gebhart/patrepeval huggingface dataset:
Efficient compression of deterministic patterns into multiple prpg seeds (2006)

Recent test-cost reduction methods are based on controlling the initial state (seed) of a pseudo-random pattern generator (PRPG) so that deterministic values are loaded in selected scan cells. Combined with an unload-data compression technique, PRPG seeding reduces test data volume and application time. This paper presents a method of mapping each scan load to multiple PRPG seeds, computed so that test pattern count, data volume, and, therefore, test cost are minimized. This method also allows smaller and fewer PRPGs, reducing the area overhead of test-compression circuitry. The results on deep-submicron industrial designs, show significant test cost reduction when this method is applied with either X-tolerant or X-free unload-data compression
P‐14: AM‐OLED Pixel Circuits Based on a‐InGaZnOThin Film Transistors (2009)

Abstract In this paper, we investigated the application of amorphous In‐Ga‐Zn‐O (a‐InGaZnO) thin film transistors (TFTs) to active‐matrix organic light emitting display (AM‐OLED) pixel circuits. SPICE model of a‐InGaZnO TFTs was developed based on experimental data. Several pixel circuits were explored, and the potential advantages of using a‐InGaZnO TFTs were discussed.
A fluorescent-labeled oligopeptide for monitoring PKA-mediated phosphorylation (2000)

A fluorescent-labeled oligopeptide (DACM-CLRRASLK-fluorescein), containing a consensus amino acid sequence (RRXSL) of cyclic AMP (cAMP) dependent protein kinase A (PKA) substrate-proteins, was designed. The fluorescent peptide was a good substrate of PKA, and the phosphorylation of its serin residue caused an intensive change in fluorescent intensity. We expect that the peptide will be useful as a fluorescent indicator for monitoring PKA activity in living cells.
A genetic analysis of the functions of LuxN: a two‐component hybrid sensor kinase that regulates quorum sensing in Vibrio harveyi (2000)

The bioluminescent marine bacterium Vibrio harveyi controls light production using two parallel quorum‐sensing systems. V. harveyi produces two autoinducers (AI‐1 and AI‐2), which are recognized by cognate membrane‐bound two‐component hybrid sensor kinases called LuxN and LuxQ respectively. Under conditions of low cell density, in the absence of autoinducer, the hybrid sensors are kinases, and under conditions of high cell density, in the presence of autoinducer, the sensors are phosphatases. These activities allow LuxN and LuxQ to modulate the level of phosphorylation of the response regulator protein LuxO. LuxO, in turn, controls the transcription of the genes encoding luciferase. The phosphorelay protein LuxU is required for signalling to LuxO. In this report, we present a genetic analysis of the activities of the AI‐1 sensor LuxN. Point mutations and in frame deletions were constructed in luxN and recombined onto the chromosome of V. harveyi for in vivo phenotypic analysis. We show that the conserved histidine (H471) in the sensor kinase domain of LuxN is required for kinase activity but not for phosphatase activity. In contrast, the conserved aspartate (D771) in the response regulator domain of LuxN is required for both activities. Furthermore, the LuxN phosphatase activity is localized to the response regulator domain. Our results indicate that the LuxN kinase activity is regulated by the presence of AI‐1, whereas the LuxN phosphatase activity is constitutive. We also show that signalling from the two V. harveyi quorum‐sensing systems is not equivalent. AI‐1 and LuxN have a much greater effect on the level of LuxO phosphate and therefore Lux expression than do AI‐2 and LuxQ.
Privacy-preserving data publishing (2010)

The collection of digital information by governments, corporations, and individuals has created tremendous opportunities for knowledge- and information-based decision making. Driven by mutual benefits, or by regulations that require certain data to be published, there is a demand for the exchange and publication of data among various parties. Data in its original form, however, typically contains sensitive information about individuals, and publishing such data will violate individual privacy. The current practice in data publishing relies mainly on policies and guidelines as to what types of data can be published and on agreements on the use of published data. This approach alone may lead to excessive data distortion or insufficient protection. Privacy-preserving data publishing (PPDP) provides methods and tools for publishing useful information while preserving data privacy. Recently, PPDP has received considerable attention in research communities, and many approaches have been proposed for different data publishing scenarios. In this survey, we will systematically summarize and evaluate different approaches to PPDP, study the challenges in practical data publishing, clarify the differences and requirements that distinguish PPDP from other related problems, and propose future research directions.
Thiazolidinediones and Fatty Acids Convert Myogenic Cells into Adipose-like Cells (1995)

Fatty acids and thiazolidinediones act as potent activators of the adipose differentiation program in established preadipose cell lines. In this report, the effects of these agents on the differentiation pathway of myoblasts have been investigated. Exposure of C2C12N myoblasts (a subclone of the C2C12 cell line) to thiazolidinediones or fatty acids prevents the expression of myogenin, alpha-actin, and creatine kinase, thus abolishing the formation of multinucleated myotubes. These treatments lead in parallel to the expression of a typical adipose differentiation program including acquisition of adipocyte morphology and activation of adipose-related genes. A similar transition toward the adipose differentiation pathway also occurs in mouse muscle satellite cells maintained in primary culture. Thiazolidinediones exert their adipogenic effects only in non-terminally differentiated myoblasts; myotubes are insensitive to the compounds. Continuous exposure to inducers after growth arrest is not required to maintain the adipose phenotype, but proliferation of adipose-like C2C12N cells leads to a complete reversion toward undifferentiated cells able to undergo either myogenic or adipogenic differentiation depending on the composition of culture medium. These results indicate that adipogenic inducers, such as thiazolidinediones or fatty acids, specifically convert the differentiation pathway of myoblasts into that of adipoblasts.
Preferential expression of CD30 by human CD4 + T cells producing Th2‐type cytokines (1995)

A large panel of human CD4+ T helper (Th) cell clones with established Th1, Th2, or Th0 profiles of cytokine secretion were examined for the expression of CD30, a member of the tumor necrosis factor receptor superfamily. Th1 clones expressed poor or no CD30 mRNA, and showed low or undetectable expression of both membrane and soluble CD30 (sCD30) protein, whereas Th2 clones showed both CD30 mRNA and membrane CD30 and released substantial amounts of sCD30. Th0 clones exhibited an intermediate pattern of CD30 expression and release. When T cells from the same donor were stimulated with three different antigens (purified protein derivative, PPD; Toxocara canis excretory/secretory antigen, TES; Lolium perenne group I, Lol p I), production of high concentrations of IFN-gamma, but not expression of CD30 or production of IL-4 and IL-5, were observed at any time after stimulation with PPD. In contrast, both CD30 expression and production of IL-4 and IL-5, but not of IFN-gamma, were concomitantly detectable in TES- and Lol p I-reactive T cells, suggesting a temporal relationship between CD30 expression and beginning of Th2-type cytokine production. Finally, CD4+CD30+ T cells specific for Lol p I and inducible to production of Th2-type cytokines were sorted out from the circulation of grass-sensitive patients in concomitance with the onset of allergic symptoms during the seasonal exposure to grass pollen. Thus, CD30 expression appears to be associated with the differentiation/activation pathway of human T cells producing Th2-type cytokines.
Effects of GH and/or sex steroids on circulating IGF-I and IGFBPs in healthy, aged women and men (2006)

Circulating GH, IGF-I, IGFBP-3, and sex steroid concentrations decrease with age. GH or sex steroid treatment increases IGFBP-3, but little is known regarding the effects of these hormones on other IGFBPs. We assessed the effects of 26 wk of administration of GH, sex steroids, or GH + sex steroids on AM levels of IGF-I, IGFBPs 1-5, insulin, glucose, and osteocalcin and 2-h urinary excretion of deoxypyridinolline (DPD) cross-links in 53 women and 71 men aged 65-88 yr. Before treatment, in women and men, IGF-I was directly related to IGFBP-3 (P < 0.001 and P < 0.0001) and IGFBP-1 to IGFBP-2 (P = 0.0001). In women, IGFBP-1 was inversely related to insulin (P < 0.0005) and glucose (P < 0.005) and IGFBP-4 to osteocalcin (P < 0.01). IGFBP-4 and IGFBP-5 were not significantly related to DPD cross-links. GH and/or sex steroid increased IGF-I levels in both sexes, with higher concentrations in men (P < 0.001). In women, the IGF-I increment after GH was attenuated by hormone replacement therapy (HRT) coadministration (P < 0.05). Hormone administration also increased IGFBP-3. IGFBP-1 was unaffected by GH + sex steroids, whereas GH decreased IGFBP-2 by 15% in men (P < 0.05). Hormone administration did not change IGFBP-4, whereas in men IGFBP-5 increased by 20% after GH (P < 0.05) and 56% after GH + testosterone (P = 0.0003). These data demonstrate sexually dimorphic IGFBP responses to GH. Additionally, HRT attenuated or prevented GH-mediated increases in IGF-I and IGFBP-3. Whether GH and/or sex steroid administration alters local tissue production of IGFBPs and whether the latter influence autocrine or paracrine actions of IGF-I remain to be determined.
C-Reactive Protein in Dilated Cardiomyopathy (1999)

The prognosis for patients with idiopathic dilated cardiomyopathy (DCM) is poor, although clinical features are variable. Prediction of outcome has been difficult in individual patients based on laboratory data. In some patients with DCM, myocardial damage secondary to viral or immune-mediated myocardial inflammation may persist. To objectively assess inflammation, we measured plasma concentrations of C-reactive protein (CRP) in 188 patients with idiopathic DCM over 5-8 years. All had dyspnea and fatigue at rest; all patients had a left ventricular ejection fraction less than 40% by echocardiography or by contrast or radionuclide ventriculography. We divided these patients into two groups: patients dying within 5 years following admission (n = 49) and the remainder surviving for at least 5 years (n = 139). CRP concentrations in the patients dying early were significantly higher than in the long-term survivors (1. 05 +/- 1.37 vs. 0.49 +/- 1.04 mg/dl, p < 0.05). Sixty-two percent of the patients with CRP>1.0 died within 5 years. In addition to other laboratory tests including electrocardiography and echocardiography, routine CRP measurements proved to be valuable for identifying high-risk patients who require special treatment strategies.
Aneuploidy in oncocytic lesions of the thyroid gland: Diffuse accumulation of mitochondria within the cell is associated with trisomy 7 and progressive numerical chromosomal alterations (2003)

Oncocytic cells are characterized by a greatly increased number of mitochondria that distend the cell cytoplasm and result in a distinctive granular appearance of the cell on conventional histology sections. Oncocytes are frequently found in metabolically active human tissues including the thyroid gland, and, as a general rule, when their proportion in a thyroid tumor is greater than 75% the tumor is referred to as oncocytic (Hürthle cell) adenoma or carcinoma. Such tumors represent a subset of thyroid lesions, and recently, both interphase fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH) studies reported that they may show aneuploidy, with widespread numerical chromosomal alterations. In contrast, very few cases have been studied by conventional cytogenetic analysis. Whether the cells with chromosomal changes are the same as those with mitochondrial accumulation or whether lesions only partially composed of oncocytic cells also have cytogenetic alterations is unclear. To investigate the relationship between acquisition of the oncocytic phenotype and numerical chromosomal changes, we analyzed a random selection of thyroid lesions with (18 cases) and without (11 cases) morphological evidence of oncocytic differentiation. Lesions with oncocytes included hyperplastic nodules, adenomas, Hürthle cell tumors, and papillary carcinomas with lymphocytic stroma (Whartin-like tumors of the thyroid). Karyotypic changes were analyzed by cytogenetic analysis, FISH, or CGH, and the results were compared with in situ analysis of mitochondrial accumulation by immunofluorescence. A striking correlation between the presence of oncocytes and the presence of aneuploid katyotypes was seen in the oncocytic follicular thyroid nodules, but not in the oncocytic papillary tumors. Structural chromosome changes or normal karyotypes were observed in the lesions lacking oncocytic features. Extending the FICTION technique to the evaluation of a cytoplasmic antigen (mitochondrial membrane antigen), we pursued the simultaneous visualization of both mitochondrial increase and numerical chromosomal alterations, and showed that oncocytes of follicular lesions are prone to become aneuploid. Our data support the contention that follicular tumors composed of oncocytes should be regarded as a distinct subset.
Presence of diabetes mellitus and steatosis is associated with liver stiffness in a general population: The Rotterdam study (2015)

In this large population-based study of older adults, LSM ≥8.0 kPa, suggestive of clinically relevant fibrosis, was present in 5.6% and was strongly associated with steatosis and DM. In the context of an aging population and an increased prevalence of DM and obesity, this study illustrates that liver fibrosis may become a more prominent public health issue in the near future.
Varietas: a functional variation database portal (2010)

Current high-throughput technologies for investigating genomic variation in large population based samples produce data on a scale of millions of variations. Browsing through these results and identifying relevant functional variations is a major hurdle in these genome-wide association studies. In order to help researchers locate the most promising associations, we have developed a web-based database portal called Varietas. Varietas can be used for retrieving information concerning genomic variations such as single-nucleotide polymorphisms (SNPs), copy number variants and insertions/deletions, while enabling users to annotate large number of variations in a batch like manner and to find information about related genes, phenotypes and diseases. Varietas also links out to various external genomic databases, allowing users to quickly browse through a set of variations and follow the most promising leads. Varietas periodically integrates data from the major SNP and genome databases, including Ensembl genome database, NCBI dbSNP database, The Genomic Association Database and SNPedia. Database URL: http://kokki.uku.fi/bioinformatics/varietas/
Whole Animal Cell Sorting of Drosophila Embryos (1991)

Use of primary culture cells has been limited by the inability to purify most types of cells, particularly cells from early developmental stages. In whole animal cell sorting (WACS), live cells derived from animals harboring a lacZ transgene are purified according to their level of beta-galactosidase expression with a fluorogenic beta-galactosidase substrate and fluorescence-activated cell sorting. With WACS, incipient posterior compartment cells that express the engrailed gene were purified from early Drosophila embryos. Neuronal precursor cells were also purified, and they differentiated into neurons with high efficiency in culture. Because there are many lacZ strains, it may be possible to purify most types of Drosophila cells. The same approach is also applicable to other organisms for which germ-line transformation is possible.
Bone marrow stem cell transplantation for cardiac repair (2005)

Cardiomyocytes respond to physiological or pathological stress only by hypertrophy and not by an increase in the number of functioning cardiomyocytes. However, recent evidence suggests that adult cardiomyocytes have the ability, albeit limited, to divide to compensate for the cardiomyocyte loss in the event of myocardial injury. Similarly, the presence of stem cells in the myocardium is a good omen. Their activation to participate in the repair process is, however, hindered by some as-yet-undetermined biological impediments. The rationale behind the use of adult stem cell transplantation is to supplement the inadequacies of the intrinsic repair mechanism of the heart and compensate for the cardiomyocyte loss in the event of injury. Various cell types including embryonic, fetal, and adult cardiomyocytes, smooth muscle cells, and stable cell lines have been used to augment the declining cardiomyocyte number and cardiac function. More recently, the focus has been shifted to the use of autologous skeletal myoblasts and bone marrow-derived stem cells. This review is a synopsis of some interesting aspects of the fast-emerging field of bone marrow-derived stem cell therapy for cardiac repair.
The effects of 1-amino-D-proline on the production of carnitine from exogenous protein-bound trimethyllysine by the perfused rat liver. (1982)

Following receptor-mediated endocytosis of trimethyllysine-labeled asialofetuin and agalacto-orosomucoid by liver parenchymal and nonparenchymal cells, respectively, the glycoproteins are degraded and the methylated lysine residues released. The free intracellular trimethyllysine is then converted, in addition to 2-N-acetyl-6-N-trimethyllysine, to 4-N-trimethylaminobutyrate, carnitine, and acetylcarnitine. In the presence of 1-amino-D-proline, a vitamin B6 antagonist, the total production from protein-bound trimethyllysine of 4-N-trimethylaminobutyrate, the immediate precursor of carnitine, carnitine, and its acetylated derivative was depressed by as much as 60-80% in perfused rat liver. The decreased synthesis of carnitine was accompanied by an accumulation of 3-hydroxy-6-N-trimethyllysine, and intermediate in the carnitine biosynthetic pathway. The extent of 3-hydroxy-6-N-trimethyllysine accumulation, which was not evident in the absence of added 1-amino-D-proline, depended on the dose of 1-amino-D-proline perfused through the liver. In addition, those effects of 1-amino-D-proline were almost completely reversed by inclusion of pyridoxine in the perfusing medium. These results support the suggestion of a requirement for pyridoxal 5'-phosphate in the biosynthesis of carnitine by the liver.
DREAM—a novel approach for robust, ultrafast, multislice B1 mapping (2012)

Abstract A novel multislice B 1 ‐mapping method dubbed dual refocusing echo acquisition mode is proposed, able to cover the whole transmit coil volume in only one second, which is more than an order of magnitude faster than established approaches. The dual refocusing echo acquisition mode technique employs a stimulated echo acquisition mode (STEAM) preparation sequence followed by a tailored single‐shot gradient echo sequence, measuring simultaneously the stimulated echo and the free induction decay as gradient‐recalled echoes, and determining the actual flip angle of the STEAM preparation radiofrequency pulses from the ratio of the two measured signals. Due to an elaborated timing scheme, the method is insensitive against susceptibility/chemical shift effects and can deliver a B 0 phase map and a transceive phase map for free. The approach has only a weak T 1 and T 2 dependence and moreover, causes only a low specific absorption rate (SAR) burden. The accuracy of the method with respect to systematic and statistical errors is investigated both, theoretically and in experiments on phantoms. In addition, the performance of the approach is demonstrated in vivo in B 1 ‐mapping and radiofrequency shimming experiments on the abdomen, the legs, and the head on an eight‐channel parallel transmit 3 T MRI system. Magn Reson Med, 2012. © 2012 Wiley Periodicals, Inc.
Cooperative Binding of the Xenopus RNA Polymerase I Transcription Factor xUBF to Repetitive Ribosomal Gene Enhancers (1992)

Upstream binding factor (UBF) is a DNA-binding transcription factor implicated in ribosomal gene promoter and enhancer function in vertebrates. UBF is unusual in that it has multiple DNA-binding domains with homology to high-mobility-group (HMG) nonhistone chromosomal proteins 1 and 2. However, a recognizable DNA consensus sequence for UBF binding is lacking. In this study, we have used gel retardation and DNase I footprinting to examine Xenopus UBF (xUBF) binding to Xenopus laevis ribosomal gene enhancers. We show that UBF has a minimum requirement for about 60 bp of DNA, the size of the short enhancer variant in X. laevis. Stronger UBF binding occurs on the longer enhancer variant (81 bp) and on multiple enhancers linked head to tail. In vivo, Xenopus ribosomal gene enhancers exist in blocks of 10 alternating 60- and 81-bp repeats within the intergenic spacer. In vitro, UBF binds cooperatively to probes with 10 enhancers, with five intermediate complexes observed in titration experiments. This suggests that, on average, one UBF dimer binds every two enhancers. A single UBF dimer can produce a DNase I footprint ranging in size from approximately 30 to about 115 bp on enhancer probes of different lengths. This observation is consistent with the hypothesis that multiple DNA-binding domains or subdomains within UBF bind independently, forming more-stable interactions on longer probes.
Phytochemical Stability and Color Retention of Copigmented and Processed Muscadine Grape Juice (2003)

Muscadine (Vitis rotundifolia) grape juice was assessed for color and phytochemical stability as influenced by anthocyanin copigmentation with a water-soluble rosemary extract, fortification with ascorbic acid, and processing by heat or high hydrostatic pressure (HHP). The roles of polyphenolic cofactors in the presence and in the absence of ascorbic acid were assessed as a means to improve the overall processing stability of the juice. Addition of rosemary extract from 0 to 0.4% (v/v) readily formed copigment complexes with anthocyanins and resulted in concentration-dependent hyperchromic shifts from 10 to 27% that corresponded to increased antioxidant activity. The presence of ascorbic acid was generally detrimental to juice quality, especially in the presence of rosemary extract, and resulted in overall anthocyanin, ascorbic acid, and antioxidant activity losses. Although thermal and high-pressure processing methods were detrimental to juice quality, HHP resulted in greater losses after processing, likely due to action from residual oxidase enzymes. Although physicochemical attributes were enhanced by copigmentation with rosemary extract, methods to inactivate residual enzymes should be addressed prior to copigmentation to prevent degradation of anthocyanins in the presence of ascorbic acid. Keywords: Muscadine; copigment; high pressure; ascorbic acid; anthocyanin; polyphenol oxidase