gebhart/patrepeval huggingface dataset:
Design and Testing of a Laboratory Ultrasonic Data Acquisition System for Tomography (2005)

Geophysical tomography allows for the measurement of stress-induced density changes inside of a rock mass or sample by non-invasive means. Tomography is a non-destructive testing method by which sensors are placed around a sample and energy is introduced into the sample at one sensor while the other sensors receive the energy. This process is repeated around the sample to obtain the desired resolution. The received information is converted by a mathematical transform to obtain a tomogram. This tomogram shows a pixelated distribution of the density within the sample. Each pixel represents an average value at that point. The project discussed in this paper takes the principle of ultrasonic tomography and applies it to geomechanics. A new instrumentation system was designed to allow rapid data collection through varying sample geometries and rock types with a low initial investment. The system is composed of sensors, an ultrasonic pulser, a source switchbox, and analog to digital converters; it is tied together using a LabVIEW virtual instrument. LabVIEW is a graphical development environment for creating test, measurement, and other control applications. Using LabVIEW, virtual instruments (VIs) are created to control or measure a process. In this application LabVIEW was used to create a virtual instrument that was automated to collect the data required to construct a tomogram. Experiments were conducted to calibrate and validate the system for ultrasonic velocity determination and stress redistribution tomography. Calibration was conducted using polymethylmethacrylate (PMMA or Plexiglas) plates. Uniaxial loads were placed on limestone and sandstone samples. The stress-induced density contrasts were then imaged using the acquisition system. The resolution and accuracy of the system is described. The acquisition system presented is a low-cost solution to laboratory geophysical tomography. The ultimate goal of the project is to further the ability to non-invasively image relative stress redistribution in a rock mass, thereby improving the engineer's ability to predict failure.
Effect of Burst Frequency and Duration of Kilohertz-Frequency Alternating Currents and of Low-Frequency Pulsed Currents on Strength of Contraction, Muscle Fatigue, and Perceived Discomfort (2008)

When comfort, strength, and fatigue are considered jointly, the LPC is advantageous. Electrically induced fatigue is affected by the number of cycles per second, rather than the number of bursts per second.
Enhanced in vitro growth of murine fibroblast cells and preimplantation embryos cultured in medium supplemented with an amphipathic peptide (1992)

Preliminary studies on the proliferative effects of lytic peptides were carried out using NIH 3T3 murine fibroblast cells and human lymphocytes. Cells were cultured in various concentrations of three different amphipathic peptides (SB-37, Shiva-1, and Vishnu), and enhanced proliferation was determined by uptake of 3H-thymidine with treated cells compared with control cultures. Enhanced proliferation of 3T3 cells was observed in cultures containing 50 microM or less SB-37. The primary study consisted of 263 four-cell- to eight-cell-stage mouse embryos from naturally bred mice and incubated in Whitten's medium containing 0.2, 1, or 10 microM of the amino terminus of an amphipathic cecropin B analog (Vishnu) or in Whitten's medium alone. Embryos were cultured to the hatched blastocyst stage, and effect of treatment was determined by the rate of growth to that stage of development. Statistical analysis revealed that culture in all three levels of Vishnu significantly accelerated in vitro growth of these stages of preimplantation embryos compared with controls. These results indicate that Vishnu promotes increased cleavage rates of embryos in vitro. A growth factor receptor clustering mechanism of action is proposed. This peptide may have some potential as an embryo culture medium additive to enhance in vitro growth rate.
Inside Front Cover: Thermally Responsive Biomineralization on Biodegradable Substrates (Adv. Funct. Mater. 16/2007) (2007)

Abstract Biomineralization offers an elegant example of how nature can design complex, hierarchical, and structurally/morphologically controllable materials. João Mano and co‐workers of the University of Minho, Portugal report on p. 3312 that modifying the surface of bioactive substrates, together with the effect of temperature, triggers the formation of apatite upon immersion in simulated body fluid. This “smart” biomineralization concept could be combined with patterning methodologies by controlling the microstructure of the surface. Such a concept could be extended in the biomimetic production of other minerals, being triggered by other kind of stimuli (e.g., pH or ionic strength), in substrates with more complex geometries. Biomineralization offers an elegant example of how nature can design complex, hierarchical, and structurally/morphologically controllable materials. In this work, the surface of bioactive substrates prepared from poly( L ‐lactic acid) and reinforced with Bioglass are modified by the graft polymerization of poly( N ‐isopropylacrylamide), (PNIPAAm) after plasma activation. It is found that such treatment, together with temperature, could trigger the formation of apatite on the biodegradable substrate upon immersion in simulated body fluid above the PNIPAAm lower critical solution temperature (LCST); in contrast, no apatite is formed at room temperature. A control experiment on a material that is not subjected to surface treatment does not show any evidence of mineral deposition at the two analyzed temperatures. This “smart” biomineralization concept is combined with patterning methodologies to control the microstructure of the surface onto which PNIPAAm is grafted. In this case, the apatite is formed at 37 °C in the modified regions. We suggest that this concept could be extended in the biomimetic production of other minerals, where it would be triggered by another kind of stimulus (e.g., pH or ionic strength) in substrates with more complex geometries.
TIGRFAMs: a protein family resource for the functional identification of proteins (2001)

TIGRFAMs is a collection of protein families featuring curated multiple sequence alignments, hidden Markov models and associated information designed to support the automated functional identification of proteins by sequence homology. We introduce the term 'equivalog' to describe members of a set of homologous proteins that are conserved with respect to function since their last common ancestor. Related proteins are grouped into equivalog families where possible, and otherwise into protein families with other hierarchically defined homology types. TIGRFAMs currently contains over 800 protein families, available for searching or downloading at www.tigr.org/TIGRFAMs. Classification by equivalog family, where achievable, complements classification by orthology, superfamily, domain or motif. It provides the information best suited for automatic assignment of specific functions to proteins from large-scale genome sequencing projects.
A pilot clinical trial of vaccination with dendritic cells pulsed with autologous tumor cells derived from malignant pleural effusion in patients with late‐stage lung carcinoma (2005)

The results indicated that it was feasible to immunize patients with lung carcinoma intranodally with DCs pulsed with necrotic tumor cells enriched from pleural effusion specimens, and this approach may generate T-cell responses and provide clinical benefit in some patients.
An abundant and specific binding site for the novel vasodilator adrenomedullin in the rat (1995)

Rat adrenomedullin is a novel 50-amino acid peptide with structural similarities to the calcitonin family of peptides, calcitonin, calcitonin gene-related peptide (CGRP), and islet amyloid polypeptide (IAPP). Using rat [125I]adrenomedullin, specific binding sites were demonstrated in heart, lung, spleen, liver, soleus, diaphragm, gastrocnemius, and spinal cord membranes. The highest binding was present in heart and lung, which was further characterized. These sites exhibited saturation, dissociation, and competition. In rat lung, only rat (IC50 = 5.8 nM) and human (IC50 = 94 nM) adrenomedullin competed with [125I]adrenomedullin. However, in rat heart, rat (IC50 = 0.2 nM) and human (IC50 = 4.2 nM) adrenomedullin, IAPP (IC50 = 240 nM), and CGRP (IC50 = 1050 nM) all competed with [125I] adrenomedullin. Saturation analysis revealed binding capacities and dissociation constants of 2.8 +/- 0.3 pmol/mg protein and 1.3 +/- 0.3 nM, respectively, in lung and 0.47 +/- 0.11 pmol/mg protein and 0.41 +/- 0.14 nM in heart. Comparison with [125I]CGRP- and [125I]IAPP-binding sites in lung showed that rat adrenomedullin could potently inhibit at these sites (IC50 = 5 and 6 nM, respectively). Chemical cross-linking demonstrated a major band of 83,000 mol wt in lung, diaphragm, spleen, and liver and a band of 94,000 mol wt in heart, soleus, and gastrocnemius. Thus, [125I]adrenomedullin-binding sites in rat lung are abundant and can be differentiated from binding sites in rat heart, both pharmacologically and by mol wt.
Ligation-anchored PCR unveils immune repertoire of TCR-beta from whole blood (2015)

We demonstrated the technical feasibility and effectiveness of ligation-anchored PCR approach in capturing the TCR-beta landscapes. Further development of this technology may enable a comprehensive delineation of immune repertoire, including other forms of TCRs as well as immunoglobulins.
Lipidation of apolipoprotein E influences its isoform-specific interaction with Alzheimer's amyloid β peptides (2000)

The inheritance of the apolipoprotein E (apoE) epsilon4 allele is a prevailing risk factor for sporadic and familial Alzheimer's disease (AD). ApoE isoforms bind directly to Alzheimer's amyloid beta (Abeta) peptides both in vitro and in vivo. Recent studies suggest that association of apoE with lipids may modulate its interaction with Abeta. We examined the binding of lipid-associated and delipidated apoE3 and apoE4 isoforms to Abeta utilizing a solid-phase binding assay and estimated the dissociation constants for the interaction of various apoE and Abeta species. Using native apoE isoforms from stably transfected RAW 264 and human embryonic kidney 293 cells, apoE3 had greater affinity than apoE4 for both Abeta1-40 and Abeta1-42. Delipidation of apoE decreased its affinity for Abeta peptides by 5-10-fold and abolished the isoform-specificity. Conversely, incorporation of apoE isoforms produced by baculovirus-infected Sf9 cells into reconstituted human high-density-lipoprotein lipoparticles restored the affinity values for Abeta peptides and resulted in preferential binding of apoE3. The data demonstrate that native lipid-associated apoE3 binds to Abeta peptides with 2-3-fold higher affinity than lipid-associated apoE4. Since the isoforms' binding efficiency correlate inversely with the risk of developing late-onset AD, the results suggest a possible involvement of apoE3 in the clearance or routing out of Abeta from the central nervous system as one of the mechanisms underlying the pathology of the disease.
Guanylyl cyclase C is a selective marker for metastatic colorectal tumors in human extraintestinal tissues (1996)

Guanylyl cyclase C (GCC) has been detected only in intestinal mucosa and colon carcinoma cells of placental mammals. However, this receptor has been identified in several tissues in marsupials, and its expression has been suggested in tissues other than intestine in placental mammals. Selective expression of GCC by colorectal tumor cells in extraintestinal tissues would permit this receptor to be employed as a selective marker for metastatic disease. Thus, expression of GCC was examined in human tissues and tumors, correlating receptor function with detection by PCR. GCC was detected by ligand binding and catalytic activation in normal intestine and primary and metastatic colorectal tumors, but not in extraintestinal tissues or tumors. Similarly, PCR yielded GCC-specific amplification products with specimens from normal intestine and primary and metastatic colorectal tumors, but not from extraintestinal tissues or tumors. Northern blot analysis employing GCC-specific probes revealed an approximately 4-kb transcript, corresponding to recombinant GCC, in normal intestine and primary and metastatic colorectal tumors, but not in extraintestinal tissues. Thus, GCC is selectively expressed in intestine and colorectal tumors in humans and appears to be a relatively specific marker for metastatic cancer cells in normal tissues. Indeed, PCR of GCC detected tumor cells in blood from some patients with Dukes B colorectal cancer and all patients examined with Dukes C and D colorectal cancer, but not in that from normal subjects or patients with Dukes A colon carcinoma or other nonmalignant intestinal pathologies.
Genetic Design and Statistical Power of Nested Association Mapping in Maize (2008)

We investigated the genetic and statistical properties of the nested association mapping (NAM) design currently being implemented in maize (26 diverse founders and 5000 distinct immortal genotypes) to dissect the genetic basis of complex quantitative traits. The NAM design simultaneously exploits the advantages of both linkage analysis and association mapping. We demonstrated the power of NAM for high-power cost-effective genome scans through computer simulations based on empirical marker data and simulated traits with different complexities. With common-parent-specific (CPS) markers genotyped for the founders and the progenies, the inheritance of chromosome segments nested within two adjacent CPS markers was inferred through linkage. Genotyping the founders with additional high-density markers enabled the projection of genetic information, capturing linkage disequilibrium information, from founders to progenies. With 5000 genotypes, 30-79% of the simulated quantitative trait loci (QTL) were precisely identified. By integrating genetic design, natural diversity, and genomics technologies, this new complex trait dissection strategy should greatly facilitate endeavors to link molecular variation with phenotypic variation for various complex traits.
Mycobacterium tuberculosis CYP130 (2007)

CYP130 is one of the 20 Mycobacterium tuberculosis cytochrome P450 enzymes, only two of which, CYP51 and CYP121, have so far been studied as individually expressed proteins. Here we characterize a third heterologously expressed M. tuberculosis cytochrome P450, CYP130, by UV-visible spectroscopy, isothermal titration calorimetry, and x-ray crystallography, including determination of the crystal structures of ligand-free and econazole-bound CYP130 at a resolution of 1.46 and 3.0A(,) respectively. Ligand-free CYP130 crystallizes in an "open" conformation as a monomer, whereas the econazole-bound form crystallizes in a "closed" conformation as a dimer. Conformational changes enabling the "open-closed" transition involve repositioning of the BC-loop and the F and G helices that envelop the inhibitor in the binding site and reshape the protein surface. Crystal structure analysis shows that the portion of the BC-loop relocates as much as 18A between the open and closed conformations. Binding of econazole to CYP130 involves a conformational change and is mediated by both a set of hydrophobic interactions with amino acid residues in the active site and coordination of the heme iron. CYP130 also binds miconazole with virtually the same binding affinity as econazole and clotrimazole and ketoconazole with somewhat lower affinities, which makes it a plausible target for this class of therapeutic drugs. Overall, binding of the azole inhibitors is a sequential two-step, entropy-driven endothermic process. Binding of econazole and clotrimazole exhibits positive cooperativity that may reflect a propensity of CYP130 to associate into a dimeric structure.
Purification of human butyrylcholinesterase from frozen Cohn fraction IV-4 by ion exchange and Hupresin affinity chromatography (2019)

Human butyrylcholinesterase (HuBChE) is being developed as a therapeutic for protection from the toxicity of nerve agents. An enriched source of HuBChE is Cohn fraction IV-4 from pooled human plasma. For the past 40 years, purification of HuBChE has included affinity chromatography on procainamide-Sepharose. The present report supports a new affinity sorbent, Hupresin, for purification of HuBChE from Cohn fraction IV-4. Nine batches of 70-80 kg frozen Cohn fraction were extracted with water, filtered, and chromatographed on 30 L of Q-Ceramic ion exchange sorbent at pH 4.5. The 4% pure Q-eluent was pumped onto 4.2 L Hupresin, where contaminants were washed off with 0.3 M NaCl in 20 mM sodium phosphate pH 8.0, before 99% pure HuBChE was eluted with 0.1 M tetramethylammonium bromide. The average yield was 1.5 g of HuBChE from 80 kg Cohn paste. Recovery of HuBChE was reduced by 90% when the paste was stored at -20°C for 1 year, and reduced 100% when stored at 4°C for 24h. No reduction in HuBChE recovery occurred when paste was stored at -80°C for 3 months or 3 years. Hupresin and procainamide-Sepharose were equally effective at purifying HuBChE from Cohn fraction. HuBChE in Cohn fraction required 1000-fold purification to attain 99% purity, but 15,000-fold purification when the starting material was plasma. HuBChE (P06276) purified from Cohn fraction was a 340 kDa tetramer of 4 identical N-glycated subunits, stable for years in solution or as a lyophilized product.
Radiolabeled anti-CD33 monoclonal antibody M195 for myeloid leukemias. (1995)

M195, a mouse monoclonal antibody reactive with the early myeloid antigen CD33, has been shown to target leukemia cells in patients and to reduce large leukemic burdens when labeled with 131I. A complementarity-determining region-grafted, humanized version (HuM195) has demonstrated similar targeting of leukemia cells without immunogenicity. We have studied two applications of therapy with 131I-M195. First, to intensify therapy prior to bone marrow transplantation (BMT), we combined 131I-M195 with busulfan and cyclophosphamide. Fifteen patients received first BMT for relapsed or refractory acute myelogenous leukemia or accelerated or blastic chronic myelogenous leukemia; four received second BMT for relapsed chronic or accelerated chronic myelogenous leukemia. Doses of 131I-M195 ranged from 120 to 230 mCi/m2. Few toxicities could be attributed to 131I-M195 therapy, and all patients engrafted. Eighteen patients achieved complete remission. Among those patients receiving first BMT, three have remained in unmaintained remission for 18+ to 29+ months. Six patients relapsed, including one with isolated central nervous system disease 32 months after BMT. Ten patients died in complete remission of transplant-related complications. Second, we studied whether 131I-M195 could reduce minimal residual disease and prolong remission and survival durations safely in patients with relapsed acute promyelocytic leukemia after they attained remission with all-trans-retinoic acid. Seven patients were treated with either 50 or 70 mCi/m2 131I-M195. Toxicity was limited to myelosuppression. As a measure of minimal residual disease, we monitored PML/RAR-alpha mRNA by reverse transcription PCR. Six patients had positive reverse transcription PCR assays prior to receiving 131I-M195; two converted transiently to negative. Median disease-free survival and overall survival of the seven patients were 8 (range, 3-14.5) months and 28 (range, 5.5-43+) months, respectively. This regimen compares favorably with others for relapsed acute promyelocytic leukemia. In an effort to avoid nonspecific cytotoxicity associated with 131I in future trials for minimal residual disease, we have conjugated short-range, alpha particle-emitting radioisotopes to HuM195 using a bifunctional chelate, 2-(p-isothiocyanatobenzyl)-cyclohexyldiethyl-enetriaminep entaacetic acid, with high efficiency and specific activities. 212Bi-HuM195 has demonstrated dose- and specific activity-dependent killing of HL60 cells in vitro. Injection of 213Bi-HuM195 into healthy BALB/c mice produced no effects on weight or viability.
Human serum antibody response to Campylobacter jejuni infection as measured in an enzyme-linked immunosorbent assay (1984)

An enzyme-linked immunosorbent assay was adapted to measure immunoglobulin A (IgA), IgG, and IgM classes of human serum antibody to Campylobacter jejuni. Sera were tested from healthy controls, from ill persons at various intervals after exposure to an epidemiologically implicated vehicle for Campylobacter sp. enteritis, from persons exposed to these same vehicles who remained well, and from persons who chronically drank raw milk. The major antigens in the C. jejuni acid-washed antigen preparations from three different strains all migrated at about 30,000 and 63,000. Persons with Campylobacter enteritis developed rising serum IgA, IgG, and IgM antibodies during the second week after infection; IgG and IgM elevations persisted longer than did IgA. Exposed persons who remained well showed similar, but lower, antibody rises. Chronic raw milk drinkers had elevated IgG levels, but not IgM or IgA levels, whether or not they were acutely exposed to an implicated vehicle.