gebhart/patrepeval huggingface dataset:
Revisiting cardiovascular regeneration with bone marrow‐derived angiogenic and vasculogenic cells (2012)

Cell-based therapy has emerged as a promising therapy for cardiovascular disease. Particularly, bone marrow (BM)-derived cells have been most extensively investigated and have shown encouraging results in preclinical studies. Clinical trials, however, have demonstrated split results in post-myocardial infarction cardiac repair. Mechanistically, transdifferentiation of BM-derived cells into cardiovascular tissue demonstrated by earlier studies is now known to play a minor role in functional recovery, and humoral and paracrine effects turned out to be main mechanisms responsible for tissue regeneration and functional recovery. With this advancement in the mechanistic insight of BM-derived cells, new efforts have been made to identify cell population, which can be readily isolated and obtained in sufficient quantity without mobilization and have higher therapeutic potential. Recently, haematopoietic CD31(+) cells, which are more prevalent in bone marrow and peripheral blood, have been revealed to have angiogenic and vasculogenic activities and strong potential for therapeutic neovascularization in ischaemic tissues. This article will cover the recent advances in BM-derived cell-based therapy and implication of CD31(+) cells.
MPI: A Message-Passing Interface Standard (1994)

process naming to allow libraries to describe their communication in terms suitable to their own data structures and algorithms, ffl The ability to &amp;quot;adorn&amp;quot; a set of communicating processes with additional user-defined attributes, such as extra collective operations. This mechanism should provide a means for the user or library writer effectively to extend a message-passing notation. In addition, a unified mechanism or object is needed for conveniently denoting communication context, the group of communicating processes, to house abstract process naming, and to store adornments. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 5.1. INTRODUCTION 131 5.1.2 MPI&amp;apos;s Support for Libraries The corresponding concepts that MPI provides, specifically to support robust libraries, are as follows: ffl Contexts of communication, ffl Groups of processes, ffl Virtual topologies, ffl Attribute caching, ffl Commun...
From ultrasoft pseudopotentials to the projector augmented-wave method (1999)

The formal relationship between ultrasoft (US) Vanderbilt-type pseudopotentials and Bl\"ochl's projector augmented wave (PAW) method is derived. It is shown that the total energy functional for US pseudopotentials can be obtained by linearization of two terms in a slightly modified PAW total energy functional. The Hamilton operator, the forces, and the stress tensor are derived for this modified PAW functional. A simple way to implement the PAW method in existing plane-wave codes supporting US pseudopotentials is pointed out. In addition, critical tests are presented to compare the accuracy and efficiency of the PAW and the US pseudopotential method with relaxed core all electron methods. These tests include small molecules $({\mathrm{H}}_{2}{,\mathrm{}\mathrm{H}}_{2}{\mathrm{O},\mathrm{}\mathrm{Li}}_{2}{,\mathrm{}\mathrm{N}}_{2}{,\mathrm{}\mathrm{F}}_{2}{,\mathrm{}\mathrm{BF}}_{3}{,\mathrm{}\mathrm{SiF}}_{4})$ and several bulk systems (diamond, Si, V, Li, Ca, ${\mathrm{CaF}}_{2},$ Fe, Co, Ni). Particular attention is paid to the bulk properties and magnetic energies of Fe, Co, and Ni.
Initial investigations into the effects of input shaping on trajectory following (2005)

The effects of input shaping on trajectory following were investigated by simulating the response of a fourth-order system with orthogonal modes and conducting experiments on an XY positioning stage. For nearly all values of damping and frequency ratio, the shaped inputs result in significantly better trajectory following than unshaped inputs. When the trajectory improvement techniques in this paper are used, the shaped inputs perform considerably better for all parameter values.
Iron substitution in the treatment of chronic heart failure (2017)

Iron deficiency is a prevalent and clinically relevant comorbidity in up to 50% of patients with chronic heart failure (CHF). Iron deficiency in CHF patients is associated with impaired quality of life, reduced exercise capacity and increased mortality, irrespective of the presence of anaemia. It is diagnosed by determining circulating ferritin levels and transferrin saturation. Three randomised trials (CONFIRM-HF, FAIR-HF, and EFFECT-HF) of intravenous ferric carboxymaltose in the treatment of iron deficiency in CHF patients with reduced left ventricular ejection fraction demonstrated improvement of symptoms, functional capacity and quality of life. These beneficial effects were independent of the presence of anaemia. In addition, CONFIRM-HF and subsequent meta-analyses indicated that treatment of iron deficiency may reduce the rate of hospitalisations for worsening CHF. Oral iron is available at lower cost than intravenous iron, but its use did not translate into beneficial effects in CHF patients with iron deficiency. Large randomised trials designed to assess long-term clinical outcomes of iron treatment in CHF patients are pending. Current guidelines advise establishing evidence-based pharmacological and device therapy to improve symptoms and prognosis in patients with CHF. In addition, screening for iron deficiency is recommended. Intravenous ferric carboxymaltose should be considered for treating iron deficiency in ambulatory symptomatic patients with reduced left ventricular ejection fraction in order to alleviate heart failure symptoms, and to improve exercise capacity and quality of life.
미국 NASW 윤리강령의 변화과정 및 2018 개정의 함의 (2018)

Ethical issues are the core principles of social welfare practice that have a great impact on social welfare identity, mission and practice as well as...
Novel strategies and underlying protective mechanisms of modulation of vagal activity in cardiovascular diseases (2014)

Cardiovascular disease remains a major cause of disability and death worldwide. Autonomic imbalance, characterized by suppressed vagal (parasympathetic) activity and increased sympathetic activity, correlates with various pathological conditions, including heart failure, arrhythmia, ischaemia/reperfusion injury and hypertension. Conventionally, pharmacological interventions, such as β-blocker treatment, have primarily targeted suppressing sympathetic over-activation, while vagal modulation has always been neglected. Emerging evidence has documented the improvement of cardiac and vascular function mediated by the vagal nerve. Many investigators have tried to explore the effective ways to enhance vagal tone and normalize the autonomic nervous system. In this review, we attempt to give an overview of these therapeutic strategies, including direct vagal activation (electrical vagal stimulation, ACh administration and ACh receptor activation), pharmacological modulation (adenosine, cholinesterase inhibitors, statins) and exercise training. This overview provides valuable information for combination therapy, contributing to establishment of a comprehensive system on vagal modulation from the aspects of clinical application and lifestyle improvement. In addition, the mechanisms contributing to the benefits of enhancing vagal tone are diverse and have not yet been fully defined. We endeavour to outline the recent findings that advance our knowledge regarding the many favourable effects exerted by vagal activation: anti-inflammatory pathways, modulation of NOS and NO signalling, regulation of redox state, improvement of mitochondrial biogenesis and function, and potential calcium regulation. This review may help to develop novel therapeutic strategies targeting enhancing vagal activity for the treatment of cardiovascular diseases.
Nuclease Resistance of Oligonucleotides Containing the Tricyclic Cytosine Analogues Phenoxazine and 9-(2-Aminoethoxy)-Phenoxazine (“G-clamp”) and Origins of Their Nuclease Resistance Properties (2001)

The tricyclic cytosine analogues phenoxazine and 9-(2-aminoethoxy)-phenoxazine ("G-clamp") are known to significantly enhance the binding affinity of oligonucleotides to their complementary target DNA or RNA strands. To investigate their effect on the nuclease resistance, they were incorporated into model oligomers with a natural phosphodiester backbone, and enzymatic degradation was monitored in an in vitro assay with snake venom phosphodiesterase as the hydrolytic enzyme. In both cases, a single incorporation at the 3'-terminus completely protected the oligonucleotides against 3'-exonuclease attack. Further investigations indicate that the observed high nuclease resistance is not due to the lack of binding affinity to the enzyme's active site, since these modified oligonucleotides were able to inhibit degradation of a natural DNA fragment by bovine intestinal mucosal phosphodiesterase in a dose-dependent manner.
The Scottish Structural Proteomics Facility: targets, methods and outputs (2010)

The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology.
Lack of the latent transforming growth factor beta binding protein in malignant, but not benign prostatic tissue. (1993)

Transforming growth factor beta (TGF-beta) is a family of proteins which act as a potent growth inhibitor for most cell types including epithelial cells. TGF-beta is synthesized as latent high molecular weight complexes, composed of TGF-beta, the NH2-terminal part of the TGF-beta precursor and the third molecule, the latent TGF-beta binding protein (LTBP). We here ascertain that TGF-beta is expressed in human prostatic cancer tissue as well as in cystectomized prostatic tissue and in materials from transurethral resections with benign prostatic hyperplasia, analyzed by immunohistochemistry. TGF-beta is observed in both epithelial cells and stromal cells. No significant correlation was obtained between TGF-beta expression in tumor cells and their degree of differentiation. However, analysis by immunohistochemistry using antibodies against LTBP revealed that specimens from histopathologically verified human prostatic cancer are mostly negative for this molecule, although it is expressed in cystectomized prostatic and benign prostatic hyperplasia tissues. These results indicate that in cystectomized prostatic and benign prostatic hyperplasia tissues, TGF-beta may be produced in a complex associated with LTBP; whereas in prostatic carcinoma, TGF-beta is produced without associating with LTBP. The biological significance of the production of TGF-beta in relation to LTBP and the possible association with prognosis are discussed.
PFLOTRAN User Manual: A Massively Parallel Reactive Flow and Transport Model for Describing Surface and Subsurface Processes (2015)

PFLOTRAN solves a system of generally nonlinear partial differential equations describing multi-phase, multicomponent and multiscale reactive flow and transport in porous materials. The code is designed to run on massively parallel computing architectures as well as workstations and laptops (e.g. Hammond et al., 2011). Parallelization is achieved through domain decomposition using the PETSc (Portable Extensible Toolkit for Scientific Computation) libraries for the parallelization framework (Balay et al., 1997). PFLOTRAN has been developed from the ground up for parallel scalability and has been run on up to 218 processor cores with problem sizes up to 2 billion degrees of freedom. Written in object oriented Fortran 90, the code requires the latest compilers compatible with Fortran 2003. At the time of this writing this requires gcc 4.7.x, Intel 12.1.x and PGC compilers. As a requirement of running problems with a large number of degrees of freedom, PFLOTRAN allows reading input data that is too large to fit into memory allotted to a single processor core. The current limitation to the problem size PFLOTRAN can handle is the limitation of the HDF5 file format used for parallel IO to 32 bit integers. Noting that 232 = 4; 294; 967; 296, this gives an estimate of the maximum problem size that can be currently run with PFLOTRAN. Hopefully this limitation will be remedied in the near future.
Depletion of L-3,5,3'-Triiodothyronine and L-Thyroxine in Euthyroid Calf Serum for Use in Cell Culture Studies of the Action of Thyroid Hormone* (1979)

GH1 cells are a clonal strain of rat pituitary tumor cells which synthesize GH and PRL. We have previously demonstrated that these cells respond to physiological concentrations of L-T3 and L-T4 when cultured with medium supplemented with thyroidectomized calf serum to achieve a thyroid hormone-depleted state under cell culture conditions. In this study, we describe a method to deplete euthyroid calf serum of L-T3 and L-T4 using an anion exchange resin. We demonstrate that the procedure only minimally alters the low molecular weight anion components of the serum and does not change the total protein content or the electrophoretic pattern of serum proteins. Moreover, we show that euthyroid calf serum depleted of L-T3 and L-T4 by this procedure yields serum which, when used as a medium supplement, results in biological responses identical to those obtained with media supplemented with thyroidectomized calf serum. In addition, resin treatment does not alter the growth-promoting properties of the serum if the thyroid hormone concentration is restored. This procedure should be useful in preparing thyroid hormone-depleted serum for cell culture studies in situations where thyroidectomy is not feasible or would require surgical procedures on a large number of small animals.
Cloning of the murine TROP2 gene: Conservation of a PIP2-binding sequence in the cytoplasmic domain of TROP-2 (1998)

Trop-2 is a novel calcium signal transducer expressed at high levels by most human carcinomas. To develop an animal model to study the function of this molecule in vivo, we have cloned the murine Trop2 gene. Using human TROP2 primers, we amplified by PCR a segment of murine Trop2. This was used as a probe to clone a full-length gene by hybridization of a genomic library. The cloned murine Trop2 gene is functional, as indicated by sequencing and by expression after transfection. The murine Trop2 is 87.4% similar to its human homologue, with the highest conservation in the extracellular region between residues 86 and 157. Essentially all cysteines are conserved between the human and the murine genes, suggesting conservation of the Trop2 disulfide bridges and of its overall structure. Intriguingly, the cytoplasmic tail of Trop2 shows a highly conserved phosphatidylinositol 4,5-bisphosphate (PIP2)-binding sequence, which overlaps with a protein kinase C phosphorylation site. Thus, we speculate that PIP2 might regulate the phosphorylation state of Trop2 and play a role in its signal transduction. Murine Trop2 mRNA is detected in normal kidney, lung, ovary and testis, similarly to the human gene. Interestingly, the highest levels of expression are found in immortalized keratinocytes. Since Trop2 is undetectable in undifferentiated spindle cell carcinomas, this suggests a preferential expression at early stages of tumor progression.
Pixel-Accurate Representation and Evaluation of Page Segmentation in Document Images (2006)

This paper presents a new representation and evaluation procedure of page segmentation algorithms and analyzes six widely-used layout analysis algorithms using the procedure. The method permits a detailed analysis of the behavior of page segmentation algorithms in terms of over- and undersegmentation at different layout levels, as well as determination of the geometric accuracy of the segmentation. The representation of document layouts relies on labeling each pixel according to its function in the overall segmentation, permitting pixel-accurate representation of layout information of arbitrary layouts and allowing background pixels to be classified as "don't care". Our representations can be encoded easily in standard color image formats like PNG, permitting easy interchange of segmentation results and ground truth
Protecting against unexpected system calls (2005)

This paper proposes a comprehensive set of techniques which limit the scope of remote code injection attacks. These techniques prevent any injected code from making system calls and thus restrict the capabilities of an attacker. In defending against the traditional ways of harming a system these techniques significantly raise the bar for compromising the host system forcing the attack code to take extraordinary steps that may be impractical in the context of a remote code injection attack. There are two main aspects to our approach. The first is to embed semantic information into executables identifying the locations of legitimate system call instructions; system calls from other locations are treated as intrusions. The modifications we propose are transparent to user level processes that do not wish to use them (so that, for example, it is still possible to run unmodified third-party software), and add more security at minimal cost for those binaries that have the special information present. The second is to back this up using a variety of techniques, including a novel approach to encoding system call traps into the OS kernel, in order to deter mimicry attacks. Experiments indicate that our approach is effective against a wide variety of code injection attacks. 1
Adaptation of Clostridium tyrobutyricum for Enhanced Tolerance to Butyric Acid in a Fibrous‐Bed Bioreactor (2003)

By immobilization in a fibrous-bed bioreactor (FBB), we succeeded in adapting and selecting an acid-tolerant strain of Clostridium tyrobutyricum that can produce high concentrations of butyrate from glucose and xylose. This mutant grew well under high butyrate concentrations (>30 g/L) and had better fermentative ability as compared to the wild-type strain used to seed the bioreactor. Kinetic analysis of butyrate inhibition on cell growth, acid-forming enzymes, and ATPase activity showed that the adapted cells from the FBB are physiologically different from the original wild type. Compared to the wild type, the adapted culture's maximum specific growth rate increased by 2.3-fold and its growth tolerance to butyrate inhibition increased by 29-fold. The key enzymes in the butyrate-forming pathway, phosphotransbutyrylase (PTB) and butyrate kinase (BK), were also more active in the mutant, with 175% higher PTB and 146% higher BK activities. Also, the mutant's ATPase was less sensitive to inhibition by butyric acid, as indicated by a 4-fold increase in the inhibition rate constant, and was more resistant to the enzyme inhibitor N,N'-dicyclohexylcarbodiimide (DCCD). The lower ATPase sensitivity to butyrate inhibition might have contributed to the increased growth tolerance to butyrate inhibition, which also might be attributed to the higher percentage of saturated fatty acids in the membrane phospholipids (74% in the mutant vs 69% in the wild type). This study shows that cell immobilization in the FBB provides an effective means for in-process adaptation and selection of mutant with higher tolerance to inhibitory fermentation product.
The chemistry of graphene oxide (2009)

The chemistry of graphene oxide is discussed in this critical review. Particular emphasis is directed toward the synthesis of graphene oxide, as well as its structure. Graphene oxide as a substrate for a variety of chemical transformations, including its reduction to graphene-like materials, is also discussed. This review will be of value to synthetic chemists interested in this emerging field of materials science, as well as those investigating applications of graphene who would find a more thorough treatment of the chemistry of graphene oxide useful in understanding the scope and limitations of current approaches which utilize this material (91 references).
Evidence that PI3K, Rac, Rho, and Rho kinase are involved in basic fibroblast growth factor‐stimulated fibroblast–Collagen matrix contraction (2007)

Fibroblast-collagen matrix contraction has been used as a model system to study how cells organize connective tissue. Previous work showed that lysophosphatidic acid (LPA)-stimulated floating collagen matrix contraction is independent of Rho kinase while platelet-derived growth factor (PDGF)-stimulated contraction is Rho kinase-dependent. The current studies were carried out to determine the signaling mechanisms of basic fibroblast growth factor (bFGF)-stimulated fibroblast-collagen matrix contraction. Both bFGF and LPA promoted equally collagen matrix contraction well. Three different inhibitors, LY294002 for phosphatidylinositol-3-kinase (PI3K), C3 exotransferase for Rho and Y27632 for Rho kinase, suppressed the bFGF-stimulated fibroblast-collagen matrix contraction. With bFGF stimulation, fibroblasts spread with prominent stress fiber network formation and focal adhesions. In the presence of Rho kinase inhibitor, focal adhesions and stress fibers were mostly lost. We demonstrated that bFGF stimulation for fibroblast caused transient Rac and Rho activation but did not activate Cdc42. In addition, bFGF enhanced fibroblast migration in wound healing assay. The present study implicates PI3K, Rac, Rho, and Rho kinase as being involved in bFGF-stimulated collagen matrix contraction. The elucidation of bFGF-triggered signal transduction may be an important clue to understand the roles of bFGF in wound healing.
DNA interstrand cross-link and free radical formation in a human multidrug-resistant cell line from mitomycin C and its analogues. (1990)

A subline of the human breast tumor cell line (MCF-7), selected for resistance to Adriamycin and having the multidrug resistance phenotype, also developed significant cross-resistance to mitomycin C and its two analogues, BMY 25282 and BMY 25067. Because mitomycin C and the analogues contain both quinone and aziridine moieties, the mechanism of tumor cell kill is thought to involve alkylation and cross-linking of DNA molecules, hence they are not expected to show cross-resistance to cells selected for resistance to a DNA intercalator. Studies to understand this novel observation show that the resistant MCF-7 cells form significantly less hydroxyl radical and DNA cross-linking in the presence of mitomycin C and BMY 25282 than the sensitive cells. Although BMY 25067 formed less free radicals in the resistant cells, similar to the other two drugs, the formation of DNA cross-links was identical in both cell lines, indicating a somewhat different mechanism of tumor cell kill by this analogue. DNA cross-link formation increased slightly with time in the sensitive cells while there was a small decrease in the resistant cells. This difference in the formation of toxic intermediates appeared to result from enhanced detoxification of reactive species (hydrogen peroxide and alkylating intermediates) as a result of significantly higher glutathione peroxidase (14-fold) and glutathione S-transferase (44-fold) activities in the resistant cell line. These events, i.e., free radical formation and DNA alkylation, showed a good correlation with the cytotoxicity in drug-sensitive cells, indicating that both mechanisms contribute to cell killing of human breast tumor cells.