gebhart/patrepeval huggingface dataset:
Modeling and validation of a molded polycarbonate continuous-flow polymerase chain reaction devic (2003)

A continuous flow polymerase chain reaction (CFPCR) system was designed, fabricated from molded polycarbonate, and tested. Finite element modeling was used to simulate the thermal and Microfluidic response of the system. The mold insert for the initial prototypes was fabricated using the X-ray LIGA microfabrication process and device components produced by hot embossing polycarbonate. Commercial thin film heaters under PID control were used to supply the necessary heat flux to maintain the steady-state temperatures in the PCR. The simulated transient temperature response at start up was compared to the experimental response. The simulated steady state temperature profile along the channel generated by the finite element analysis was compared to the experimental temperature profile displayed by liquid crystals. Experimental and simulated results were within 5% of each other, validating the thermal design of the CFPCR device.
The relative importance of alkalinity, temperature, and the washout effect of bicarbonate-buffered, multidose cardioplegic solution. (1984)

Recent experimental and clinical studies from our institution have shown that the administration of cold, bicarbonate-buffered, hyperkalemic crystalloid cardioplegic solution resulted in a significant rise in intramyocardial pH. This rise could theoretically be caused by (1) the alkalinity of the solution administered (pH 8.2 at 25 degrees C), (2) the washout of acid metabolites with each administration, and (3) hypothermia per se. To investigate the relative effects of each of these three factors on intramyocardial pH, dogs on cardiopulmonary bypass received crystalloid cardioplegic solution either at 10 degrees C (n = 9) or at 37 degrees C (n = 8) every 30 min during 2 hr of aortic cross-clamping. Myocardial temperature, intramyocardial pH, and CO2 tension (Pmco2) were measured continuously. Needle biopsy specimens were taken every 30 min for biochemical and ultrastructural analysis. Before aortic cross-clamping, intramyocardial pH was 7.07 +/- 0.06 in both groups (+/- SEM). Upon each administration of cardioplegic solution, hearts in the 10 degrees C group cooled to 10 degrees to 15 degrees C and intramyocardial pH increased on the average by 0.31 +/- 0.03 units (p less than .001). In the 37 degrees C group intramyocardial pH was unaffected by cardioplegic solution. At the end of the cross-clamping period, intramyocardial pH had declined to 6.49 +/- 0.13 in the 10 degrees C group and to 5.60 +/- 0.08 in the 37 degrees C group, the fall in pH being significantly greater in the 37 degrees C group than in the 10 degrees C group (p less than .01).(ABSTRACT TRUNCATED AT 250 WORDS)
Autophagy-Dependent Anticancer Immune Responses Induced by Chemotherapeutic Agents in Mice (2011)

Antineoplastic chemotherapies are particularly efficient when they elicit immunogenic cell death, thus provoking an anticancer immune response. Here we demonstrate that autophagy, which is often disabled in cancer, is dispensable for chemotherapy-induced cell death but required for its immunogenicity. In response to chemotherapy, autophagy-competent, but not autophagy-deficient, cancers attracted dendritic cells and T lymphocytes into the tumor bed. Suppression of autophagy inhibited the release of adenosine triphosphate (ATP) from dying tumor cells. Conversely, inhibition of extracellular ATP-degrading enzymes increased pericellular ATP in autophagy-deficient tumors, reestablished the recruitment of immune cells, and restored chemotherapeutic responses but only in immunocompetent hosts. Thus, autophagy is essential for the immunogenic release of ATP from dying cells, and increased extracellular ATP concentrations improve the efficacy of antineoplastic chemotherapies when autophagy is disabled.
Evidence for non-V3-specific neutralizing antibodies that interfere with gp120/CD4 binding in human immunodeficiency virus 1-infected humans. (1991)

Total anti-gp120 antibodies (total anti-gp120 Abs) were purified from a pool of four human immunodeficiency virus-positive (HIV+) sera by affinity chromatography on a gp120SF2-Sepharose column and exhibited both type- and group-specific neutralizing activities. To dissect the epitope specificity of the group-specific neutralizing antibodies, CD4 attachment site-specific antibodies (CD4-site Abs) were isolated from total anti-gp120 Abs by using a CD4-blocked gp120SF2-Sepharose column. The CD4-site Abs exhibited group-specific neutralizing activities. Another approach to dissecting type- and group-specific neutralizing activities of total anti-gp120 Abs was to separate the third variable region (V3)-specific antibodies (V3-region Abs) from non-V3-region-specific antibodies (non-V3 Abs). The results indicated that V3-region Abs exhibited type-specific neutralizing activities, whereas non-V3 Abs exhibited group-specific neutralizing activities. By comparing the neutralizing activities of V3-region Abs to those of non-V3 Abs, we concluded that V3-region Abs are more effective than non-V3 Abs in neutralizing a specific HIV isolate. Collectively, this study indicates that group-specific neutralizing anti-gp120 antibodies are specific for the CD4 attachment site.
Purification and characterization of acidic fibroblast growth factor from bovine brain. (1984)

Acidic brain fibroblast growth factor has been purified a minimum of 35,000-fold to apparent homogeneity by a combination of differential salt precipitation, ion exchange chromatography, gel filtration, isoelectric focusing, and hydrophobic chromatography on a C4 reversed-phase HPLC column. Two microheterogeneous forms of the molecule are obtained with apparent molecular masses of 16,600 and 16,800 daltons. The mitogen is highly active with half-maximal stimulation of BALB/c 3T3 fibroblasts at about 40 pg/ml in an assay using incorporation of [methyl-3H]thymidine into DNA.
Inaccuracies in self-reported intake identified by comparison with the doubly labelled water method (1990)

To test the accuracy of self-reported energy intake, reported intake was compared with measured energy expenditure. Results from nine studies were reviewed in which intake data were obtained by recall or weighed record for at least 7 days. Expenditure was measured for 7 days or more by the doubly labelled water method. Individual differences between reported intake and expenditure were large (range +25 to -76%). Group mean differences were smaller. Lean, nonathletic groups living in industrialized countries demonstrated the smallest mean difference between self-reported energy intakes and expenditure (0 to -20%). Obese populations demonstrated the largest mean differences (-35 and -50%), but women living in the Gambia and elite athletes also demonstrated large mean differences. Most of the difference appears to be due to under-reporting, but some subjects lost weight during the reporting period indicating that some of the difference was due to undereating. Because the greatest bias was observed in obese subjects, current methods for self-reported energy intake are not recommended for use in obesity research.
A chemiluminescense-based assay for S-nitrosoalbumin and other plasma S-nitrosothiols (2000)

The lack of a simple assay for the quantification of S-nitrosothiols in complex biological matrices has hampered our understanding of their contribution to normal physiology and pathophysiological states. In this paper we describe an assay based upon the release of nitric oxide by reaction with a mixture consisting of Cu(I), iodine and iodide with subsequent quantification by chemiluminescense. With this method we can detect levels of S-nitrosothiols down to 5 nM in plasma. Following alkylation of free thiols with N-ethylmaleimide, and removal of nitrite with acidified sulfanilamide, we were able to measure known amounts of S-nitrosoalbumin added to plasma or whole blood, with an inter-assay variation for plasma S-nitrosothiols of approximately 4%. Further studies showed that the mean concentration of circulating S-nitrosothiols in venous plasma of healthy human volunteers was 28+/-7 nM.
Cys2/His2 zinc-finger protein family of petunia: Evolution and general mechanism of target-sequence recognition (1998)

The EPF family is a group of Cys2/His2zinc-finger proteins in petunia. In these proteins, characteristically long spacer regions have been found to separate the zinc fingers. Our previous DNA-binding studies demonstrated that two-fingered proteins (ZPT2-1 and ZPT2-2), which have spacers of different lengths, bind to two separate AGT core motifs in a spacing specific manner. To investigate the possibility that these proteins might distinguish between the target sequences on the basis of spacing between the core motifs, we screened petunia cDNA library for other proteins belonging to this family. Initial screening by PCR and subsequent cloning of full-length cDNAs allowed us to identify the genes for 10 new proteins that had two, three or four zinc fingers. Among the two-fingered proteins the spacing between zinc fingers varied from 19 to 65 amino acids. The variation in the length of spacers was even more extensive in three- and four-fingered proteins. The presence of such proteins is consistent with our hypothesis that the spacing between the core motifs might be important for target sequence recognition. Furthermore, comparison of diverse protein structures suggests that three- and two-fingered proteins might have resulted due to successive loss of fingers from a four-fingered protein during molecular evolution. We also demonstrate that a highly conserved motif (QALGGH) among the members of EPF family and other Cys2/His2 zinc-finger proteins in plants is critical for the DNA-binding activity.
A New Mechanism of NK Cell Cytotoxicity Activation: The CD40–CD40 Ligand Interaction (1997)

NK recognition is regulated by a delicate balance between positive signals initiating their effector functions, and inhibitory signals preventing them from proceeding to cytolysis. Knowledge of the molecules responsible for positive signaling in NK cells is currently limited. We demonstrate that IL-2-activated human NK cells can express CD40 ligand (CD40L) and that recognition of CD40 on target cells can provide an activation pathway for such human NK cells. CD40-transfected P815 cells were killed by NK cell lines expressing CD40L, clones and PBL-derived NK cells cultured for 18 h in the presence of IL-2, but not by CD40L-negative fresh NK cells. Cross-linking of CD40L on IL-2-activated NK cells induced redirected cytolysis of CD40-negative but Fc receptor-expressing P815 cells. The sensitivity of human TAP-deficient T2 cells could be blocked by anti-CD40 antibodies as well as by reconstitution of TAP/MHC class I expression, indicating that the CD40-dependent pathway for NK activation can be downregulated, at least in part, by MHC class I molecules on the target cells. NK cell recognition of CD40 may be important in immunoregulation as well as in immune responses against B cell malignancies.
Sphingosine 1-Phosphate Contracts Canine Basilar Arteries In Vitro and In Vivo (2001)

S1P induces vasocontraction in the canine basilar artery in vitro and in vivo, possibly through a mechanism involving activation of the Rho/Rho-kinase pathway. Thus, S1P might be considered as a novel spasmogenic substance involved in cerebral vasospasm after subarachnoid hemorrhage.
Changes of transforming growth factor beta 1 in rat periodontal tissue during orthodontic tooth movement. (2000)

Changes in TGF-beta 1 levels play an important role in the remodeling of periodontal tissue during orthodontic tooth movement, and can powerfully promote bone formation.
Combination of Prostate-Specific Antigen, Clinical Stage, and Gleason Score to Predict Pathological Stage of Localized Prostate Cancer (1997)

<h3>Objective.</h3> —To combine the clinical data from 3 academic institutions that serve as centers of excellence for the surgical treatment of clinically localized prostate cancer and develop a multi-institutional model combining serum prostate-specific antigen (PSA) level, clinical stage, and Gleason score to predict pathological stage for men with clinically localized prostate cancer. <h3>Design.</h3> —In this update, we have combined clinical and pathological data for a group of 4133 men treated by several surgeons from 3 major academic urologic centers within the United States. Multinomial log-linear regression was performed for the simultaneous prediction of organ-confined disease, isolated capsular penetration, seminal vesicle involvement, or pelvic lymph node involvement. Bootstrap estimates of the predicted probabilities were used to develop nomograms to predict pathological stage. Additional bootstrap analyses were then obtained to validate the performance of the nomograms. <h3>Patients and Settings.</h3> —A total of 4133 men who had undergone radical retropubic prostatectomy for clinically localized prostate cancer at The Johns Hopkins Hospital (n=3116), Baylor College of Medicine (n=782), and the University of Michigan School of Medicine (n=235) were enrolled into this study. None of the patients had received preoperative hormonal or radiation therapy. <h3>Outcome Measures.</h3> —Simultaneous prediction of organ-confined disease, isolated capsular penetration, seminal vesicle involvement, or pelvic lymph node involvement using updated nomograms. <h3>Results.</h3> —Prostate-specific antigen level, TNM clinical stage, and Gleason score contributed significantly to the prediction of pathological stage (<i>P</i>&lt;.001). Bootstrap estimates of the median and 95% confidence interval of the predicted probabilities are presented in the nomograms. For most cells in the nomograms, there is a greater than 25% probability of qualifying for more than one of the pathological stages. In the validation analyses, 72.4% of the time the nomograms correctly predicted the probability of a pathological stage to within 10% (organ-confined disease, 67.3%; isolated capsular penetration, 59.6%; seminal vesicle involvement, 79.6%; pelvic lymph node involvement, 82.9%). <h3>Conclusions.</h3> —The data represent a multi-institutional modeling and validation of the clinical utility of combining PSA level measurement, clinical stage, and Gleason score to predict pathological stage for a group of men with localized prostate cancer. Clinicians can use these nomograms when counseling individual patients regarding the probability of their tumor being a specific pathological stage; this will enable patients and physicians to make more informed treatment decisions based on the probability of a pathological stage, as well as risk tolerance and the values they place on various potential outcomes.
Raman Spectroscopy for Non-Invasive Characterization of Ocular Tissue: Potential for Detection of Biological Molecules (1997)

The ability of Raman spectroscopy to remotely characterize ocular tissues using a rapid fibre-optic-based system was explored in this study. An argon ion laser operating at 514.5 nm and a charge-coupled-device-based Raman system were used. Raman spectra from aqueous humour specimens of rabbits and humans, as well as spectra from biological molecules obtained through fresh excised rabbit corneas, were obtained. Prominent peaks were observed which qualitatively matched the known locations of biological molecular peaks such as glucose, lactate and urea. In the rabbit aqueous humour spectra, peak positions were also observed indicative of amino acids and proteins. Raman spectra were also obtained from the rabbit lens showing peak positions indicative of amide I and III modes, sulphydryl and CH stretching modes and amino acids. This study demonstrated that it may be possible to characterize ocular tissue structures and to determine in a qualitative manner the presence of various biological molecules in aqueous humour by means of a Raman-based fibre optic instrument. © 1997 by John Wiley & Sons, Ltd.
Constant, but Not Pulsed Calcitriol Suppresses Hemodialysis Patients’ Antigen-Induced Lymphocyte Proliferation (2000)

The decline of TT response with constant 1,25-(OH)(2)D(3) corresponds with findings on immunosuppressive action of 1,25-(OH)(2)D(3) in previous studies done on normal subjects' cells. This was not seen with intermittently applied 1,25-(OH)(2)D(3). These results support the previous concept that intermittent 1,25(OH)(2)D(3) therapy is not immunosuppressive in hemodialysis patients.
Blood separation on microfluidic paper-based analytical devices (2012)

A microfluidic paper-based analytical device (μPAD) for the separation of blood plasma from whole blood is described. The device can separate plasma from whole blood and quantify plasma proteins in a single step. The μPAD was fabricated using the wax dipping method, and the final device was composed of a blood separation membrane combined with patterned Whatman No.1 paper. Blood separation membranes, LF1, MF1, VF1 and VF2 were tested for blood separation on the μPAD. The LF1 membrane was found to be the most suitable for blood separations when fabricating the μPAD by wax dipping. For blood separation, the blood cells (both red and white) were trapped on blood separation membrane allowing pure plasma to flow to the detection zone by capillary force. The LF1-μPAD was shown to be functional with human whole blood of 24-55% hematocrit without dilution, and effectively separated blood cells from plasma within 2 min when blood volumes of between 15-22 μL were added to the device. Microscopy was used to confirm that the device isolated plasma with high purity with no blood cells or cell hemolysis in the detection zone. The efficiency of blood separation on the μPAD was studied by plasma protein detection using the bromocresol green (BCG) colorimetric assay. The results revealed that protein detection on the μPAD was not significantly different from the conventional method (p > 0.05, pair t-test). The colorimetric measurement reproducibility on the μPAD was 2.62% (n = 10) and 5.84% (n = 30) for within-day and between day precision, respectively. Our proposed blood separation on μPAD has the potential for reducing turnaround time, sample volume, sample preparation and detection processes for clinical diagnosis and point-of care testing.
Human Trabecular Meshwork Cell Responses Induced by Bimatoprost, Travoprost, Unoprostone, and other FP Prostaglandin Receptor Agonist Analogues (2003)

The pharmacology of the h-TM cell FP-receptor-mediated PI turnover and [Ca(2+)](i) mobilization was defined using numerous synthetic (FP-selective) PG agonist analogues and an FP receptor antagonist, AL-8810. Bimatoprost, travoprost, latanoprost, unoprostone isopropyl ester, and their respective free acids were shown to be FP agonists in the h-TM cells.
Femtosecond electron diffraction: heralding the era of atomically resolved dynamics (2011)

One of the great dream experiments in Science is to directly observe atomic motions as they occur. Femtosecond electron diffraction provided the first 'light' of sufficient intensity to achieve this goal by attaining atomic resolution to structural changes on the relevant timescales. This review covers the technical progress that made this new level of acuity possible and gives a survey of the new insights gained from an atomic level perspective of structural dynamics. Atomic level views of the simplest possible structural transition, melting, are discussed for a number of systems in which both thermal and purely electronically driven atomic displacements can be correlated with the degree of directional bonding. Optical manipulation of charge distributions and effects on interatomic forces/bonding can be directly observed through the ensuing atomic motions. New phenomena involving strongly correlated electron–lattice systems are also discussed in which optically induced changes in the potential energy landscape lead to ballistic structural changes. Concepts such as the structural order parameters are now directly observable at the atomic level of inspection to give a remarkable view of the extraordinary degree of cooperativity involved in strongly correlated electron–lattice systems. These recent examples, in combination with time-resolved real space imaging now possible with electron probes, are truly defining an emerging field that holds great promise to make a significant impact in how we understand structural dynamics.
Defective Development of γ/δ T Cells in Interleukin 7 Receptor–Deficient Mice Is Due to Impaired Expression of T Cell Receptor γ Genes (1999)

Mice lacking the interleukin 7 receptor (IL-7R) generate alpha/beta T cells at a detectable but greatly reduced rate, but gamma/delta T cells are completely absent. The special role of IL-7R signaling in gamma/delta T cell development has remained unclear. IL-7Ralpha(-/-) mice exhibit a paucity of gamma gene rearrangements. This striking observation can be explained by a defect in T cell receptor (TCR)-gamma gene rearrangement, a defect in TCR-gamma gene transcription leading to death of gamma/delta lineage cells, and/or a requirement for IL-7R in commitment of cells to the gamma/delta lineage. To determine the role of IL-7R signaling in gamma/delta T cell development, we examined transcription of a prerearranged TCR-gamma transgene in IL-7Ralpha(-/-) mice, as well as the effects of IL-7 on transcription of endogenous, rearranged TCR-gamma genes in alpha/beta lineage cells. The results demonstrate that IL-7R-mediated signals are necessary for the normal expression of rearranged TCR-gamma genes. Equally significant, the results show that the poor expression of TCR-gamma genes in IL-7Ralpha(-/-) mice is responsible for the selective deficit in gamma/delta cells in these mice, since a high copy TCR-gamma transgene exhibited sufficient residual expression in IL-7Ralpha(-/-) mice to drive gamma/delta cell development. The results indicate that the absence of gamma/delta T cells in IL-7Ralpha(-/-) mice is due to insufficient TCR-gamma gene expression.
Internal magnetic field measurement on C-2 field-reversed configuration plasmas (2012)

A long-lived field-reversed configuration (FRC) plasma has been produced in the C-2 device by dynamically colliding and merging two oppositely directed, highly supersonic compact toroids (CTs). The reversed-field structure of the translated CTs and final merged-FRC state have been directly verified by probing the internal magnetic field structure using a multi-channel magnetic probe array near the midplane of the C-2 confinement chamber. Each of the two translated CTs exhibits significant toroidal fields (B(t)) with opposite helicity, and a relatively large B(t) remains inside the separatrix after merging.