gebhart/patrepeval huggingface dataset:
Cryotreatment as a simple method for cell preparation in autologous tumor cell-based vaccination (2010)

Immunotherapies using autologous whole tumor cell vaccines have great potential in the treatment of cancer. Very few studies report the use of cryotreatment for the preparation of cells in cell-based vaccines. In this study, we demonstrated that a preparation containing cryotreated human breast cancer cells has the same capacity as a preparation containing irradiated human breast cancer cells to induce the activation of immune cells in vivo. The vaccine strategy proposed in this study may provide the experiment basis for the use of autologous or allogeneic breast cancer cells in the cell-based vaccine approach for the treatment of breast cancer and other types of cancer as well.
A Sensitive Cell Line, HL Cells, for Isolation and Propagation of Chlamydia pneumoniae Strain TWAR (1990)

The sensitivity of a human line, HL cells, for growth of Chlamydia pneumonia was compared with HeLa 229 cells using laboratory-adapted and wild strains. HL cells were more sensitive for growth of HeLa-adapted C. pneumoniae strains and more sensitive for isolation of the organism from patient specimens. Adaptation of new isolates to continuous cell culture growth has been much more successful in HL cells. Centrifugation of inoculum and incorporation of cycloheximide in the medium enhanced the infectivity. Microscopic observation of cultures from days 2 to 6 showed that C. pneumoniae undergoes a second cycle of growth in HL cells. However, the optimal time of harvesting is 3 days after inoculation.
Extracellular Matrix-Associated Bone Morphogenetic Proteins Are Essential for Differentiation of Murine Osteoblastic Cellsin Vitro1 (1999)

Osteoblastic differentiation is an essential part of bone formation that compensates resorbed bone matrix to maintain its structural integrity. Cells in an osteoblast lineage develop differentiated phenotypes during a long-term culture in vitro. However, intrinsic mechanisms whereby these cells differentiate into mature osteoblasts are yet unclear. Bone morphogenetic proteins (BMPs) stimulate osteoblastic differentiation and bone formation. We demonstrate that mouse osteoblastic MC3T3-E 1 cells constitutively expressed messenger RNAs (mRNAs) for BMP-2 and BMP-4 and accumulated BMPs in collagen-rich extracellular matrices. BMPs associated with the extracellular matrices were involved in the induction of osteoblastic differentiation of nonosteogenic mesenchymal cells as well as cells in the osteoblast lineage. MC3T3-E1 cells constitutively expressed type IA and type II BMP receptors. When a kinase-deficient type IA BMP receptor was stably transfected to MC3T3-E 1 cells to obliterate BMP-2/4 signaling, these cells not only failed to respond to exogenous BMP-2 but lost their capability of differentiation into osteoblasts that form mineralized nodules. These observations strongly suggest that endogenous BMP-2/4 accumulated in extracellular matrices are essential for the osteoblastic differentiation of cells in the osteoblast lineage. Therefore, the regulatory mechanism of BMP-2/4 actions in osteoblastic cells is a principal issue to be elucidated for better understanding of pathogenesis of bone losing diseases such as osteoporosis.
MOCZ for Blind Short-Packet Communication: Basic Principles (2019)

We introduce a novel blind (noncoherent) communication scheme, called modulation on conjugate-reciprocal zeros (MOCZ), pronounced as “Moxie,” to reliably transmit sporadic short-packets over unknown wireless multipath channels. In MOCZ, the information is modulated onto the zeros of the transmitted discrete-time baseband signal's z-transform, which yields to a codebook of non-orthogonal signals. In the absence of additive noise, the zero structure of the signal is perfectly preserved at the receiver, no matter what the channel impulse response (CIR) is. Furthermore, by a proper selection of the zeros, we show that MOCZ is not only invariant to the CIR but also robust against additive noise. Starting with the maximum-likelihood estimator, we define a low complexity and reliable decoder and compare it to various state-of-the-art noncoherent multipath schemes, such as OFDM index-modulation (IM), OFDM pilot-aided, OFDM differential-modulation, and pulse-position-modulation. Our scheme outperforms all schemes and maintains its performance even if the length becomes shorter than the CIR.
Phase II Trial of a Transplantation Regimen of Yttrium-90 Ibritumomab Tiuxetan and High-Dose Chemotherapy in Patients With Non-Hodgkin's Lymphoma (2007)

Adding 90Y ibritumomab tiuxetan to high-dose BEAM with autologous stem-cell transplantation is feasible and has a toxicity and tolerability profile similar to that observed with BEAM alone. Rates of progression-free survival seen in these patients are promising and warrant additional study.
Identification of Adenovirus (Ad) Penton Base Neutralizing Epitopes by Use of Sera from Patients Who Had Received Conditionally Replicative Ad (Ad dl 1520) for Treatment of Liver Tumors (2003)

Sera from 17 patients with primary and secondary liver tumors who had been administered oncolytic adenovirus (Ad) mutant Addl1520 were analyzed for anti-Ad neutralization titers and antibodies to the Ad major capsid proteins hexon, penton base (Pb), and fiber. The antibodies recognized mainly conformational epitopes in hexon and both linear and conformational epitopes in Pb and fiber. Pb-specific antibodies were isolated from serum samples that had been obtained prior to and during the course of the treatment of four of these patients. We found that the Pb antibodies had a significant contribution toward anti-Ad neutralization, and this mainly occurred at the step of virus internalization. The Pb antigenic epitopes were determined by phage biopanning and were mapped to 10 discrete regions, which made up three major immunodominant domains within residues 51 to 120, 193 to 230, and 311 to 408, respectively. One of these domains (residues 311 to 408) overlapped the highly conserved, integrin-binding RGD (Arg-Gly-Asp) motif. The contribution of antibodies directed to RGD and other epitopes in Ad neutralization activity was determined indirectly by using a phage-mediated depletion assay. Our results suggested that circulating RGD antibodies were not prevalent and were poorly neutralizing and that other peptide motifs within residues 51 to 60, 216 to 226, and 311 to 408 in Pb sequence represented major target sites for neutralizing antibodies.
Transrectal ultrasound in the diagnosis and staging of prostatic carcinoma. (1989)

Indications for TRUS are: (a) for diagnosis of nonpalpable cancer, or detection of cancer with greater accuracy than is possible at present; (b) for guidance of transrectal biopsies of hypoechoic lesions for histologic confirmation of cancer; (c) for guidance of staging biopsies to ensure diagnoses of extraprostatic extension; and (d) for staging previously diagnosed prostate cancer.
Novel and potent inhibitors targeting DHODH are broad-spectrum antivirals against RNA viruses including newly-emerged coronavirus SARS-CoV-2 (2020)

Emerging and re-emerging RNA viruses occasionally cause epidemics and pandemics worldwide, such as the on-going outbreak of the novel coronavirus SARS-CoV-2. Herein, we identified two potent inhibitors of human DHODH, S312 and S416, with favorable drug-likeness and pharmacokinetic profiles, which all showed broad-spectrum antiviral effects against various RNA viruses, including influenza A virus, Zika virus, Ebola virus, and particularly against SARS-CoV-2. Notably, S416 is reported to be the most potent inhibitor so far with an EC<sub>50</sub> of 17 nmol/L and an SI value of 10,505.88 in infected cells. Our results are the first to validate that DHODH is an attractive host target through high antiviral efficacy in vivo and low virus replication in DHODH knock-out cells. This work demonstrates that both S312/S416 and old drugs (Leflunomide/Teriflunomide) with dual actions of antiviral and immuno-regulation may have clinical potentials to cure SARS-CoV-2 or other RNA viruses circulating worldwide, no matter such viruses are mutated or not.
Model of interaction of the IL‐1 receptor accessory protein IL‐1RAcP with the IL‐1β/IL‐1RI complex (2001)

A preliminary model has been calculated for the activating interaction of the interleukin 1 receptor (IL-1R) accessory protein IL-1RAcP with the ligand/receptor complex IL-1beta/IL-1R(I). First, IL-1RAcP was modeled on the crystal structure of IL-1R(I) bound to IL-1beta. Then, the IL-1RAcP model was docked using specific programs to the crystal structure of the IL-1beta/IL-1R(I) complex. Two types of models were predicted, with comparable probability. Experimental data obtained with the use of IL-1beta peptides and antibodies, and with mutated IL-1beta proteins, support the BACK model, in which IL-1RAcP establishes contacts with the back of IL-1R(I) wrapped around IL-1beta.
An Investigation of the Cause of the Eosinophilia–Myalgia Syndrome Associated with Tryptophan Use (1990)

The outbreak of the eosinophilia-myalgia syndrome in 1989 resulted from the ingestion of a chemical constituent that was associated with specific tryptophan-manufacturing conditions at one company. The chemical constituent represented by peak E may contribute to the pathogenesis of the eosinophilia-myalgia syndrome, or it may be a surrogate for another chemical that induces the syndrome.
A rendt, H annah (2017)

Arendt is best known as a political rather than a social theorist but much of her work may be read as a rich contribution to social theory and in particular to the critique of political modernity. This reading reflects her own emphasis on the importance of the activity of understanding and her debt to the understanding of society to be found in classical philosophy and sociology.
Stable insulating tethered bilayer lipid membranes (2008)

Tethered bilayer lipid membranes have been shown to be an excellent model system for biological membranes. Coupling of a membrane to a solid supports creates a stable system that is accessible for various surface analytical tools. Good electrical sealing properties also enable the use of the membranes in practical sensing applications. The authors have shown that tethered membranes have extended lifetimes up to several months. Air-stability of the bilayer can be achieved by coating the membrane with a hydrogel. The structure of a monolayer and its stability under applied dc potentials have been investigated by neutron scattering.
Damage diagnosis using time series analysis of vibration signals (2001)

A novel time series analysis is presented to locate damage sources in a mechanical system, which is running in various operational environments. The source of damage is located by solely analyzing the acceleration time histories recorded from a structure of interest. First, a data normalization procedure is proposed. This procedure selects a reference signal that is `closest' to a newly obtained signal from an ensemble of signals recorded when the structure is undamaged. Second, a two-stage prediction model (combining auto-regressive (AR) and auto-regressive with exogenous inputs (ARX) techniques) is constructed from the selected reference signal. Then, the residual error, which is the difference between the actual acceleration measurement for the new signal and the prediction obtained from the AR-ARX model developed from the reference signal, is defined as the damage-sensitive feature. This approach is based on the premise that if there were damage in the structure, the prediction model previously identified using the undamaged time history would not be able to reproduce the newly obtained time series measured from the damaged structure. Furthermore, the increase in residual errors would be maximized at the sensors instrumented near the actual damage locations. The applicability of this approach is demonstrated using acceleration time histories obtained from an eight degrees-of-freedom mass-spring system.
Identification of a tightly regulated hypoxia-response element in the promoter of human plasminogen activator inhibitor–1 (2002)

Plasminogen activator inhibitor-1 (PAI-1) plays a key role in control of coagulation and tissue remodeling and has been shown to be regulated by a number of cell stimuli, among those hypoxia. In this study we characterize the hypoxia-mediated induction of PAI-1 in human hepatoma cell line HepG2. We found that PAI-1 is tightly regulated in a narrow oxygen gradient. After incubation at oxygen concentrations of 1% to 2%, a 60-fold increase in PAI-1 messenger RNA levels was observed, whereas mild hypoxic conditions of more than 3.5% did not appear to induce transcription. Moreover, increased levels of PAI-1 protein were observed after incubation at low oxygen tensions. Through sequence analysis, several putative hypoxia-response elements (HREs 1-5) were identified in the human PAI-I promoter. Reporter gene assays showed that the HRE-2 (-194 to -187) was necessary and sufficient for the hypoxia-mediated response. By electrophoretic mobility assay we observed hypoxia-dependent binding of a protein complex to the HRE-2 motif. Further analysis demonstrated that HRE-2 was specifically recognized by the hypoxia-inducible transcription factor 1alpha-arylhydrocarbon nuclear translocator complex. Taken together, our data demonstrate that hypoxia-induced transcription is mediated through HIF-1 interaction with the HRE-2 site of the human PAI-1 promoter.
Recent Updates on the Calcium-Sensing Receptor as a Drug Target (2008)

Parathyroid hormone (PTH) secreted from parathyroid cells is a key regulator of circulating levels of calcium ion, which is maintained within a narrow physiological range mainly by the action of a cell surface Ca2+-sensing receptor (CaSR) residing on parathyroid cells. The CaSR belongs to the family C of G-protein-coupled receptors (GPCRs), all members of which have a large extra cellular domain called Venus flytrap, akin to bacterial nutrient sensor. Promiscuity of the CaSR is reflected in its binding to several physiologically relevant di- or polyvalent cations that could elicit cellular signaling, yet the ligand specificity remains poor. This problem has been circumvented by the discovery of calcimimetics, the positive allosteric modulators of the CaSR that activate the CaSR on parathyroid cells, immediately suppressing PTH secretion. Out of several small molecules that act as calcimimetics, cinacalcet is the most extensively studied. The discovery of the CaSR and these specific agonists provides important insights into the discovery of new drugs that will be discussed in this review from the perspective of their structure-activity relationship. The calcimimetic compound cinacalcet has obtained regulatory approval for the treatment of hyperparathyroidism and is the first positive allosteric modulator of any GPCR to reach the market. It has other important uses in dialysis patients with end-stage renal disease, in whom it decreases Ca X P product. Pharmaceutically converse to calcimimetics are calcilytic compounds, which antagonize parathyroid CaSR and stimulate PTH secretion. Antagonism of the CaSR has the potential to yield an anabolic therapy for osteoporosis that awaits clinical validation.
Rodent obesity models: An overview (2001)

Animal obesity models differ widely in type and extent of obesity. They are either based on environmental factors (eg. high fat diet induced obesity), spontaneous mutants (i.e. ob/ob mice), genetically engineered animals (eg. mice with melanocortin receptor subtype-4 gene disruption (knock-out)) or mechanical intervention (eg. chemical lesion of the ventromedial hypothalamus). This article reviews available rodent models to study obesity and attempts to highlight the greatest utility for each model.
Delayed thymocyte development induced by augmented expression of p56lck. (1991)

Accumulating evidence supports the contention that CD4 and CD8 receptor molecules play a critical signaling role during thymocyte development. The lymphocyte-specific protein tyrosine kinase (p56lck), by virtue of its physical association with these surface components, provides a likely candidate for the biochemical signal transducing element required for these effects. To investigate the function of p56lck in T lymphocytes, transgenic mice were produced that carry either the wild-type lck gene or a mutated lck gene encoding a constitutively activated form of p56lck (p56lckF505). Both transgenes were expressed in thymocytes under the control of the lck proximal promoter element. A large set of founder animals was obtained in which steady-state accumulation of lck transgene mRNA directly correlated with transgene copy number, suggesting that this transgene contains a dominant control region. Progeny of these founders exhibited a transgene-dependent dose-related decrease in the production of thymocytes bearing functional antigen receptors. This effect was strictly dependent on p56lck activity, in that both wild-type and mutated versions of the genes induced similar effects with differing efficiencies. Remarkably, even a twofold increase in p56lck abundance was sufficient to substantially disrupt the appearance of functional thymocytes. These results indicate that thymocyte maturation is regulated in part by signals derived from p56lck.
Feasibility Study on Using Two Mixer Pumps for Tank 241-AY-102 Waste Mixing (2004)

The current waste retrieval plan at Hanford calls for using two mixer pumps to mix the waste stored in double-shell Tank 214-AY-102. The objective of this evaluation was to determine whether two rotating 300-hp mixer pumps placed 22 ft (6.7 m) off-center in the tank could adequately mix the AY-102 waste. The tank currently contains high-level waste that is 248 inches (6.3 m) deep, comprising 62 inches (1.58 m) of sludge and 186 inches (4.72 m) of supernatant liquid (Galbraith et al. 2002). Based on the available data, AY-102 waste properties were determined, including the densities of liquid and agglomerated settled solids and crystals, the volume fraction of settled solids, the solid particle size distribution, the liquid and slurry viscosities, and the yield stress in shear (shear strength) of the settled solids layer. To evaluate the likely and bounding cases of AY-102 waste mixing, sludge erosion modeling was performed with a median value of 1,090 Pa (likely condition) and a conservative (more difficult to erode) 97.5 percentile value of 2,230 Pa for shear strength. According to model predictions, the two rotating mixer pumps would erode 89% of the sludge with shear strength of 1,090 Pa. They would erode sludge up to 41 ft (12.5 m) away from the mixer pumps but would not mobilize the bottom 2.5 inches (0.06-m) of sludge or sludge in the areas next to the tank wall, more than 26 ft (7.9 m) away. Once the sludge is mobilized, the solids were predicted to be uniformly suspended within the tank within a 1-vol% concentration variation except those in few inches at the bottom. With shear strength of 2,230 Pa, the two pumps would erode 85% of the sludge, slightly less than the 1,090-Pa shear strength case. In this case, the pump jets would mobilize the sludge up to 38 ft (11.6 m), except the bottom 2.5 inches of sludge. The mixer pumps would also leave the sludge at the tank wall, which is 20 ft or more from the pumps. Similar to the 1,090 Pa case, the solids were predicted to be uniformly suspended except within few inches of the tank bottom. These results indicate that the greater the sludge shear strength, the less the mixer pumps can erode, although the differences in the amount eroded and the maximum erosion distance from the pumps are fairly small. Thus, two 300-hp mixer pumps would suffice to mobilize the sludge and uniformly mix it with the supernatant liquid for both the likely and conservative conditions. Two additional mixer pumps, for a total of four, would most likely increase the sludge erosion amount by approximately 10 to 14 vol%.
Purification and properties of rabbit brain and liver 4-aminobutyrate aminotransferases isolated by monoclonal-antibody immunoadsorbent chromatography (1985)

The use of a monoclonal-antibody immunoaffinity column for the rapid isolation of 4-aminobutyrate aminotransferases (EC 2.6.1.19) from rabbit brain and liver is described. Homogeneous enzyme protein is eluted from the immunoadsorbent with 100mM-citrate buffer, pH5, and remains stable at 4 degrees C for several days. One such column (bed volume 8 ml) has been used 40 times in a 9-month period to isolate 10-15 units of enzyme activity (specific activity approx. 3.5-7.5 units/mg) per extraction. Kinetic and spectral analysis of the enzymes from the two tissues revealed a close similarity. Sodium dodecyl sulphate/polyacrylamide-gel electrophoresis showed the isolated enzyme to have a monomeric Mr of 52 000, and this was confirmed by h.p.l.c. gel exclusion at pH 5.0. The results of Sephadex G-100 chromatography at different pH values are taken to indicate that the enzyme behaves as a dimer at pH 7.0 and above, but as a monomer at pH 5.0. 4-Aminobutyrate aminotransferase isolated from the brain by the procedure of Fowler & John [(1981) Biochem. J. 197, 149-152] is more stable than the immunoaffinity-purified material, and has been shown to contain a contaminant protein of Mr 84 000 that exhibits succinic semialdehyde dehydrogenase activity.
Guidelines for the laboratory diagnosis and susceptibility testing of methicillin-resistant Staphylococcus aureus (MRSA) (2005)

These evidence-based guidelines have been produced after a literature review of the laboratory diagnosis and susceptibility testing of methicillin-resistant Staphylococcus aureus (MRSA). We have considered the detection of MRSA in screening samples and the detection of reduced susceptibility to glycopeptides in S. aureus. Recommendations are given for the identification of S. aureus and for suitable methods of susceptibility testing and screening for MRSA and for S. aureus with reduced susceptibility to glycopeptides. These guidelines indicate what tests should be used but not when the tests are applicable, as aspects of this are dealt with in guidelines on control of MRSA. There are currently several developments in screening media and molecular methods. It is likely that some of our recommendations will require modification as the new methods become available.
Complex I Defect in muscle from patients with Huntington's disease (1998)

Abstract We found a variable defect of complex I of the mitochondrial respiratory chain, ranging in severity from 25% to 63% of control values, in muscle of patients with Huntington's disease (HD). The most severe defect was observed in the patient with the greatest expansion of CAG triplets. Muscle morphology showed myopathic changes such as moth‐eaten fibers, angulated fibers, increased subsarcolemmal oxidative activities, or an increased number of enlarged mitochondria with abnormal cristae. Multiple mitochondrial DNA deletions were found by polymerase chain reaction (PCR) analysis in muscle of the patient with the most severe defect of complex I. Our data further support the involvement of energetic defects and oxidative damage in muscle of patients with HD.