gebhart/patrepeval huggingface dataset:
Survivin is required for stable checkpoint activation in taxol-treated HeLa cells (2003)

Survivin is an essential chromosomal passenger protein whose function remains unclear. Here, we have used RNA interference to specifically repress Survivin in cultured HeLa cells. Immunoblot analysis showed that Survivin was no longer detectable in cultures 60 hours after transfection with Survivin-specific siRNA. Live cell analysis showed that many Survivin-depleted cells were delayed in mitosis, and immunofluorescence analysis of fixed specimens revealed that Survivin-depleted cells accumulated in prometaphase with misaligned chromosomes. The chromosomal passenger proteins, INCENP and Aurora-B, which can interact directly with Survivin, were absent from the centromeres of Survivin-depleted cells. These data contribute to the emerging picture that Survivin operates together with INCENP and Aurora-B to perform its mitotic duties. Some Survivin-depleted cells eventually exited mitosis without completing cytokinesis. This resulted in a gradual increase in the percentage of multinucleated cells in the culture. Time-lapse imaging of synchronized cultures revealed that control and Survivin-depleted cells arrested in mitosis in the presence of nocodazole; however, the latter failed to arrest in mitosis when treated with taxol. Immunofluorescence studies revealed that Survivin-depleted cells were unable to stably maintain BubR1 at the kinetochores in the presence of either taxol or nocodazole. Our data reveal that Survivin is not required for the spindle assembly checkpoint when it is activated by the loss of microtubules. However, Survivin is required for the maintenance of the checkpoint when it is activated by taxol, which is generally thought to cause a loss of spindle tension.
The epidermal architecture of an in vitro reconstructed human skin equivalent (Advanced Tissue Sciences Skin2 Models ZK 1300/2000). (1993)

We investigated the epidermal ultrastructure of an organotypic skin culture model over a culture period of one week. At delivery, the stratified keratinizing epidermis consists of a basal layer with hemidesmosomes, a spinous layer with desmosomes, a granular layer with keratohyalin and membrane coating granules, a horny layer enclosing many lipid droplets. At the epidermal-dermal junction laminae lucida and densa are evident. After 7 days of culture the multilayered cornifying aspect persists; the number of viable cell layers remains constant. Spinous cells display abundant glycogen deposits. In the granular layer keratohyalin granules are more abundant. Both the size and number of hemidesmosomes increase. Anchoring fibrils are observed. From a structural point of view the model remains stable and well differentiated in culture and, therefore, may be well suited for pharmacological purposes.
Long-period fibre grating fabrication with focusedCO 2 laser pulses (1998)

A new, simple method of fabricating long-period fibre gratings by direct exposure of the fibre to focused 10.6 µm wavelength CO2 laser pulses is presented. No ultraviolet exposure is used. Hydrogen loading is found to enhance the writing sensitivity.
Clinical Significance and Therapeutic Potential of the Programmed Death-1 Ligand/Programmed Death-1 Pathway in Human Pancreatic Cancer (2007)

Our data suggest for the first time that PD-L1 status may be a new predictor of prognosis for patients with pancreatic cancer and provide the rationale for developing a novel therapy of targeting the PD-L/PD-1 pathway against this fatal disease.
Regional specificity of iron uptake by small intestinal brush-border membranes from normal and iron-deficient mice (1985)

Fe(II)-ascorbate uptake by purified small intestinal brush-border membrane vesicles prepared from proximal and distal segments was studied in normal and iron-deficient mice. Iron was maintained in a reduced, soluble form by a 20-fold excess of ascorbate at a physiological pH of 7.2-7.4. In normal mice, iron uptake by proximal membrane vesicles was three- to fourfold greater (approximately 1,700 pmol/mg prot) than from distal segments (approximately 500 pmol/mg prot). In iron-deficient mice, uptake of Fe(II) was also greater in proximal membranes (approximately 3,200 pmol/mg prot) than uptake from distal segments (approximately 350 pmol/mg prot), and the regional difference was almost 10-fold, without any change in distal segmental iron uptake. These results are consistent with the pattern of intestinal iron absorption in iron-replete and iron-deficient animals and indicate that regulatory changes in proximal intestinal brush-border membranes may account for the increased iron absorption known to occur in iron deficiency.
Matrix Metalloproteinase Expression and Inhibition After Sciatic Nerve Axotomy (2001)

Wallerian degeneration is characterized by breakdown of myelin and axons with subsequent macrophage infiltration and removal of the degenerating nerve components. Proteinases of the matrix metalloproteinase (MMP) family seem to play an important role in demyelinating processes, since some of their members have been shown to cleave myelin basic protein. In the present study we investigated the expression of MMP-2 and MMP-9 (gelatinases A and B) during myelin removal after peripheral nerve trauma. After transection of the sciatic nerve an upregulation of MMP-2 and MMP-9 with a first peak 12 h and a second peak 48 h after axotomy was observed by zymography. These peaks correlate with the breakdown of the blood-nerve barrier, the accumulation of granulocytes, and the invasion of macrophages into the damaged nerves, respectively. Furthermore, MMP-2 was found to be upregulated in the contralateral nontransected nerves. Immunocytochemistry for MMP-9 and in situ zymography identified MMP-reactive cells within the distal nerve stump. Chloracetate esterase staining was used to detect granulocytes, which accumulated at the transection site and were colocalized with the in situ zymography signal. Wallerian degeneration of the transected nerve could be delayed either by intraperitoneal injections of hydroxamate (Ro 31-9790), a nonspecific MMP inhibitor, or by local application of an MMP-9-specific antibody. Following these treatment strategies, a decreased number of invading macrophages was seen in the nerves associated with an increased amount of preserved myelin sheaths. These results suggest that the invasion of macrophages into a transected peripheral nerve is accompanied by an increased expression of MMPs, particularly MMP-9. Thus, MMPs may seem to play an important role in the breakdown of the blood-nerve barrier and subsequent cell recruitment from the systemic circulation into the damaged nerve.
Pteroylpolyglutamate hydrolase from human jejunal brush borders. Purification and characterization. (1986)

Pteroylpolyglutamate hydrolase was solubilized with Triton X-100 from human jejunal mucosal brush borders and purified approximately 5,000-fold using organomercurial affinity chromatography, DEAE-cellulose chromatography, and gel filtration. The apparent molecular weight of the purified enzyme in the Triton micelle was estimated as 700,000 using Bio-Gel A-1.5m gel filtration. Sodium dodecyl sulfate/urea-polyacrylamide gel electrophoresis followed by Coomassie stain demonstrated two polypeptide bands at 145,000 and 115,000 daltons. The purified enzyme had an isoelectric point of 7.2, was maximally active at pH 5.5, and was stable above pH 6.5 and at temperatures up to 65 degrees C for at least 90 min. Human jejunal brush-border pteroylpolyglutamate hydrolase is an exopeptidase which liberated [14C]Glu as the sole labeled product of PteGlu2[14C]Glue (where PteGlun represents pteroylpolyglutamate), failed to liberate a radioactive product from PteGlu2[14C]GluLeu2, and released all possible labeled PteGlun products during incubation with Pte[14C]GluGlu6 with the accumulation of Pte[14C]Glu. PteGlu2, PteGlu3, and PteGlu7 were substrates, each with Km = 0.6 microM, whereas PteGlu was a weak inhibitor of the hydrolysis of PteGlu3 with Ki = 20 microM. Components of the pteroyl moiety, Glu, and short chain Glun in alpha or gamma linkages were not inhibitory. The enzyme was activated by Zn2+ or Co2+. The properties of brush-border pteroylpolyglutamate hydrolase are different from those described for the soluble intracellular pteroylpolyglutamate hydrolase in other species and in human mucosa, yet are consistent with previous data on the process of hydrolysis of PteGlun in the intact human intestine.
Reversible and irreversible labeling and autoradiographic localization of the cerebral histamine H2 receptor using [125I]iodinated probes. (1990)

Iodoaminopotentidine (I-APT)--i.e., N-[2-(4-amino-3-iodobenzamido)ethyl]-N'-cyano-N''-(3-[3- (1-piperidinylmethyl)phenoxy]propyl)guanidine--represents one of the most potent H2-receptor antagonists known so far. In membranes of guinea pig brain 125I-APT bound reversibly, selectively, and with high affinity (Kd = 0.3 nM) to a homogeneous population of sites unambiguously identified as H2 receptors by inhibition studies conducted with a large panel of antagonists. 125I-APT binding was also inhibited by histamine, and the effect was modulated by a guanyl nucleotide, which is consistent with the association of the H2 receptor with a guanine nucleotide binding regulatory protein. The low nonspecific binding of 125I-APT generated high contrast autoradiographic pictures in brain sections and established the precise distribution of H2 receptors. Their highly heterogeneous distribution and laminated pattern in some areas--e.g., cerebral and hippocampal cortices--suggest their major association with neuronal elements. These localizations were more consistent than those of H1 receptors with the distribution of histaminergic projections, indicating that H2 receptors mediate a larger number of postsynaptic actions of histamine--e.g., in striatum. Colocalizations of H1 and H2 receptors in some areas account for their known synergistic interactions in cAMP formation induced by histamine. The distribution of 125I-APT binding sites did not strictly parallel that of the H2-receptor-linked adenylate cyclase activity, which may reflect heterogeneity among H2 receptors. After UV irradiation and SDS/PAGE analysis, [125I]iodoazidopotentidine (125I-AZPT), a photoaffinity probe derived from 125I-APT, was covalently incorporated in several peptides, among which the labeling of two peptides of 59 and 32 kDa was prevented by H2 antagonists, suggesting that they correspond to H2-receptor binding peptides or proteolysis products of the latter. These probes should be useful for sensitive radioassays, localization, purification, and molecular studies of the H2 receptor, which were previously impracticable.
Human C5a modulates monocyte Fc and C3 receptor expression. (1985)

FcIgG and C3 (CR1 and CR3) receptors are responsible for binding opsonized particles, phagocytosis, and immune adherence reactions by circulating and tissue-fixed mononuclear phagocytes. Alterations in the expression of these receptors may thus significantly influence the function of these cells. Because chemoattractants have been shown to both recruit and modulate the function of monocytes, this study specifically examines the effects of human C5a and N-formyl-methionyl-leucyl-phenyl-alanine (FMLP) on human peripheral blood monocyte FcIgG and C3 receptor expression in vitro. Adherent, elutriator-purified monocytes were incubated with C5a (10(-7) to 10(-10) M) or FMLP (10(-5) to 10(-10) M) for 30 min at 37 degrees C, and FcIgG receptor expression was assessed by rosetting with sheep erythrocytes sensitized with limiting dilutions of IgG. Human C5a caused dose-related increases in Fc rosettes of 28% at 10(-9) M, 63% at 10(-8) M, and 167% at 10(-7) M (p less than 0.01). In contrast, no significant increases in monocyte Fc receptor expression were induced by FMLP. Similar rosetting experiments were performed with sheep erythrocytes opsonized with limiting amounts of human C3b to assess C3b receptor expression on adherent human monocytes stimulated with C5a (10(-7) to 10(-10) M) or FMLP (10(-6) to 10(-9) M) for 30 min at 37 degrees C. Again, human C5a caused dose-related increases in monocyte C3b rosette formation; at 10(-8) M and 10(-7) M concentrations of C5a, these increases equaled 119% and 196%, respectively (p less than 0.05). In these experiments, 10(-6) M FMLP also caused a significant increase of 110% in monocyte C3b rosette formation (p less than 0.05). Modulation of monocyte cell surface receptors by human C5a or FMLP was also examined by measuring cell fluorescence and side scatter by dual channel flow cytometry after staining normal leukocytes in citrated venous blood with receptor-specific monoclonal antibodies. These flow cytometric studies demonstrated that both C5a and FMLP induce dose-related increases in CR1 (C3b receptor) and CR3 (iC3b receptor) expression in both monocytes and neutrophils.(ABSTRACT TRUNCATED AT 400 WORDS)
Molecular Epidemiology of Staphylococcus spp. Contamination in the Ward Environment: Study on mecA and femA Genes in Methicillin-Resistant Strains (1995)

Staphylococcus spp. were isolated from the ward environment and antibiotic susceptibility tests were performed. Twenty-nine strains out of 274 isolates were S. aureus, and 41.4% of the S. aureus strains were methicillin resistant (MRSA). All 12 strains of MRSA were also resistant to oxacillin, ceftizoxime, ampicillin and clindamycin. Among the coagulase-negative staphylococci (CNS), methicillin-resistant (MR) strains of S. epidermidis, S. capitis, S. warneri, S. haemolyticus, S. hominis, S. auricularis, S. saprophyticus and S. cohnii were isolated. Eight of the 10 S. Haemolyticus strains were methicillin resistant. The femA gene was detected in S. aureus (MSSA and MRSA), but not in CNS by polymerase chain reaction (PCR) analysis and Southern blot analysis. The mecA gene was found in all the MRSA and MR-S. epidermidis strains tested, and one of the two MR-S. hominis strains, but not in MSSA, MS-S. epidermidis, MS-S. hominis, or MS-S. haemolyticus. DNA from one strain of MR-S. hominis and 2 strains of MR-S. haemolyticus was not amplified by PCR using the mecA gene primer, or hybridized by Southern blotting. The ambiguity that mecA was detected in some MR-CNS strains, but not in others is discussed.
CdSe Core−Shell Nanoparticles as Active Materials for Up-Converted Emission (2011)

In this study, we investigate CdSe based core−shell quantum dots as potential active materials for nonlinear optical applications. A detailed characterization of the linear and nonlinear optical properties is carried out for QDs in solution and within two electronically similar sol−gel hosts, hafnia and zirconia. The favorable absorption and emission properties of the solid-state hybrid sol−gel/QD matrices are exploited for the realization of up cavity-less laser.
Flucelvax (Optaflu) for seasonal influenza (2015)

Conventional egg-based manufacturing technology for seasonal influenza vaccines has several drawbacks, including its inflexibility, reliance on egg supplies, risk of contamination, absence of growth of some isolates and egg-adaptive viral mutations that threaten vaccine matching. To overcome these limitations, cell culture-derived vaccines have been designed, including the trivalent inactivated vaccine Flucelvax®/Optaflu® (brand names in the US/EU, respectively). Flucelvax®/Optaflu® has gained wide regulatory approval and is currently implemented in several countries. Non-clinical studies have assuaged hypothetical concerns regarding oncogenicity and use in persons allergic to dogs. Ample clinical data suggest the non-inferiority of Flucelvax®/Optaflu® to egg-based vaccines in terms of immunogenicity, safety and tolerability, and it has fulfilled American and European mandatory requirements. Although Flucelvax®/Optaflu® is currently indicated only for adults and the elderly, pediatric data indicate its good immunogenicity and safety. This paper provides an update on the clinical development of Flucelvax®/Optaflu®, its seasonal trials and available post-marketing surveillance data.
Review number 14.3181 of Adger, D. (2003) Core Syntax : A Minimalist Approach. Oxford University Press. Oxford (2003)

Review number 14.3181 of Adger, D. (2003) Core Syntax : A Minimalist Approach. Oxford University Press. Oxford
Antigenic Changes of Borrelia burgdorferi as a Result of in Vitro Cultivation (1987)

The article by Spriggs [I] was a very well done summary of the microbial ecology of Legionella. I would like to correct one small but significant point regarding my work on the association between Legionella and cyanobacteria [2]. The in situ as well as the in vitro temperature at which we documented the growth of Legionella pneumophi/a with cyanobacteria was 45 C, not 35 C as stated by Spriggs [I]. This temperature was significant at the time our study was done because growth of Legionella at temperatures greater than 37 C had not been demonstrated [3]. Later reports of Legionella isolations from hot-water systems [4] confirmed the thermotolerance of this organism-a characteristic that contributes significantly to the epidemiology of Legionnaires' disease.
Image processing of multiphase images obtained via X‐ray microtomography: A review (2014)

Abstract Easier access to X‐ray microtomography (μCT) facilities has provided much new insight from high‐resolution imaging for various problems in porous media research. Pore space analysis with respect to functional properties usually requires segmentation of the intensity data into different classes. Image segmentation is a nontrivial problem that may have a profound impact on all subsequent image analyses. This review deals with two issues that are neglected in most of the recent studies on image segmentation: (i) focus on multiclass segmentation and (ii) detailed descriptions as to why a specific method may fail together with strategies for preventing the failure by applying suitable image enhancement prior to segmentation. In this way, the presented algorithms become very robust and are less prone to operator bias. Three different test images are examined: a synthetic image with ground‐truth information, a synchrotron image of precision beads with three different fluids residing in the pore space, and a μCT image of a soil sample containing macropores, rocks, organic matter, and the soil matrix. Image blur is identified as the major cause for poor segmentation results. Other impairments of the raw data like noise, ring artifacts, and intensity variation can be removed with current image enhancement methods. Bayesian Markov random field segmentation, watershed segmentation, and converging active contours are well suited for multiclass segmentation, yet with different success to correct for partial volume effects and conserve small image features simultaneously.
Point clouds can be represented as implicit surfaces for constraint-based haptic rendering (2012)

We present a constraint-based strategy for haptic rendering of arbitrary point cloud data. With the recent proliferation of low-cost range sensors, dense 3D point cloud data is readily available at high update rates. Taking a cue from the graphics literature, we propose that point data should be represented as an implicit surface, which can be formulated to be mathematically smooth and efficient for computing interaction forces, and for which haptic constraint algorithms are already well-known. This method is resistant to sensor noise, makes no assumptions about surface connectivity or orientation, and data pre-processing is fast enough for use with streaming data. We compare the performance of two different implicit representations and discuss our strategy for handling time-varying point clouds from a depth camera. Applications of haptic point cloud rendering to remote sensing, as in robot telemanipulation, are also discussed.
Phase I Study of Decitabine Alone or in Combination With Valproic Acid in Acute Myeloid Leukemia (2007)

Low-dose decitabine was safe and showed encouraging clinical and biologic activity in AML, but the addition of VA led to encephalopathy at relatively low doses. On the basis of these results, additional studies of decitabine (20 mg/m(2)/d for 10 days) alone or with an alternative deacetylating agent are warranted.
Maintenance of integrity in aortic endothelium. (1980)

Although on the average aortic endothelium is a highly stable tissue, available data indicate that there are areas of high, spontaneous, focal cell turnover. This may be significant since the response to experimental endothelial denudation includes thrombosis and smooth muscle proliferation, both components of atherosclerosis lesion formation. Thus questions about mechanisms of endothelial injury and about the role of the repair process in maintenance of endothelial integrity are likely to be important in attempting to understand the pathogenesis of atherosclerosis. Our approach is to ask what factors control endothelial regeneration. Studies include both in vitro and in vivo data. Regeneration in vivo is strongly dependent on the geometry of the vessel; recovery is much more rapid along the vessel axis. This appears to explain the localization of smooth muscle lesions following mechanical removal of the endothelium, since rapidly recovered areas do not develop smooth muscle proliferation. In vitro, regeneration is independent of a requirement for growth factors, implying that the signal for this process is intrinsic to the monolayer. Cytochalasin B inhibits both movement and replication, implying that movement may be required for transition from G0 to G1. Finally, we have discovered that cultured endothelial cells themselves produce a growth factor. This is of potential importance for interactions between smooth muscle cells and endothelial cells in the vascular response to injury.
MASS: Masked Sequence to Sequence Pre-training for Language Generation (2019)

Pre-training and fine-tuning, e.g., BERT, have achieved great success in language understanding by transferring knowledge from rich-resource pre-training task to the low/zero-resource downstream tasks. Inspired by the success of BERT, we propose MAsked Sequence to Sequence pre-training (MASS) for the encoder-decoder based language generation tasks. MASS adopts the encoder-decoder framework to reconstruct a sentence fragment given the remaining part of the sentence: its encoder takes a sentence with randomly masked fragment (several consecutive tokens) as input, and its decoder tries to predict this masked fragment. In this way, MASS can jointly train the encoder and decoder to develop the capability of representation extraction and language modeling. By further fine-tuning on a variety of zero/low-resource language generation tasks, including neural machine translation, text summarization and conversational response generation (3 tasks and totally 8 datasets), MASS achieves significant improvements over the baselines without pre-training or with other pre-training methods. Specially, we achieve the state-of-the-art accuracy (37.5 in terms of BLEU score) on the unsupervised English-French translation, even beating the early attention-based supervised model.
Cabozantinib (XL184) for the Treatment of Locally Advanced or Metastatic Progressive Medullary Thyroid Cancer (2013)

Cabozantinib (XL184) is an oral multiple receptor tyrosine kinase inhibitor manufactured by Exelixis Inc., CA, USA. It mainly inhibits three tyrosine kinase receptors: MET, VEGFR2 and RET. In both preclinical and clinical studies it has been shown to inhibit tumor angiogenesis, invasiveness and metastases. The most frequent side effects are fatigue, diarrhea, decreased appetite, nausea, weight loss and palmar-plantar erythrodysesthesia. A Phase III clinical trial (EXAM study) of XL184 versus placebo in advanced and progressive medullary thyroid cancer showed a 28 versus 0% overall response rate and a progression-free survival of 11.2 versus 4.0 months (hazard ratio: 0.28; 95% CI: 0.19-0.40; p < 0.0001) in patients treated with cabozantinib and placebo, respectively. The drug has been approved by the US FDA for the treatment of advanced/progressive metastatic medullary thyroid cancer in the USA. The EMA is now evaluating its approval in Europe.