gebhart/patrepeval huggingface dataset:
Cytoskeletal Reorganization Internalizes Multiple Transient Receptor Potential Channels and Blocks Calcium Entry into Human Neutrophils (2004)

Store-operated calcium entry (SOCE) is required for polymorphonuclear neutrophil (PMN) activation in response to G protein-coupled agonists. Some immunocytes express proteins homologous to the Drosophila transient receptor potential gene (trp) calcium channel. TRP proteins assemble into heterotetrameric ion channels and are known to support SOCE in overexpression systems, but the evidence that TRP proteins support SOCE and are functionally important in wild-type cells remains indirect. We therefore studied the expression and function of TRP proteins in primary human PMN. TRPC1, TRPC3, TRPC4, and TRPC6 were all expressed as mRNA as well as membrane proteins. Immunofluorescence microscopy demonstrated localization of TRPC1, TRPC3, and TRPC4 to the PMN cell membrane and their internalization after cytoskeletal reorganization by calyculin A (CalyA). Either TRPC internalization by CalyA or treatment with the inositol triphosphate receptor inhibitor 2-aminoethoxydiphenyl borane resulted in the loss of PMN SOCE. Cytochalasin D (CytoD) disrupts actin filaments, thus preventing cytoskeletal reorganization, and pretreatment with CytoD rescued PMN SOCE from inhibition by CalyA. Comparative studies of CytoD and 2-aminoethoxydiphenyl borane inhibition of PMN cationic entry after thapsigargin or platelet-activating factor suggested that SOCE occurs through both calcium-specific and nonspecific pathways. Taken together, these studies suggest that the multiple TRPC proteins expressed by human PMN participate in the formation of at least two store-operated calcium channels that have differing ionic permeabilities and regulatory characteristics.
SWL (2007)

As mobile phones become increasingly multifunctional, the number and size of applications installed in phones are rapidly increasing. Consequently, mobile phones require more hardware resources such as NOR/NAND flash memory and DRAM, and their production cost is accordingly becoming higher. One candidate solution to reduce production cost is demand paging using MMU. However, demand paging causes unpredictably long page fault latency, and as such mobile phone manufacturers are reluctant to deploy this scheme. In this paper, we present a method that reduces the long latency of page faults by performing page fault handling in a parallelized manner, considering the characteristics of NAND-Type flash memory. We also discuss how to modify the existing page cache replacement policies so that they can exploit the benefits of the parallelized page fault handler. Experimental results show that the parallelized page fault handler improves the worst case latency of page faults significantly, by up to roughly 20%, and that the modified page cache replacement policies improve both the average and worst instruction fetch time.
Sequence of the Saccharomyces cerevisiae CATI gene and amino acid sequence of catalase A derived from it (1988)

The nucleotide sequence of a 2785-base-pair stretch of DNA containing the Saccharomyces cerevisiae catalase A (CTA1) gene has been determined. This gene contains an uninterrupted open reading frame encoding a protein of 515 amino acids (relative molecular mass 58,490). Catalase A, the peroxisomal catalase of S. cerevisiae was compared to the peroxisomal catalases from bovine liver and from Candida tropicalis and to the non-peroxisomal, presumably cytoplasmic, catalase T of S. cerevisiae. Whereas the peroxisomal catalases are almost colinear, three major insertions have to be introduced in the catalase T sequence to obtain an optimal fit with the other proteins. Catalase A is most closely related to the C. tropicalis enzyme. It is also more similar to the bovine liver catalase than to the second S. cerevisiae catalase. The differences between the two S. cerevisiae enzymes are most striking within four blocks of amino acids consisting of a total of 37 residues with high homology between the three peroxisomal, but low conservation between the S. cerevisiae catalases. The results obtained indicate that the peroxisomal catalases compared have very similar three-dimensional structures and might have similar targeting signals.
BMP and BMP Inhibitors in Bone (2006)

Bone morphogenetic proteins (BMPs) are signaling molecules that act locally on target cells to affect cell survival, proliferation, and differentiation. While first identified as bone-inducing agents, BMPs are now known to affect the formation and function of many organ systems. Here we focus only on the roles of BMPs in the skeleton. In the developing mouse embryo, BMPs direct skeletal patterning, chondrogenesis, and bone formation. In postnatal animals, BMPs are potent bone regeneration factors, affecting both the amount of new bone formed and the rate at which bone healing occurs. The amount of BMP available for signaling is tightly regulated in both the embryo and postnatally, and in the context of the skeleton, several structurally distinct BMP ligand antagonists have been shown to alter the ability of BMPs to bind to their receptors, blocking BMP activity in physiologically important circumstances. For example, noggin knockout mice display cartilage hyperplasia during skeletal development that results in the loss of joint formation (too much BMP activity), while mice that overexpress noggin in skeletal cells display severe osteopenia and bone fragility (too little BMP activity). Sclerostin, chordin, CTGF, follistatin, and gremlin are additional BMP antagonists that may act in the skeleton to regulate BMP availability. Another class of BMP inhibitors are the proteins that bind to BMP receptors but have no inherent signaling function and thus act as BMP receptor antagonists. To date, inhibin and BMP-3 have been identified as BMP receptor antagonists that can block BMP signaling in bone. Identification of BMP antagonists allows us to investigate their role in diseases that affect skeletal function, such as osteopenia and nonunion fracture, and may provide a novel therapeutic intervention point for treatment.
Aspects on Tail‐Flick, Hot‐Plate and Electrical Stimulation Tests for Morphine Antinociception (1998)

The objective of this study was to compare the results of three nociceptive tests, tail-flick, hot-plate and electrical stimulation vocalisation, reflecting the responses from different sites in the CNS. A subcutaneous morphine dose (5 mg/kg) was administered to three parallel groups of rats in which the nociceptive response was measured by one of the three methods. The baseline decreased during the period of measurement for the hot-plate test, but remained stable for the other methods. The spinally mediated tail-flick response was more sensitive to the morphine effects as compared to the supraspinally mediated hot-plate and electrical stimulation vocalisation responses. The electrical stimulation vocalisation-test demonstrated more even effect-time profiles and less variability among the rats than did the tail-flick and the hot-plate methods. In the tail-flick group, 59% of the observations attained the cut-off latency at this morphine dose, leading to underestimation of the peak effect, the area under the effect curve (AUEC), and the variability among the rats. In the hot-plate group, 13% of the observations were at the cut-off latency, and 2% in the electrical stimulation vocalisation group. Different ways of presenting the data are discussed. In conclusion, the test selected for measuring the nociceptive response will influence the effect-time profile and subsequently any pharmacodynamic parameters describing it.
Distinctive roles of different β‐amyloid 42 aggregates in modulation of synaptic functions (2009)

To determine how endogenously secreted beta-amyloid 42 (Abeta42) aggregates regulate synaptic functions, we examined effects of Abeta42 at the neuromuscular junction of Drosophila larvae. Voltage-clamp recordings of synaptic transmission and optical analysis of vesicle recycling at presynaptic terminals show that expression of Abeta42 in neurons leads to a reduction of neurotransmitter release. However, expression of Abeta42 in postsynaptic muscle cells enhanced neurotransmitter release. Both effects are neutralized by Abeta antibody, suggesting a role for secreted Abeta42 peptides. Application of exogenously prepared Abeta42 oligomers leads to a reduction in synaptic responses, whereas mixed Abeta42 aggregates with mainly fibrils elicit an opposite effect by increasing synaptic transmission. Further analysis of long-term depression (LTD) confirms differential effects of different Abeta42 aggregates. Taken together, our data suggest that Abeta42 is secreted from neurons primarily as oligomers that inhibit neurotransmitter release and exert no effect on LTD. Whereas larger-sized aggregates, possibly fibrils, are major components secreted from muscle cells, which enhance synaptic transmission and LTD. Thus, different types of cells may secrete distinct forms of Abeta42 aggregates, leading to different modulation of synaptic functions.
One-Year Safety and Clinical Outcomes of a Transcatheter Interatrial Shunt Device for the Treatment of Heart Failure With Preserved Ejection Fraction in the Reduce Elevated Left Atrial Pressure in Patients With Heart Failure (REDUCE LAP-HF I) Trial (2018)

ClinicalTrials.gov identifier: NCT02600234.
Effect of low‐dose cyclosporin a on systemic lupus erythematosus disease activity (1994)

The favorable responses observed in our patients strongly suggest that low-dose CSA can reduce the disease activity of SLE.
5-Fluorodeoxyuridine as an alternative to the synthesis of mixed hybridization probes for the detection of specific gene sequences. (1988)

Synthetic complementary oligonucleotides are useful hybridization probes for the detection of mRNAs and genes encoding proteins for which only a partial amino acid sequence is known. Usually this involves the synthesis of mixtures of oligonucleotides complementary to all possible bases in degenerate positions of codons. As an alternative we have prepared and characterized a series of unique oligonucleotides containing a pyrimidine analog, 5-fluorodeoxyuridine (F). Thermodynamic parameters and the melting temperatures of hybrid duplexes containing A.F and G.F base pairs showed that they are considerably more stable than duplexes containing A.T and G.T base pairs. The stability of a duplex decreased linearly with the number of mismatches introduced at positions at least a codon apart. A 5-fluorodeoxyuridine-substituted oligonucleotide cDNA detects rat liver pyruvate carboxylase mRNA on a RNA gel blot with a dissociation temperature only 10 degrees C below the measured melting temperature in solution. We suggest that the complexity of oligonucleotide cDNAs used for screening gene libraries can be reduced by the design of single hybridization probes containing the substituted bases--5-fluorodeoxyuridine to pair with adenosine or guanosine, guanosine to pair with cytidine or thymidine, and deoxyinosine to pair with adenosine or cytidine at positions of codon degeneracy--and still retain near-maximum stability of hybrid duplexes.
Vaccination-Associated Relapse of Immune Thrombocytopenia (1981)

Many patients with immune thrombocytopenia require splenectomy to achieve remission. They are therefore at risk for postsplenectomy septicemia and should receive vaccination against Streptococcus pneumoniae. In experiment situations, antigens contained within this vaccine cell initiate a polyclonal B-lymphocyte activation and increased production of specific and nonspecific antibodies. In certain animal models, a polyclonal B-lymphocyte stimulatory response can trigger an autoimmune disorder. Two patients with immune thrombocytopenia had relapses of their immune thrombocytopenia after the administration of pneumococcal and influenza vaccines. These observations suggest that patients with a history of immune thrombocytopenia should be monitored after vaccination.
MD-2, a Novel Accessory Molecule, Is Involved in Species-Specific Actions ofSalmonellaLipid A (2002)

Salmonella lipid A is inactive in human macrophages despite being potently active in murine macrophages. We investigated the molecular basis for this species-specific action of Salmonella lipid A. When murine CD14 (mCD14), mTLR4, and mMD-2 were all expressed in human monocytic THP-1 cells, these cells were capable of responding to Salmonella lipid A. Expressing each of these proteins separately did not impart such responsiveness. Expression of mTLR4 plus mMD-2, but not mCD14 plus mTLR4 or mCD14 plus mMD-2, conferred this responsiveness. In THP-1 cells expressing mCD14, mTLR4, and mMD-2, replacing mCD14 with human CD14 had no effect on responsiveness to Salmonella lipid A or synthetic Salmonella-type lipid A (compound 516). When mTLR4 was replaced with human TLR4, the responses to these lipid A preparations were decreased to half, and the replacement of mMD-2 decreased responsiveness to one-third, although the responses to Escherichia coli lipid A or synthetic E. coli-type lipid A (compound 506) were not affected. These results indicate that both TLR4 and MD-2 participate in the species-specific action of Salmonella lipid A.
Women managers, Perception vs Performance analysis (2003)

Cytoplasmic and cell membrane associated hepatitis B core antigen (HBcAg) were found to be more widespread within infected liver using indirect immunofluorescence on frozen sections than with the widely used direct immunofluorescence method. Fixation of frozen sections with carbon tetrachloride improved tissue histology without reducing the sensitivity of antigen detection. In tissue blocks fixed with formalin or ethanol-acetic acid, detection of HBcAg was reduced in comparison with frozen sections, and many cells containing low concentrations of (usually cytoplasmic and membranous) HBcAg could not be identified even using indirect immunofluorescence or peroxidase-antiperoxidase reactions. In contrast, intracellular hepatitis B surface antigen (HBsAg) was well detected in fixed sections, but membrane associated HBsAg was not detectable after fixation.
A Nationwide Case-Control Study of Escherichia coli O157:H7 Infection in the United States (1998)

Risk factors for Escherichia coli O157:H7 infection were investigated in a case-control study at 10 medical centers throughout the United States. Among 73 case-patients and 142 matched controls, exposures in the 7 days before illness associated with E. coli O157:H7 infection in univariate analysis included consumption of hamburger (matched odds ratio [MOR], 3.8; 95% confidence interval [CI], 1.9-7.9), undercooked hamburger (MOR, 4.5; 95% CI, 1.6-12.2), or hot dogs (MOR, 2.2; 95% CI, 1.1-4.4); eating at a fast-food restaurant (MOR, 2.3; 95% CI, 1.1-4.6); drinking unchlorinated well water (MOR, 2.4; 95% CI, 1.1-5.7); swimming in a pond (MOR, 5.4; 95% CI, 1.1-26.0); and having a household member with diarrhea (MOR, 11.9; 95% CI, 2.7-53.5). In multivariate analysis, only eating undercooked hamburger remained associated with infection. Seven (8%) of 93 patients developed hemolytic uremic syndrome and 1 died. Prevention strategies aimed at modifying risk factors may help to reduce the risk of infection with E. coli O157:H7.
Self-association of a 1,3,4-oxadiazole-containing dendrimer (1996)

A. Kraft, Chem. Commun., 1996, 77 DOI: 10.1039/CC9960000077
Frequency-domain interferometer for femtosecond time-resolved phase spectroscopy (1992)

A new femtosecond time-resolved interferometer was developed that utilizes interference fringes in the frequency domain to obtain simultaneously difference phase spectra (DPS) and difference transmission spectra with a multichannel spectrometer. For the first time to our knowledge, transient oscillations were observed in DPS and the spectral shift of a probe pulse was time resolved together with the rise in DPS, which is clear evidence for induced phase modulation in absorptive materials.
The Association of Real-World CA 19-9 Level Monitoring Patterns and Clinical Outcomes Among Patients With Metastatic Pancreatic Ductal Adenocarcinoma (2021)

In one of the largest, contemporary, real-world studies of patients with mPDAC, elevated CA 19-9 level at treatment initiation demonstrated a prognostic impact. Routine serial monitoring of CA 19-9 levels during treatment may be warranted, in addition to clinical and radiographic assessment, and may translate into better patient outcomes. Further validation studies are needed to understand the generalizability of these results.
In vivo retinal imaging by optical coherence tomography (1993)

We describe what are to our knowledge the first in vivo measurements of human retinal structure with optical coherence tomography. These images represent the highest depth resolution in vivo retinal images to date. The tomographic system, image-processing techniques, and examples of high-resolution tomographs and their clinical relevance are discussed.
GATA6 regulates HNF4 and is required for differentiation of visceral endoderm in the mouse embryo (1998)

GATA6 belongs to a family of zinc finger transcription factors that play important roles in transducing nuclear events that regulate cellular differentiation and embryonic morphogenesis in vertebrate species. To examine the function of GATA6 during embryonic development, gene targeting was used to generate GATA6-deficient (GATA6(-/-)) ES cells and mice harboring a null mutation in GATA6. Differentiated embryoid bodies derived from GATA6(-/-) ES cells lack a covering layer of visceral endoderm and severely attenuate, or fail to express, genes encoding early and late endodermal markers, including HNF4, GATA4, alpha-fetoprotein (AFP), and HNF3beta. Homozygous GATA6(-/-) mice died between embryonic day (E) 6.5 and E7. 5 and exhibited a specific defect in endoderm differentiation including severely down-regulated expression of GATA4 and absence of HNF4 gene expression. Moreover, widespread programmed cell death was observed within the embryonic ectoderm of GATA6-deficient embryos, a finding also observed in HNF4-deficient embryos. Consistent with these data, forced expression of GATA6 activated the HNF4 promoter in nonendodermal cells. Finally, to examine the function of GATA6 during later embryonic development, GATA6(-/-)-C57BL/6 chimeric mice were generated. lacZ-tagged GATA6(-/-) ES cells contributed to all embryonic tissues with the exception of the endodermally derived bronchial epithelium. Taken together, these data suggest a model in which GATA6 lies upstream of HNF4 in a transcriptional cascade that regulates differentiation of the visceral endoderm. In addition, these data demonstrate that GATA6 is required for establishment of the endodermally derived bronchial epithelium.
DBD: a transcription factor prediction database (2005)

Regulation of gene expression influences almost all biological processes in an organism; sequence-specific DNA-binding transcription factors are critical to this control. For most genomes, the repertoire of transcription factors is only partially known. Hitherto transcription factor identification has been largely based on genome annotation pipelines that use pairwise sequence comparisons, which detect only those factors similar to known genes, or on functional classification schemes that amalgamate many types of proteins into the category of 'transcription factor'. Using a novel transcription factor identification method, the DBD transcription factor database fills this void, providing genome-wide transcription factor predictions for organisms from across the tree of life. The prediction method behind DBD identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains. Thus, it is limited to factors that are homologus to those HMMs. The collection of HMMs is taken from two existing databases (Pfam and SUPERFAMILY), and is limited to models that exclusively detect transcription factors that specifically recognize DNA sequences. It does not include basal transcription factors or chromatin-associated proteins, for instance. Based on comparison with experimentally verified annotation, the prediction procedure is between 95% and 99% accurate. Between one quarter and one-half of our genome-wide predicted transcription factors represent previously uncharacterized proteins. The DBD (www.transcriptionfactor.org) consists of predicted transcription factor repertoires for 150 completely sequenced genomes, their domain assignments and the hand curated list of DNA-binding domain HMMs. Users can browse, search or download the predictions by genome, domain family or sequence identifier, view families of transcription factors based on domain architecture and receive predictions for a protein sequence.
A mechanistic study on the effect of dexamethasone in moderating cell death in Chinese Hamster Ovary cell cultures (2011)

Dexamethasone (DEX) was previously shown (Jing et al., Biotechnol Bioeng. 2010;107:488-496) to play a dual role in increasing sialylation of recombinant glycoproteins produced by Chinese Hamster Ovary (CHO) cells. DEX addition increased sialic acid levels of a recombinant fusion protein through increased expression of α2,3-sialyltransferase and β1,4-galactosyltransferase, but also decreased the sialidase-mediated, extracellular degradation of sialic acid through slowing cell death at the end of the culture period. This study examines the underlying mechanism for this cytoprotective action by studying the transcriptional response of the CHO cell genome upon DEX treatment using DNA microarrays and gene ontology term analysis. Many of those genes showing a significant transcriptional response were associated with the regulation of programmed cell death. The gene with the highest change in expression level, as validated by Quantitative PCR assays with TaqMan® probes and confirmed by Western Blot analysis, was the antiapoptotic gene Tsc22d3, also referred to as GILZ (glucocorticoid-induced leucine zipper). The pathway by which DEX suppressed cell death towards the end of the culture period was also confirmed by showing involvement of glucocorticoid receptors and GILZ through studies using the glucocorticoid antagonist mifepristone (RU-486). These findings advance the understanding of the mechanism by which DEX suppresses cell death in CHO cells and provide a rationale for the application of glucocorticoids in CHO cell culture processes.
Nucleotide sequence and functions of mrk determinants necessary for expression of type 3 fimbriae in Klebsiella pneumoniae (1991)

The nucleotide sequence of six genes involved in the expression of type 3 fimbriae of Klebsiella pneumoniae was determined. In addition to the genes that encode the fimbrial subunit (mrkA) and adhesion (mrkD), the mrkB, mrkC, and mrkE genes appear to be involved in assembly of the fimbrial filament and regulation of type 3 fimbrial expression. The mrkF gene product is required to maintain the stability of the fimbrial filament on the cell surface.
Fully-depleted strained-Si on insulator NMOSFETs without relaxed SiGe buffers (2004)

Fully-depleted strained Si n-channel MOSFETs were demonstrated on a compliant borophosphorosilicate insulator (BPSG) without an underlying SiGe buffer layer. Stress balance of a SiGe/Si structure, transferred onto BPSG by wafer bonding and Smart-cut processes, is utilized for the first time to make strained-Si on insulator (sSOI) by a process that does not involve the introduction of misfit dislocations. Strained-Si n-channel MOSFETs with a strain level of 0.6%, equivalent to that of a conventional strained Si layer grown on a relaxed Si/sub 0.85/Ge/sub 0.15/ buffer, exhibit 60% mobility enhancement over the control, in good agreement with theory. This approach to fabricating strained Si overcomes any potential process or device complexity due to the presence of a SiGe layer in the final devices.