gebhart/patrepeval huggingface dataset:
Methylation Markers for the Identification of Body Fluids and Tissues from Forensic Trace Evidence (2016)

The identification of body fluids is an essential tool for clarifying the course of events at a criminal site. The analytical problem is the fact that the biological material has been very often exposed to detrimental exogenous influences. Thereby, the molecular substrates used for the identification of the traces may become degraded. So far, most protocols utilize cell specific proteins or RNAs. Instead of measuring these more sensitive compounds this paper describes the application of the differential DNA-methylation. As a result of two genome wide screenings with the Illumina HumanMethylation BeadChips 27 and 450k we identified 150 candidate loci revealing differential methylation with regard to the body fluids venous blood, menstrual blood, vaginal fluid, saliva and sperm. Among them we selected 9 loci as the most promising markers. For the final determination of the methylation degree we applied the SNuPE-method. Because the degree of methylation might be modified by various endogenous and exogenous factors, we tested each marker with approximately 100 samples of each target fluid in a validation study. The stability of the detection procedure is proved in various simulated forensic surroundings according to standardized conditions. We studied the potential influence of 12 relatively common tumors on the methylation of the 9 markers. For this purpose the target fluids of 34 patients have been analysed. Only the cervix carcinoma might have an remarkable effect because impairing the signal of both vaginal markers. Using the Illumina MiSeq device we tested the potential influence of cis acting sequence variants on the methylation degree of the 9 markers in the specific body fluid DNA of 50 individuals. For 4 marker loci we observed such an influence either by sole SNPs or haplotypes. The identification of each target fluid is possible in arbitrary mixtures with the remaining four body fluids. The sensitivity of the individual body fluid tests is in the same range as for the forensic STR-analysis. It is the first forensic body fluid protocol which considers the exogenic and endogenic parameters potentially interfering with the true results.
Remyelination by Oligodendrocytes Stimulated by Antiserum to Spinal Cord (1987)

The new synthesis of myelin and the proliferation of oligodendrocytes was stimulated by serum from syngeneic mice immunized with homogenized spinal cord (SCH). Treatment with this antiserum produced a 10-fold increase in the area of remyelination in spinal cords that had become demyelinated previously as a result of infection by Theiler's murine encephalomyelitis virus. Inflammation was decreased in regions of white matter that showed remyelination. Oligodendrocytes exposed to anti-SCH in vitro incorporated three to five times more [3H]thymidine than resting cells did and expressed more myelin basic protein in their cytoplasm, suggesting stimulation of myelinogenesis. Thus, there is a factor present in anti-SCH antiserum that stimulates central nervous system-type remyelination. This finding may provide clues for the therapy of patients with demyelinating disorders such as multiple sclerosis.
Graded-field microscopy with white light (2006)

We present a general imaging technique called graded-field microscopy for obtaining phase-gradient contrast in biological tissue slices. The technique is based on introducing partial beam blocks in the illumination and detection apertures of a standard white-light widefield transillumination microscope. Depending on the relative aperture sizes, one block produces phase-gradient contrast while the other reduces brightfield background, allowing a full operating range between brightfield and darkfield contrast. We demonstrate graded-field imaging of neurons in a rat brain slice.
A medical nutriment has supportive value in the treatment of colorectal cancer (2003)

MSC (Avemar) is a medical nutriment of which preclinical and observational clinical studies suggested an antimetastatic activity with no toxicity. This open-label cohort trial has compared anticancer treatments plus MSC (9 g once daily) vs anticancer treatments alone in colorectal patients, enrolled from three oncosurgical centres; cohort allocation was on the basis of patients' choice. Sixty-six colorectal cancer patients received MSC supplement for more than 6 months and 104 patients served as controls (anticancer therapies alone): no statistical difference was noted in the time from diagnosis to the last visit between the two groups. End-point analysis revealed that progression-related events were significantly less frequent in the MSC group (new recurrences: 3.0 vs 17.3%, P<0.01; new metastases: 7.6 vs 23.1%, P<0.01; deaths: 12.1 vs 31.7%, P<0.01). Survival analysis showed significant improvements in the MSC group regarding progression-free (P=0.0184) and overall survivals (P=0.0278) probabilities. Survival predictors in Cox's proportional hazards were UICC stage and MSC treatment. Continuous supplementation of anticancer therapies with MSC for more than 6 months is beneficial to patients with colorectal cancer in terms of overall and progression-free survival.
Quadrupole ion traps (2009)

The extraordinary story of the three-dimensional radiofrequency quadrupole ion trap, accompanied by a seemingly unintelligible theoretical treatment, is told in some detail because of the quite considerable degree of commercial success that quadrupole technology has achieved. The quadrupole ion trap, often used in conjunction with a quadrupole mass filter, remained a laboratory curiosity until 1979 when, at the American Society for Mass Spectrometry Conference in Seattle, George Stafford, Jr., of Finnigan Corp., learned of the Masters' study of Allison Armitage of a combined quadrupole ion trap/quadrupole mass filter instrument for the observation of electron impact and chemical ionization mass spectra of simple compounds eluting from a gas chromatograph. Stafford developed subsequently the mass-selective axial instability method for obtaining mass spectra from the quadrupole ion trap alone and, in 1983, Finnigan Corp. announced the first commercial quadrupole ion trap instrument as a detector for a gas chromatograph. In 1987, confinement of ions generated externally to the ion trap was demonstrated and, soon after, the new technique of electrospray ionization was shown to be compatible with the ion trap.
Electrooptic Liquid Crystal Devices: Principles and Applications (1972)

The principles governing the operation and performance of devices utilizing mesomorphic anisotropic fluids (liquid crystals) am reviewed and systematized according to materials, dielectric type, and mode of operation. A further breakdown is made into whether the phenomenon is a change in optical density (color), diffraction, or scattering. Some of the possible directions for optical applications are indicated for which liquid crystals may be unique. Performance, life, circuit parameters, and drive characteristics are considered.
Fairness in routing and load balancing (2003)

We consider the issue of network routing subject to explicit fairness conditions. The optimization of fairness criteria interacts in a complex fashion with the optimization of network utilization and throughput; in this work, we undertake an investigation of this relationship through the framework of approximation algorithms. In this work we consider the problem of selecting paths for routing so as to provide a bandwidth allocation that is as fair as possible (in the max-min sense). We obtain the first approximation algorithms for this basic optimization problem, for single-source unsplittable routings in an arbitrary directed graph. Special cases of our model include several fundamental load balancing problems, endowing them with a natural fairness criterion to which our approach can be applied. Our results form an interesting counterpart to the work of Megiddo (1974), who considered max-min fairness for single-source fractional flow. The optimization problems in our setting become NP-complete, and require the development of new techniques for relating fractional relaxations of routing to the equilibrium constraints imposed by the fairness criterion.
Alternate operating strategies for Hot Dry Rock geothermal reservoirs (1991)

Flow testing and heat extraction experiments in prototype Hot Dry Rock (HDR) geothermal reservoirs have uncovered several challenges which must be addressed before commercialization of the technology is possible. Foremost among these is the creation of a reservoir which simultaneously possesses high permeability pathways and a large volume of fractured rock. The current concept of heat extraction -- a steady state circulation system with fluid pumping from the injection well to a single, low pressure production well -- may limit our ability to create heat extraction systems which meet these goals. A single injection well feeding two production wells producing fluid at moderate pressures is shown to be a potentially superior way to extract heat. Cyclic production is also demonstrated to have potential as a method for sweeping fluid through a larger volume of rock, thereby inhibiting flow channeling and increasing reservoir lifetime. 10 refs., 4 figs., 2 tabs.
Key semantics extraction by dependency tree mining (2005)

We propose a new text mining system which extracts characteristic contents from given documents. We define Key semantics as characteristic sub-structures of syntactic dependencies in the given documents, and consider the following three tasks in this paper: 1)Key semantics extraction: extracting characteristic syntactic dependency structures not only as ordered trees but also as unordered trees and free trees, 2)Redundancy reduction: from the result of extraction, deleting redundant dependency structures such as sub-structures or equivalent structures of the others, and 3)Phrase/sentence reconstruction: generating a phrase or sentence in a natural language corresponding to the extracted structure.Our system is a combination of natural language processing techniques and tree mining techniques. The system consists of the following five units: 1) syntactic dependency analysis unit, 2) input filters, 3) characteristic ordered subtree extraction unit, 4) output filters, and 5) phrase/sentence reconstruction unit. Although ordered trees are extracted in the third unit, the overall behavior of the system can be switched into the extraction of ordered trees, unordered trees, or free trees depending on which of the input filters is/are applied in the second step. The output filters delete redundant trees from the extraction result for efficient knowledge discovery. Finally, phrases or sentences corresponding to the extracted subtrees are reconstructed by utilizing the input documents.We demonstrate the validity of our system by showing experimental results using real data collected at a help desk and TDT pilot corpus.
Alterations of ocular nitric oxide synthase in human glaucoma. (1995)

Abnormalities in NO or NO-containing cells occur in POAG. These abnormalities may be causally related to glaucoma or may be a manifestation of the disease or its treatment. In either case, such alterations, together with recent pharmacologic studies showing that NO-mimicking nitrovasodilators alter IOP, indicate that NO has relevance to the course, treatment, or both, or some forms of this disease.
Plasma levels of progesterone, Provera, oestradiol-17β, and 13,14-dihydro-15-keto-prostaglandin F in cows treated with Provera-impregnated intravaginal sponges (1979)

Plasma concentrations of progesterone and Provera were measured daily in 3 cows during 21 days of treatment with Provera-impregnated intravaginal sponges. Plasma concentrations of oestradiol-17beta and 13,14-dihydro-15-keto-prostaglandin F (PGFM) were measured hourly from 5 h before until 62 h after sponge removal. The profile of progesterone concentrations indicated that luteolysis occurred at the expected time (Days 19 to 23 of the cycle), even though plasma Provera concentrations were 150-250 pg/ml. The occurrence of peaks of PGFM after sponge withdrawal suggests that PGF-2alpha release is stimulated by falling levels of progestagen.
A Strategy for Shuffling Numerous Bacillus thuringiensis Crystal Protein Domains (2004)

Bacillus thuringiensis that produce Cry1Ba are toxic to Lucilia cuprina Wiedemann blow fly maggots in vivo, and when applied in quantity to sheep fleece, provide up to 6 wk protection against flystrike in the field. These strains also are toxic to Epiphyas postvittana (Walker) light brown apple moth caterpillars. B. thuringiensis expressing Cry1Db are toxic only to E. postvittana. When Cry1Ba and Cry1Db proteins are expressed within Escherichia coli, the recombinant bacteria have the same toxicity profile as the wild-type B. thuringiensis strain. In an effort to develop a Cry protein with improved blow fly toxicity, three different internal regions of Cry1Ba coding DNA, encoding all or part of domains I, II and III respectively were systematically exchanged with the corresponding region from a pool of other Cry protein coding DNAs. The chimeric products were then expressed in recombinant E. coli, and the resulting bacteria assayed for toxicity on L. cuprina and E. postvittana. Clones having insecticide bioactivity were characterized to identify the source of the replacement Cry domain. Despite successfully expressing a large number and variety of chimeric proteins within E. coli, many with measurable insecticidal activity, none of the chimeras had greater potency against L. cuprina than the wild-type Cry1Ba. Chimeric replacements involving domains I and II were rarely active, whereas a much higher proportion of domain III chimeras had some bioactivity. We conclude that shuffling of Cry coding regions through joining at the major conserved sequence motifs is an effective means for the production of a diverse number of chimeric Cry proteins but that such toxins with enhanced bioactive properties will be rare or nonexistent.
Hydropathic influences on the quantification of equine heart cytochromec using relative ion abundance measurements by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (1999)

The number of publications documenting the utility of electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) for the analysis of biological molecules has increased in geometric proportion spanning diverse areas of research. Currently, we are investigating the capabilities of ESI-FTICR to quantify relative molecular ion abundances of biopolymers, an area which has not been explored rigorously. We present here the results of an investigation of a two-component system utilizing equine heart cytochrome c (EH) as the analyte and bovine heart cytochrome c (BH) as a constant concentration internal standard. As these compounds are relatively large ( approximately 12 kDa), they will become multiply charged during the electrospray process. Using appropriate solution and instrument conditions, the 7(+) and 8(+) charge states were enhanced for both cytochrome c species. We report that using the average of the ion abundances for the two charge states observed for each species, the linear curve (intensity ratio vs concentration ratio) had a dynamic range of 0.045-2.348 microM (1.7 orders of magnitude). Linear least-squares regression analysis (LLSRA) of these averaged ion abundances (i.e. [(EH + 7H(+))(7+)/(BH + 7H(+))(7+) + (EH + 8H(+))(8+)/(BH + 8H(+))(8+)]/2) yielded the equation y = 1.005x + 0.027. The slope of the line with its calculated precision, reported as one standard deviation, is 1.005 +/- 0.0150, which is statistically ideal (i.e. equal to unity). However, LLSRA of the ion abundances of the two individual charge states were significantly different (i.e. the slope of the (EH + 7H(+))(7+)/(BH + 7H(+))(7+) peak intensity ratio vs molar ratio data was 0.885 +/- 0.0183 and the slope of the (EH + 8H(+))(8+)/(BH + 8H(+))(8+) data was 1.125 +/- 0.0308). We attribute this difference to the variation in primary amino acid sequence for the two cytochrome c species. Both have 104 amino acids, but there are three residue substitutions between EH and BH; one of the substitutions confers an additional basic site to EH. While this extra basic residue may imply an additional charging site, the low charge states observed under the solution conditions employed indicate that most (>66%) basic sites are not protonated. However, the extra basic site also renders EH slightly more hydrophilic. These results present significant considerations when choosing internal standards for the quantification of large proteins by ESI-FTICR-MS and demonstrate that relative molecular ion signals in FTICR can be used to quantify macromolecular species in the nanomolar regime.
<i>Stability and Fluorescence Quantum Yield of CdSe–ZnS Quantum Dots—Influence of the Thickness of the ZnS Shell</i> (2008)

We investigated the correlation between the thickness of the ZnS shell of CdSe-ZnS quantum dots (QDs), the stability of the particles, and the fluorescence quantum yield. As a measure for stability, a new shell quality test was developed. This test is based on the reaction of the QDs with photochemically formed thiophenol radicals and communicates an imperfect ZnS shell by a rapid and complete loss of fluorescence. The quantum yield increases from less than 5% for unshelled CdSe up to 50%, with an increase in ZnS shell thickness up to 0.6-0.8 nm. At the same time, the particles become significantly more stable, as revealed by the shell test.
Long-lasting Disease Stabilization in the Absence of Toxicity in Metastatic Lung Cancer Patients Vaccinated with an Epitope Derived from Indoleamine 2,3 Dioxygenase (2013)

Abstract Purpose: To investigate targeting of indoleamine 2,3 dioxygenase (IDO) enzyme using a synthetic peptide vaccine administered to patients with metastatic non–small cell lung cancer (NSCLC). Experimental Design: In a clinical phase I study, we treated 15 HLA-A2–positive patients with stage III–IV NSCLC in disease stabilization after standard chemotherapy. Patients were treated with imiquimod ointment and subcutaneous vaccinations (100 μg IDO5 peptide, sequence ALLEIASCL, formulated in 900 μL Montanide). Primary endpoint was toxicity. Clinical benefit and immunity were assessed as secondary endpoints. Results: No severe toxicity was observed. One patient developed a partial response (PR) after one year of vaccine treatment, whereas long-lasting stable disease (SD) ≥ 8.5 months was demonstrated in another six patients. The median overall survival (OS) was 25.9 months. Patients demonstrated significant improved OS (P = 0.03) when compared with the group of patients excluded because of HLA-A2 negativity. IDO-specific CD8+ T-cell immunity was demonstrated by IFN-γ Elispot and Tetramer staining. Fluorescence-activated cell sorting analyses demonstrated a significant reduction of the Treg population (P = 0.03) after the sixth vaccine (2.5 months) compared with pretreatment levels. Furthermore, expression of IDO was detected in nine of ten tumor biopsies by immunohistochemistry. High-performance liquid chromatography analyses of kynurenine/tryptophan (Kyn/Trp) ratio in sera were performed. In long-term analyses of two clinical responding patients, the ratio of Kyn/Trp remained stable. Conclusions: The vaccine was well tolerated with no severe toxicity occurring. A median OS of 25.9 months was demonstrated and long-lasting PR+SD was seen in 47% of the patients. Clin Cancer Res; 20(1); 221–32. ©2013 AACR.
REAL-TIME MIXED REALITY WITH GPU TECHNIQUES (2008)

In this paper, we propose a combination of modern GPU-based methods that are able to generate high-quality, interactive real-time rendering for augmented and mixed reality applications. We also present a new approach to estimate surface reflection functions and materials from images using genetic algorithms.
Hg<sup>II</sup> Ion Specifically Binds with T:T Mismatched Base Pair in Duplex DNA (2010)

Metal-mediated base pair formation, resulting from the interaction between metal ions and artificial bases in oligonucleotides, has been developed for its potential application in nanotechnology. We have recently found that the T:T mismatched base pair binds with Hg(II) ions to generate a novel metal-mediated base pair in duplex DNA. The thermal stability of the duplex with the T-Hg-T base pair was comparable to that of the corresponding T:A or A:T. The novel T-Hg-T base pair involving the natural base thymine is more convenient than the metal-mediated base pairs involving artificial bases due to the lack of time-consuming synthesis. Here, we examine the specificity and thermodynamic properties of the binding between Hg(II) ions and the T:T mismatched base pair. Only the melting temperature of the duplex with T:T and not of the perfectly matched or other mismatched base pairs was found to specifically increase in the presence of Hg(II) ions. Hg(II) specifically bound with the T:T mismatched base pair at a molar ratio of 1:1 with a binding constant of 10(6) M(-1), which is significantly higher than that for nonspecific metal ion-DNA interactions. Furthermore, the higher-order structure of the duplex was not significantly distorted by the Hg(II) ion binding. Our results support the idea that the T-Hg-T base pair could eventually lead to progress in potential applications of metal-mediated base pairs in nanotechnology.
Supramolekulare Strukturen bei Polymeren: Ein Weg zu „Intelligenten” Materialien? (1992)

Abstract Metallhaltige Polymermicellen und oberflächenmodifizierte Mikrolatices sind zwei Beispiele für supramolekulare Systeme aus synthetischen Polymeren mit funktionellen Gruppen. Über den technischen Nutzen solcher Systeme darf spekuliert werden.
Lipid‐lowering properties of TAK‐475, a squalene synthase inhibitor, <i>in vivo</i> and <i>in vitro</i> (2003)

1. Squalene synthase is the enzyme that converts farnesyl pyrophosphate to squalene in the cholesterol biosynthesis pathway. We examined the lipid-lowering properties of 1-[[(3R,5S)-1-(3-acetoxy-2,2-dimethylpropyl)-7-chloro-5-(2,3-dimethoxyphenyl)-2-oxo-1,2,3,5-tetrahydro-4,1-benzoxazepin-3-yl]acetyl]piperidine-4-acetic acid (TAK-475), a novel squalene synthase inhibitor. 2. TAK-475 inhibited hepatic cholesterol biosynthesis in rats (ED(50), 2.9 mg kg(-1)) and showed lipid-lowering effects in beagle dogs, marmosets, cynomolgus monkeys and Wistar fatty rats. 3. In marmosets, TAK-475 (30, 100 mg kg(-1), p.o., for 4 days) lowered both plasma non-high-density lipoprotein (HDL) cholesterol and triglyceride, but did not affect plasma HDL cholesterol. On the other hand, atorvastatin (10, 30 mg kg(-1), p.o., for 4 days) lowered the levels of all these lipids. A correlation between decrease in triglyceride and increase in HDL cholesterol was observed, and TAK-475 increased HDL cholesterol with a smaller decrease in triglyceride than did atorvastatin. 4. TAK-475 (60 mg kg(-1), p.o., for 15 days) suppressed the rate of triglyceride secretion from the liver in hypertriglyceridemic Wistar fatty rats, which show an enhanced triglyceride secretion rate from the liver compared with their lean littermates. 5. In HepG2 cells, TAK-475 and its pharmacologically active metabolite, T-91485, increased the binding of (125)I-low-density lipoprotein (LDL) to LDL receptors. 6. These results suggest that TAK-475 has clear hypolipidemic effects in animals via inhibition of hepatic triglyceride secretion and upregulation of LDL receptors, and that TAK-475 might increase HDL cholesterol by decreasing triglyceride. Thus, TAK-475 is expected to be useful for the treatment of dyslipidemia.