cell response the role of complement activation in acute graft rejection has become evident in recent years. Here, modern complement analysis as an integral part of posttransplantation monitoring may contribute to early recognition of impeding graft rejection. Hyperacute graft rejection is a rare occurrence in the clinic. It may occur immediately after allotransplantation due to preexisting blood group directed or anti-HLA antibodies. In xentransplantation, hyperacute rejection is a major barrier to organ survival. The binding of pre-existing, so-called natural antibodies, mostly of the IgM class, to donor cells leads to fulminant activation of the complement and clotting systems with rapid loss of graft function. Therapeutic substitution of appropriate complement regulators appears to be a reasonable approach to reduce undesirable complement-mediated inflammatory reactions in the grafted organ.