gebhart/patrepeval huggingface dataset:
A surface analytical study of the formation and adhesion of chromium films on alumina (1992)

Chromium-alumina bonding was characterized by using surface analysis techniques. The metal-ceramic interface was produced by vapour deposition of the metal at room temperature in an ultra-high vacuum chamber equipped with AES (Auger electron spectroscopy), EELS (electron energy loss spectroscopy), and XPS (X-ray photoelectron spectroscopy) facilities. Two kinds of alumina surface were used as the support for Cr condensation: a stoichiometric (1×1) α-Al2O3 surface (called the perfect surface or class a) and an oxygen-deficient surface giving rise to LEED patterns (called the reduced surface or class b). It is shown that on perfect surfaces the Cr film grows layer by layer but on reduced surfaces a three-dimensional (3D) growth process is observed. These results are explained by a strong chemical interaction between Cr and the class a surface, and by 3D nucleation on defect sites on the class b surface. After ageing for a few days under vacuum, the thick Cr film deposited on the reduced surface delaminates. This behaviour can be interpreted as competition between Cr atoms and Al ions to form an interfacial oxide layer.
T-cell-epitope mapping of the major secreted mycobacterial antigen Ag85A in tuberculosis and leprosy (1994)

Lymphoproliferation and gamma interferon (IFN-gamma) secretion in response to 28 overlapping 20-mer synthetic peptides covering the complete sequence of the mature (295-amino-acid) 85A component of the major secreted, fibronectin-binding antigen 85 complex from Mycobacterium tuberculosis and Mycobacterium bovis BCG (MTAg85A) was examined by using peripheral blood mononuclear cell (PBMC) cultures from healthy tuberculin- and lepromin-positive volunteers and from patients with tuberculosis and leprosy. Peptide recognition was largely promiscuous, with a variety of human leukocyte antigen haplotypes reacting to the same peptides. PBMC from all tuberculin-positive subjects reacted to Ag85, and the majority proliferated in response to peptide 6 (amino acids 51 to 70), peptides 13, 14, and 15 (amino acids 121 to 160), or peptides 20 and 21 (amino acids 191 to 220). PBMC from tuberculosis patients demonstrated a variable reactivity to Ag85 and its peptides, and the strongest proliferation was observed against peptide 7 (amino acids 61 to 80). MTAg85A peptides were also recognized by PBMC from healthy lepromin-positive volunteers and paucibacillary leprosy patients (again in a promiscuous manner), but despite a 90% homology between the 85A proteins of M. leprae and M. tuberculosis, the peptides recognized were different. PBMC from lepromin-positive healthy contacts reacted against peptide 2 (amino acids 11 to 30), peptide 5 (amino acids 41 to 60), and peptides 25 and 26 (amino acids 241 to 270). PBMC from paucibacillary patients reacted preferentially against peptide 1 (amino acids 1 to 20) and peptide 5. Multibacillary patients were not reactive to Ag85 or the MT85A peptides. IFN-gamma production was generally detected simultaneously with positive lymphoproliferative responses, although peptide 1 mostly stimulated proliferation and peptides 27 and 28 mostly elicited an IFN-gamma response. In conclusion, regions 41 to 80 and 241 to 295 demonstrated powerful and promiscuous T-cell-stimulatory properties, resulting in proliferative responses and IFN-gamma secretion, respectively, in the majority of reactive subjects tested in this study. These results could be of value in the development of a subunit vaccine for tuberculosis and leprosy.
Physiologically based pharmacokinetic model for fluorocarbon elimination after the administration of an octafluoropropane-albumin microsphere sonographic contrast agent. (1999)

A physiologically based pharmacokinetic model was developed to evaluate the kinetics of one of the newest sonographic contrast agents available, FS069 or Optison. This material consists of octafluoropropane gas encapsulated in proteinaceous microspheres, injected intravenously for use as a myocardial contrast agent in humans. This model has six compartments: two lung compartments (alveolar and dead volume), and compartments for the heart, slowly perfused tissue, richly perfused tissue, and gastrointestinal tract. The model was developed to determine the distribution and excretion of the octafluoropropane in the body. Despite the high affinity of octafluoropropane for tissue, the model predicted that nearly 100% of the material would be exhaled from the lungs within 6 min. The model verified the results of a phase I clinical trial with 10 healthy subjects. Ventilation rate was found to play a critical role in the complete excretion of this contrast agent. The physiologically based pharmacokinetic model was a useful tool for evaluating the safety of FS069. This model can be used a basis for developing similar models for other types of contrast agents.
Post-Prandial Blood Glucose Determination by Quantitative Mid-Infrared Spectroscopy (1992)

The multivariate calibration method of partial least-squares (PLS) was applied to the mid-infrared spectra of whole blood for quantitatively determining blood glucose concentrations. Separate calibration models were developed on the basis of spectra of whole blood obtained from six diabetic subjects from either in vitro glucose-supplemented blood or blood obtained from the same subjects in the post-prandial state during meal tolerance tests. The cross-validated PLS calibrations yielded average errors in glucose concentration of 11 and 13 mg/dL, respectively. It is desirable to use the calibration models based on the in vitro glucose-supplemented blood for determining glucose concentrations in unknown blood samples. However, when these multivariate calibration models based upon in vitro blood spectra were applied to the spectra of the postprandial blood samples, a subject-dependent concentration bias was observed. The source of this bias was not identified, but when the glucose determinations were corrected for the bias, average concentration errors were found to be 14 mg/dL. Changes in spectrometer design or calibrations based on large numbers of subjects are expected to eliminate the presence of this bias. If these measures do not succeed in eliminating the bias, then methods are demonstrated that significantly reduce the bias while retaining the sensitive outlier detection capabilities of the PLS methods. These latter methods require that the infrared spectrum and reference glucose levels be obtained from a single blood sample from each subject.
Use of a Fluorescently Labeled Poly-Caspase Inhibitor for in Vivo Detection of Apoptosis Related to Vascular-Targeting Agent Arsenic Trioxide for Cancer Therapy (2007)

Arsenic trioxide (ATO, Trisenox) is a potent anti-vascular agent and significantly enhances hyperthermia and radiation response. To understand the mechanism of the anti-tumor effect in vivo we imaged the binding of a fluorescently-labeled poly-caspase inhibitor (FLIVO) in real time before and 3 h or 24 h after injection of 8 mg/kg ATO. FSaII tumors were grown in dorsal skin-fold window chambers or on the rear limb and we observed substantial poly-caspase binding associated with vascular damage induced by ATO treatment at 3 and 24 h after ATO injection. Flow cytometric analysis of cells dissociated from the imaged tumor confirmed cellular uptake and binding of the FLIVO probe. Apoptosis appears to be a major mode of cell death induced by ATO in the tumor and the use of fluorescently tagged caspase inhibitors to assess cell death in live animals appears feasible to monitor and/or confirm anti-tumor effects of therapy.
Bacterial Competition for Human Nasal Cavity Colonization: Role of Staphylococcal agr Alleles (2003)

We examined the bacterial aerobic nasal flora of 216 healthy volunteers to identify potential competitive interactions among different species, with special emphasis on the influence of staphylococcal agr alleles. The Staphylococcus aureus colonization rate correlated negatively with the rate of colonization by Corynebacterium spp. and non-aureus staphylococci, especially S. epidermidis, suggesting that both Corynebacterium spp. and S. epidermidis antagonize S. aureus colonization. Most of the S. aureus and S. epidermidis isolates were agr typed by a PCR method. Only one S. aureus agr (agr(Sa)) allele was detected in each carrier. Multiple logistic regression of the two most prevalent agr(Sa) alleles (agr-1(Sa) and agr-2(Sa)) and the three S. epidermidis agr (agr(Se)) alleles showed a specific influence of the agr system. The results of this model did not support conclusions drawn from previous in vitro agr-specific cross-inhibition experiments. Our findings suggest that the agr alleles, which are strongly linked to the bacterial genetic background, may simply be associated with common biological properties--including mediators of bacterial interference--in the strains that bear them.
Recruitment and Derecruitment During Acute Respiratory Failure (2001)

We aimed to elucidate the relationships between pleural (Ppl), esophageal (Pes), and superimposed gravitational pressures in acute lung injury, and to understand the mechanisms of recruitment and derecruitment. In six dogs with oleic acid respiratory failure, we measured Pes and Ppl in the uppermost, middle, and most dependent lung regions. Each dog was studied at positive end-expiratory pressure (PEEP) of 5 and 15 cm H2O and three levels of tidal volume (VT; low, medium, and high). For each PEEP-VT combination, we obtained a computed tomographic (CT) scan at end-inspiration and end-expiration. The variations of Ppl and Pes pressures were correlated (r = 0.86 +/- 0.07, p < 0.0001), as was the vertical gradient of transpulmonary (PL) and superimposed pressure (r = 0.92, p < 0.0001). Recruitment proceeded continuously along the entire volume-pressure curve. Estimated threshold opening pressures were normally distributed (mode = 20 to 25 cm H2O). The amount of end-expiratory collapse at the same PEEP and PL was significantly lower when ventilation was performed at high VT. End-inspiratory and end-expiratory collapse were highly correlated (r = 0.86, p < 0.0001), suggesting that as more tissue is recruited at end-inspiration, more remains recruited at end-expiration. When superimposed pressure exceeded applied airway pressure (Paw), collapse significantly increased.
Cell biology and molecular mechanisms of injury in ischemic acute renal failure (2000)

The pathogenesis of acute renal failure has been attributed to persistent vasoconstriction and leukocyte-endothelial interactions, resulting in inflammation and compromise of local blood flow to the outer medulla, the loss of tubular epithelial cell polarity with multiple functional sequelae, necrosis or apoptosis of epithelial cells, and the de-differentiation, migration and proliferation of surviving cells. In this paper, the authors present their views of pathophysiology of ischemic acute renal failure.
Potent Peptide Inhibitors of Human Hepatitis C Virus NS3 Protease Are Obtained by Optimizing the Cleavage Products (1998)

In the absence of a broadly effective cure for hepatitis caused by hepatitis C virus (HCV), much effort is currently devoted to the search for inhibitors of the virally encoded protease NS3. This chymotrypsin-like serine protease is required for the maturation of the viral polyprotein, cleaving it at the NS3-NS4A, NS4A-NS4B, NS4B-NS5A, and NS5A-NS5B sites. In the course of our studies on the substrate specificity of NS3, we found that the products of cleavage corresponding to the P6-P1 region of the substrates act as competitive inhibitors of the enzyme, with IC50s ranging from 360 to 1 microM. A detailed study of product inhibition by the natural NS3 substrates is described in the preceding paper [Steinkühler, C., et al. (1997) Biochemistry 37, 8899-8905]. Here we report the results of a study of the structure-activity relationship of the NS3 product inhibitors, which suggest that the mode of binding of the P region-derived products is similar to the ground-state binding of the corresponding substrates, with additional binding energy provided by the C-terminal carboxylate. Optimal binding requires a dual anchor: an "acid anchor" at the N terminus and a "P1 anchor" at the C-terminal part of the molecule. We have then optimized the sequence of the product inhibitors by using single mutations and combinatorial peptide libraries based on the most potent natural product, Ac-Asp-Glu-Met-Glu-Glu-Cys-OH (Ki = 0.6 microM), derived from cleavage at the NS4A-NS4B junction. By sequentially optimizing positions P2, P4, P3, and P5, we obtained several nanomolar inhibitors of the enzyme. These compounds are useful both as a starting point for the development of peptidomimetic drugs and as structural probes for investigating the substrate binding site of NS3 by modeling, NMR, and crystallography.
Recombinant Human Bone Morphogenetic Protein‐2 Potentiates the In Vivo Osteogenic Ability of Marrow/Hydroxyapatite Composites (2001)

A composite of marrow mesenchymal stem cells (MSCs) and porous hydroxyapatite (HA) has bone-forming capability. To promote the capability, we added recombinant human bone morphogenetic protein-2 (BMP) to the composite. The bone formation was assessed by rat subcutaneous implantation of 4 different kinds of implants, i.e., HA alone, BMP/HA composites, MSCs/HA composites, and the composites containing BMP (MSCs/BMP/HA). Both HA and the BMP/HA composites did not show bone formation at any time after implantation. The MSCs/HA composites showed moderate bone formation at 4 weeks and extensive bone formation at 8 weeks. The MSCs/BMP/HA composites showed obvious bone formation together with active osteoblasts at 2 weeks and more bone formation at 4 and 8 weeks. The MSCs/BMP/HA composites demonstrated high alkaline phosphatase and osteocalcin expression at both the protein and gene levels. These results indicate that the combination of MSCs, porous HA, and BMP synergistically enhances osteogenic potential and provides a rational basis for their clinical application in bone reconstruction surgery.
Human prostate cancer cells lack feedback regulation of low-density lipoprotein receptor and its regulator, SREBP2 (2000)

The low-density lipoprotein receptor (LDLR) pathway provides cells with essential fatty acids for prostaglandin E2 (PGE2) synthesis. Regulation of LDLR expression by LDL was compared between the human normal and cancer prostate cells using semi-quantitative RT-PCR and LDL uptake assays. LDLR mRNA expression and LDL uptake by LDLR were down-regulated in the presence of exogenous LDL or whole serum in the normal prostate cells, but not in the prostate cancer cells. Addition of exogenous cholesterol down-regulated both LDLR and a potent regulator of the ldlr promoter, sterol regulatory element binding protein 2 (SREBP2), in normal cells but not in cancer cells. PGE2 synthesis in prostate cancer cells was significantly increased in response to LDL. Our study suggests that over-production of LDLR is an important mechanism in cancer cells for obtaining more essential fatty acids through LDLR endocytosis, allowing increased synthesis of prostaglandins, which subsequently stimulate cell growth. The data also suggest that the sterol regulatory element and SREBP2 play a role in the loss of sterol feedback regulation in cancer cells.
Associations Between Pathogen-Specific Cases of Clinical Mastitis and Somatic Cell Count Patterns (2004)

Associations were estimated between pathogen-specific cases of clinical mastitis (CM) and somatic cell count (SCC) patterns based on deviations from the typical curve for SCC during lactation and compared with associations between pathogen-specific CM and lactation average SCC. Data from 274 Dutch herds recording CM over an 18-mo period were used. Pathogens found were Staphylococcus aureus, coagulase-negative staphylococci, Escherichia coli, Streptococcus dysgalactiae, Streptococcus uberis, streptococci other than Strep. dysgalactiae and Strep. uberis, and culture-negative samples. The dataset contained 245,595 test-day records on SCC, recorded in 24,012 lactations of 19,733 cows of different parities. Pattern definitions were based on three or five consecutive test-day records. The patterns differentiated between a short or longer period of increased SCC and also between lactations with and without recovery. Logistic regression was applied to identify associations between presence of patterns and occurrence of pathogens. Occurrence of overall CM in a lactation is equally or even more accurately predicted by the presence of SCC in that lactation, than by a lactation average SCC of more than 200,000 cells/mL. Patterns can also distinguish between chances of risk for specific mastitis-causing pathogens. Clinical E. coli mastitis was significantly associated with the presence of a short peak in SCC, whereas Staph. aureus was associated with long increased SCC. Streptococcus dysgalactiae was not strongly associated with any of the defined patterns of peaks in SCC, and no single unambiguous pattern was found for Strep. uberis.
Preparation of oligodeoxyribonucleoside phosphoro-dithioates by a triester method (1994)

A method to prepare thymidine phosphorodithioate dimers (ref. 1) has been extended to allow the preparation of oligo-2'-deoxyribonucleotide phosphorodithioates containing all four bases. The method is suitable for large-scale synthesis and gives phosphorodithioates without phosphorothioate impurities (31P nmr, detection limit 0.5 to 1%). Oligonucleotides up to octamers which contain -0-(PS2-)-0- linkages at all positions have been prepared by block synthesis in solution. The phosphorodithioate linkage is introduced by the reaction of a 5'-O, N-protected nucleoside (or oligonucleotide) with a dithiophosphorylating agent RSP(S)(ODhbt)2, R = 2,4-dichlorobenzyl, Dhbt = 3,4-dihydro-4-oxo-benzotriazin-3-yl, followed by coupling of the product to a 3'-O,N-protected nucleoside (or oligonucleotide). This method gives pure protected oligodeoxyribonucleoside phosphorodithioates, and phosphorothioate linkages are only introduced if contact with conc. aqueous ammonia during or after deblocking is unduly prolonged.
Zinc Acetate Treatment in Wilson's Disease (1998)

Zinc acetate is an effective maintenance therapy for patients with Wilson's disease. Negligible toxicity, compared with that of previously approved treatments, is a major advantage.
Single-shot spectral interferometry with chirped pulses (2001)

We present a method for obtaining time-resolved measurements of the amplitude modulation and the phase shift of a chirped probe pulse interacting with a femtosecond-laser-produced plasma. Based on spectral interferometry, the technique allows for single-shot measurements and keeps the temporal resolution associated with the full bandwidth of the probe pulse. We demonstrate the efficiency of this technique by probing femtosecond-laser breakdown of plastic targets.
The oxyhemoglobin reaction of nitric oxide (1999)

The oxidation of nitric oxide (NO) to nitrate by oxyhemoglobin is a fundamental reaction that shapes our understanding of NO biology. This reaction is considered to be the major pathway for NO elimination from the body; it is the basis for a prevalent NO assay; it is a critical feature in the modeling of NO diffusion in the circulatory system; and it informs a variety of therapeutic applications, including NO-inhalation therapy and blood substitute design. Here we show that, under physiological conditions, this reaction is of little significance. Instead, NO preferentially binds to the minor population of the hemoglobin's vacant hemes in a cooperative manner, nitrosylates hemoglobin thiols, or reacts with liberated superoxide in solution. In the red blood cell, superoxide dismutase eliminates superoxide, increasing the yield of S-nitrosohemoglobin and nitrosylated hemes. Hemoglobin thus serves to regulate the chemistry of NO and maintain it in a bioactive state. These results represent a reversal of the conventional view of hemoglobin in NO biology and motivate a reconsideration of fundamental issues in NO biochemistry and therapy.
Platelet factor 4 gene expression in a human megakaryocytic leukemia cell line (CMK) and its differentiated subclone (CMK11-5). (1991)

The human cell line CMK spontaneously expresses megakaryocytic characteristics and can be induced to differentiate into mature megakaryocytes after exposure to 12-O-tetradecanoylphorbol-13-acetate (TPA). In comparison with CMK, we have examined the characteristics of a subclone, designated as CMK11-5, that is morphologically larger than the parent clone CMK and contains multinucleated giant cells. All CMK11-5 cells were positive for platelet peroxidase (PPO) activity, and some contained abundant alpha-granules and well-developed demarcation membranes. CMK cells had few demarcation membranes and alpha-granules, and 10% of these cells were found not to possess PPO activity. Phenotypic analysis revealed the percentage of CMK11-5 cells for platelet glycoprotein (GP) IIb/IIIa (CD41a), and GPIIIa (CD61) was greater than that for CMK cells. On the basis of these findings, CMK11-5 cells were considered to be more differentiated than CMK cells. We further examined the expression of GPIIb and platelet factor 4 (PF4) mRNA by Northern blot hybridization using 32P-labeled cDNA probes for GPIIb and PF4 in CMK and CMK11-5 cells. CMK cells exhibited mRNA for GPIIb, and its expression was augmented by TPA addition, but not PF4. In contrast, CMK11-5 cells were found to contain mRNA for GPIIb and PF4, and their mRNA levels were increased by the addition of TPA. The immunoreactive PF4 antigen was not detected in the TPA-treated CMK11-5 cells or in the culture medium of these cells. These results indicate that expression of mRNA for PF4 is a useful marker for the identification of mature megakaryocytes. Detection of mRNA for PF4 is a more sensitive method for characterization of megakaryocytic cells than that for the PF4 antigen.
Estrogen inhibits the growth of estrogen receptor-negative, but not estrogen receptor-positive, human mammary epithelial cells expressing a recombinant estrogen receptor. (1993)

Estrogen is essential for the growth of the normal mammary gland and most estrogen receptor (ER)-positive mammary carcinomas. To better understand the differences between the estrogen response pathways in normal and tumor cells, we have stably transfected ER-negative immortal, nontumorigenic human mammary epithelial cells and ER-negative breast cancer cells with an ER-encoding expression vector. Unexpectedly, estrogen treatment (1.0 nM) inhibited the proliferation of ER-transfected nontumorigenic and tumor-derived cells. The control transfectants and parental cells exhibited no response to estrogen concentrations as high as 1.0 microM. This inhibitory effect was attributed to a decreased growth rate and a perturbation of the cell cycle distribution by estrogen treatment of the ER transfectants. The inhibitory response was blocked by cotreatment with the antiestrogen ICI 164,384 as predicted for a pure antagonist of estrogen action. However, treatment with the antiestrogen hydroxytamoxifen caused growth inhibition, implying that hydroxytamoxifen acts as an agonist of estrogen action in ER-transfected cells. Since estrogen is a mitogenic and not a growth-inhibitory stimulus for ER-positive breast cancers and cell lines, we tested the effect of constitutive, high level expression of the ER in ER-positive tumor cells. Stable transfection of ER-positive MCF-7 and T47D cells with the ER expression vector yielded cells with varying amounts of ER. At ER levels comparable to those found in the ER-negative transfected cells, the MCF-7 and T47D ER transfectants were not inhibited by estrogen. These data suggest that ER-positive breast cancer cells can tolerate higher constitutive levels of ER expression than ER-negative cells. The mechanism by which this is accomplished may be an essential step in the process which yields ER-positive tumors.