gebhart/patrepeval huggingface dataset:
Inhibition of collagenase type I expression by psoralen antisense oligonucleotides in dermal fibroblasts (1995)

Type I collagenase plays an important role in both tumor metastasis and the remodeling of connective tissue in normal human skin, during wound healing, for example, and may participate in the pathophysiology of some dermatological diseases such as skin cancer and a chronic blistering disease, recessive dystrophic epidermolysis bullosa. In an effort specifically to inhibit collagenase expression, we have designed phosphorothioate antisense oligonucleotides, linked at the 5' ends with photoreactive 4'-(hydroxyethoxymethyl)-4,5',8-trimethyl-psoralen (HMT), and directed them against the 5' end of the collagenase mRNA. Two antisense-HMT molecules targeting a region overlapping the initiation codon were compared. Only one contained the HMT moiety targeting a 5'TpA on its complementary sense strand, and we observed greater than 50-fold improvement on the cross-linking of this antisense oligonucleotide to its target sequence after ultraviolet A (UVA) irradiation. Likewise, sequence complementary to the 5'TpA target was also required to demonstrate specific inhibition of in vitro translation of collagenase mRNA. Tissue culture experiments, conducted by incubation of collagenase-specific antisense-HMT oligonucleotides with fibroblasts in monolayer or in 3-dimensional dermal equivalents, showed lowered collagenase levels 24 h after UVA irradiation as compared to controls. Initial screening of antisense oligomers for specific hybridization and photo-cross-linking is a useful step in the design of antisense oligonucleotides, and allowed us to design an HMT-linked antisense phosphorothioate oligonucleotide that specifically inhibits the expression of fibroblastic collagenase.
Egg Yolk Antibodies, State of the Art and Future Prospects. (1996)

Immunization of chickens and extraction of antibodies from egg yolk belongs to the alternative methods since the animals suffering is reduced by non-invasive antibody-sampling. Also, the number of animals needed to produce a certain amount of antibody can be reduced since chickens produce a significant higher antibody quantity than rabbits. Despite its several advantages this technology (IgY-technology) is rather scarcely used. Traditional behavior as well as limited or no information at all may hamper a broader acceptance at present. However, significant arguments exist in chicken housing, the choice of appropriate IgY-extraction methods and a lack of information regarding the use of IgY-antibodies. This paper intends to give a short introduction in the IgY-technology, to briefly discuss the state of the art and to inform on recent developments and discussions in this field. The suitability of IgY for special fields of application (as a result of the structural differences between IgY and IgG) is emphasized (e.g. assays combining IgG and IgY, immunization of chickens against highly conserved anti-genes). In addition, it is stressed that the IgY-technology as an alternative method can particularly integrate requirements of animal protection (reduce, replace, refine), science (characteristics of avian immune system and resulting properties of IgY) and economy (amount of IgY produced from one chicken).
Amino acid sequence of human liver cathepsin B (1985)

The complete amino acid sequence of cathepsin B (EC 3.4.22.1) from human liver was determined. The 252‐residue sequence was obtained by automated solid‐phase Edman degradation of the light and heavy chain resulting from limited proteolysis of the single‐chain enzyme and of fragments produced by cyanogen bromide and enzymatic cleavage of the heavy chain. Human liver cathepsin B has 83.7% identical residues with the corresponding enzyme from rat liver. Comparison of both mammalian cathepsin B sequences with the sequence of papain provides further evidence that lysosomal and plant cysteine proteinases have evolved from a common ancestor and share a similar catalytic mechanism.
An underestimated combination of opposites resulting in enhanced thrombotic tendency (2005)

Heterozygous carriers of factor V (FV) Leiden who also carry FV deficiency often develop venous thromboembolism, but the thrombosis risk associated with this rare condition (pseudohomozygous activated protein C resistance) is still unclear. The thrombosis risk of genetically characterized pseudohomozygotes (n = 6) was compared with that of FV Leiden heterozygotes (n = 683) and homozygotes (n = 50) recruited within a large cohort study on familial thrombophilia. Both thrombin generation and Kaplan-Meier thrombosis-free survival analyses were performed in different FV genotype groups. FV Leiden pseudohomozygotes showed significantly higher thrombosis risk than heterozygotes. The thrombin generation test in pseudohomozygotes showed a pattern similar to homozygotes. Accordingly, early thrombotic manifestations occurred in pseudohomozygotes at a similar rate as in homozygotes. Thus, failure to recognize FV deficiency in FV Leiden heterozygotes may result in an underestimate of the thrombosis risk and inadequate management of affected patients.
The secondary structure of influenza A M2 transmembrane domain A circular dichroism study (1992)

Using circular dichroism, this study investigated the secondary structure of the influenza A M2 transmembrane domain. When reconstituted into 1,2-dioleoyl-sn-glycero-3-phosphocholine liposomes, the M2 transmembrane domain was found to adopt a predominantly alpha-helical secondary structure which was unaffected by both temperature and the addition of 1-aminoadamantane hydrochloride. Reconstitution into 1,2-dioleoyl-sn-glycero-3-phosphoglycerol liposomes resulted in a marked decrease in helical content.
Investigating levodopa-induced dyskinesias in the parkinsonian primate. (2000)

Research into the cause of dyskinesias arising from levodopa treatment has been vexingly limited, partly due to the lack of an inexpensive and widely available animal model. Rodents do not develop levodopa-induced dyskinesias in a clinically recognizable form. However, nonhuman primates with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced parkinsonism readily develop levodopa-induced dyskinesias that are virtually indistinguishable from those seen in patients with Parkinson's disease. We have developed and validated a five-point Global Primate Dyskinesia Rating Scale to accurately measure these dyskinesias. Monkeys with MPTP-induced parkinsonism were then investigated to evaluate the relationship between dyskinesias, parkinsonism and severity of the nigrostriatal lesion. All parkinsonian animals were responsive to levodopa, and developed dyskinesias within 2-3 days of levodopa administration. Monkeys treated with only a single injection of MPTP also developed dyskinesias, even though they were not parkinsonian. It would appear that there is a different threshold of striatal dopamine depletion for parkinsonism and dyskinesias in the monkey. Finally, three hypotheses, put forward to explain the genesis of dyskinesias, are reviewed, and various experimental approaches suggested for each.
Water-in-CO2 Microemulsions Studied by Small-Angle Neutron Scattering (1997)

Aggregate structures in water-in-CO2 microemulsions were studied by high-pressure small-angle neutron scattering (SANS). With liquid CO2 at 15 °C, the partially fluorinated, di-chain surfactant bis(1H,1H,5H-octafluoro-n-pentyl) sodium sulfosuccinate (di-HCF4) stabilized single-phase microemulsions at pressures above ∼400 bar. The maximum water loading (w) investigated was 30 ([water]/[di-HCF4]), representing formation of relatively large water droplets in the microemulsion. Between w = 5 and 30, the SANS data were consistent with a model for attractive polydisperse spherical droplets. A linear relationship between the water droplet radius (Rc) and w was found, which gave an apparent head group area for the surfactant of 87 Å2 at the water−CO2 interface. In Winsor II type microemulsions the value of Rc, measured in the presence of excess water, increased with pressure from 36 Å at 400 bar to 56 Å at 550 bar.
Program-based static allocation policies for highly parallel computers (2002)

Static space sharing is a promising processor allocation strategy for highly-parallel computers. Parallel jobs or tasks are allocated fixed distinct subsets of processors. Thread scheduling can be carried out directly by the applications so as to reduce its cost, interference among jobs is reduced, and a wide range of compiler and runtime optimizations, including static data distribution and binding, are possible. The fundamental problem with static space sharing is processor fragmentation. In this paper we study and compare several no-folding and unlimited-folding program-based static space sharing processor allocation policies. A job is always allocated the number of processors it requests in the no-folding schemes, whereas it can be allocated any number of processors that does not exceed its request in the unlimited-folding policies. The results of a detailed simulation study show that unlimited folding is superior to no folding under medium to high system loads when the speedup curves of applications are significantly sublinear. However, no folding is superior under most or all loads, depending on workload characteristics, when the applications are highly efficient. The unlimited-folding policies suffer more processor fragmentation under most loads, but they exploit the increase in efficiency that typically results when a job executes on fewer processors. In addition, we study schemes based on the assumption that the execution times of jobs when they execute on number of processors they request are known. The results show that giving priority to shorter jobs can result in significant improvement in mean response times.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Factors influencing the stability of live oral attenuated bacterial vaccines. (1996)

Live oral attenuated vaccines against typhoid fever (Salmonella typhi Ty21a) and cholera (Vibrio cholerae CVD 103-HgR) have been licensed for human use. Vaccine potency is dependent upon each dose containing a minimum number of viable organisms and galenic parameters. To ensure long-term stability, such vaccines must be stored at 5 degrees C +/- 3 degrees C. However, exposure to ambient temperatures (25 degrees C) for short periods of time (< 7 days) does not compromise vaccine potency. Brief exposures (< or = 24 hours) to temperatures as high as 37 degrees C will also not render the vaccine unsuitable for use. The Ty21a vaccine is available either as enteric-coated capsules or as a "liquid formulation", while CVD 103-HgR is presented only in the latter form. Each galenic formulation presents unique challenges with regard to the production of stable vaccines. Residual moisture, excipients, and processing temperatures during manufacturing were all found to markedly affect vaccine stability.
Identification of a Transcriptional Activator (ChnR) and a 6-Oxohexanoate Dehydrogenase (ChnE) in the Cyclohexanol Catabolic Pathway in Acinetobacter sp. Strain NCIMB 9871 and Localization of the Genes That Encode Them (1999)

We identified chnR, a gene encoding an AraC-XylS type of transcriptional activator that regulates the expression of chnB, the structural gene for cyclohexanone monooxygenase (CHMO) in Acinetobacter sp. strain NCIMB 9871. The gene sequence of chnE, which encodes an NADP(+)-linked 6-oxohexanoate dehydrogenase, the enzyme catalyzing the fifth step of cyclohexanol degradation, was also determined. The gene arrangement is chnB-chnE-chnR. The predicted molecular masses of the three polypeptides were verified by radiolabeling by using the T7 expression system. Inducible expression of cloned chnB in Escherichia coli depended upon the presence of chnR. A transcriptional chnB::lacZ fusion experiment revealed that cyclohexanone induces chnB expression in E. coli, in which a 22-fold increase in activity was observed.
A 24 km fiber-based discretely signaled continuous variable quantum key distribution system (2009)

We report a continuous variable key distribution system that achieves a final secure key rate of 3.45 kilobits/s over a distance of 24.2 km of optical fiber. The protocol uses discrete signaling and post-selection to improve reconciliation speed and quantifies security by means of quantum state tomography. Polarization multiplexing and a frequency translation scheme permit transmission of a continuous wave local oscillator and suppression of noise from guided acoustic wave Brillouin scattering by more than 27 dB.
Tumor-Associated Macrophages Promote Invasion while Retaining Fc-Dependent Anti-Tumor Function (2012)

Tumor-associated macrophages (TAMs) have been shown to promote tumor progression, and increased TAM infiltration often correlates with poor prognosis. However, questions remain regarding the phenotype of macrophages within the tumor and their role in mAb-dependent cytotoxicity. This study demonstrates that whereas TAMs have protumor properties, they maintain Fc-dependent anti-tumor function. CD11b(+)CD14(+) TAMs isolated from primary human breast tumors expressed activating FcγRs. To model breast cancer TAMs in vitro, conditioned medium from breast cancer cells was used to drive human peripheral monocyte differentiation into macrophages. Tumor-conditioned macrophages were compared with in vitro derived M1 and M2a macrophages and were found to promote tumor cell invasion and express M2a markers, confirming their protumor potential. However, unlike M2a macrophages, tumor-conditioned macrophages expressed FcγRs and phagocytosed tumor cells in the presence of a tumor Ag-targeting mAb, unmasking an underappreciated tumoricidal capacity of TAMs. In vivo macrophage depletion reduced the efficacy of anti-CD142 against MDA-MB-231 xenograft growth and metastasis in SCID/beige mice, implicating a critical role for macrophages in Fc-dependent cell killing. M-CSF was identified in tumor-conditioned media and shown to be capable of differentiating macrophages with both pro- and anti-tumor properties. These results highlight the plasticity of TAMs, which are capable of promoting tumor progression and invasion while still retaining tumoricidal function in the presence of tumor-targeting mAbs.
Regression of extranodal natural killer/T-cell lymphoma, nasal type with denileukin diftitox (Ontak®) and bexarotene (Targretin®): report of a case (2006)

Denileukin diftitox (Ontak) is a fusion protein comprising a diphtheria toxin and an interleukin (IL)-2 moiety that specifically targets CD25 (IL-2 receptor)-positive tumour cells. We report a patient with rapidly progressive Epstein-Barr virus-positive nasal type extranodal natural killer/T-cell lymphoma (extranodal NKTCL), treated with a combination of denileukin diftitox (Ontak) and oral bexarotene (Targretin). A significant regression of the cutaneous tumours was observed already after the first cycle of denileukin diftitox and was maintained for a period of 5 months with monthly cycles of denileukin diftitox. The treatment was well tolerated. Following this response the patient decided to stop the treatment. He was then followed by his oncologist and lost from dermatological follow-up. Shortly after treatment withdrawal the disease progressed and the patient received one cycle of doxorubicin (Caelyx). He died from septic shock syndrome 2 months later. To our knowledge this is the first case of extranodal NKTCL treated with denileukin diftitox and bexarotene. A striking, albeit transient, response occurred with this therapy. Combination treatment with denileukin diftitox and bexarotene should be further assessed in this aggressive type of cutaneous lymphoma.
Enhancement of Schottky barrier height to n-GaAs using NiAl, NiAl/Al/Ni, and Ni/Al/Ni layer structures (1994)

The Schottky barrier height of NiAl/n-GaAs, NiAl/Al/Ni/n-GaAs, and Ni/Al/Ni/n-GaAs diodes has been studied by the current–voltage (I–V) and the capacitance–voltage (C–V) techniques. A NiAl alloy with 50 at. % Al was sputter deposited. An overall concentration of 50 at. % Al in NiAl/Al/Ni/n-GaAs contact structure, and two different overall concentrations of 25 and 60 at. % Al in Ni/Al/Ni/n-GaAs contact structure were prepared by sputter depositing different thicknesses of Ni and Al. An enhancement of the Schottky barrier height ranging from 0.1 to 0.13 eV was observed for each of the above contacts. The maximum barrier heights range from 0.95 to 0.98 eV for both the alloy and layered structure contacts, with ideality factors smaller than or equal to 1.1. The interfacial stability between the contacts and GaAs has been examined by cross-sectional transmission electron microscopy, glancing angle x-ray diffraction, and scanning Auger microscopy. A planar interface between contacts and GaAs was observed for both the alloy and layered contacts. A regrowth mechanism has been demonstrated to explain the enhancement of Schottky barrier height for these contacts.
An implantable cardioverter defibrillator but not amiodarone reduced risk of death in congestive heart failure (2006)

：Seventy eight patientssuspected of intrauterine adhesion (IUA) were scanned with two-dimensional (2D) andthree-dimensional (3D) transvaginal uhrasonography, the results were analyzed withhysteroscopic findings as the gold standard. The sensitivity, specificity, accuracy,positive predictive value and negative predictive value of three-dimensional transvaginalultrasonography in diagnosis of IUA were 97% (58/60), 18/18, 97% (76/78), 100% (58/58) and90% (18/20). Three-dimensional transvaginal ultrasonography was more accurate in diagnosisof IUA than two-dimensional ultrasonography ( P < 0. 01 ),and the IUA classificationand grading with three-dimensional transvaginal ultrasonography was better correlated withhysteroscopic findings.
Accuracy of Respiratory Inductive Plethysmograph over Wide Range of Rib Cage and Abdominal Compartmental Contributions to Tidal Volume in Normal Subjects and in Patients with Chronic Obstructive Pulmonary Disease (1984)

We assessed the accuracy of the respiratory inductive plethysmograph in the supine position to spirometry by the two-body position, least squares calibration and single-body position, isovolume calibration procedures. The comparison was carried out simultaneously in normal subjects breathing naturally and with voluntarily controlled abdominal or thoracic breathing, and in patients with COPD breathing naturally and with voluntarily controlled abdominal breathing patterns. In both groups, there was no significant difference in estimation of tidal volume between the 2 calibration procedures for the various breathing patterns. There was greater deviation from spirometric tidal volume values for both calibration methods in patients with COPD during abdominal than during natural breathing. In the normal subjects, agreement between the rib cage and abdominal partitioning of tidal volume for both calibration methods was good, but in the patients with COPD there was greater variability. In normal subjects, over a wide range of rib cage and abdominal compartmental contributions to tidal volume, either calibration procedure appears satisfactory. For patients with COPD, if large changes occur in the distribution of rib cage and abdominal contributions to tidal volume, then validation of respiratory inductive plethysmography to spirometry must be rechecked.
Introduction to Computational Biology: Maps, Sequences and Genomes. (1998)

Preface Introduction Molecular Biology Mathematics, Statistics, and Computer Science Some Molecular Biology DNA and Proteins The Central Dogma The Genetic Code Transfer RNA and Protein Sequences Genes Are Not Simple Biological Chemistry Restriction Maps Introduction Graphs Interval Graphs Measuring Fragment Sizes Multiple Maps Double Digest Problem Classifying Multiple Solutions Algorithms for DDP Algorithms and Complexity DDP is N P-Complete Approaches to DDP Simulated Annealing: TSP and DDP Mapping with Real Data Cloning and Clone Libraries A Finite Number of Random Clones Libraries by Complete Digestion Libraries by Partial Digestion Genomes per Microgram Physical Genome Maps: Oceans, Islands, and Anchors Mapping by Fingerprinting Mapping by Anchoring An Overview of Clone Overlap Putting It Together Sequence Assembly Shotgun Sequencing Sequencing by Hybridization Shotgun Sequencing Revisited Databases and Rapid Sequence Analysis DNA and Protein Sequence Databases A Tree Representation of a Sequence Hashing a Sequence Repeats in a Sequence Sequence Comparison by Hashing Sequence Comparison with at most l Mismatches Sequence Comparison by Statistical Content Dynamic Programming Alignment of Two Sequences The Number of Alignments Shortest and Longest Paths in a Network Global Distance Alignment Global Similarity Alignment Fitting One Sequence into Another Local Alignment and Clumps Linear Space Algorithms Tracebacks Inversions Map Alignment Parametric Sequence Comparisons Multiple Sequence Alignment The Cystic Fibrosis Gene Dynamic Programming in r-Dimensions Weighted-Average Sequences Profile Analysis Alignment by Hidden Markov Models Consensus Word Analysis Probability and Statistics for Sequence Alignment Global Alignment Local Alignment Extreme Value Distributions The Chein-Stein Method Poisson Approximation and Long Matches Sequence Alignment with Scores Probability and Statistics for Sequence Patterns A Central Limit Theorem Nonoverlapping Pattern Counts Poisson Approximation Site Distributions RNA Secondary Structure Combinatorics Minimum Free-energy Structures Consensus folding Trees and Sequences Trees Distance Parsimony Maximum Likelihood Trees Sources and Perspectives Molecular Biology Physical Maps and Clone Libraries Sequence Assembly Sequence Comparisons Probability and Statistics RNA Secondary Structure Trees and Sequences References Problem Solutions and Hints Mathematical Notation Algorithm Index Author Index Subject Index
Isolation and deduced amino acid sequence of the gene encoding gp115, a yeast glycophospholipid-anchored protein containing a serine-rich region (1991)

gp115 is a N- and O-glycosylated protein of Saccharomyces cerevisiae. It is also modified by addition of glycosylphosphatidylinositol, which anchors the protein to the plasma membrane. The gene encoding gp115 (GGP1) has been cloned by a two-step procedure. By an immunoscreening of a yeast genomic DNA library in the expression vector lambda gt11, a 3'-terminal 0.9-kilobase portion of the gene has been isolated and then used as a molecular probe to screen a yeast genomic DNA library in YEp24. In this way, the whole GGP1 gene has been cloned. Its identity with the gp115 gene has been confirmed by gene disruption, which has also indicated that the function of gp115 is not essential for cell viability. The features of the sequence are also entirely consistent with it corresponding to the gp115 gene. The nucleotide sequence of GGP1 predicts a 60-kDa polypeptide, in agreement with the molecular mass of the gp115 precursor detected in sec53 mutant cells at restrictive temperature. Two hydrophobic sequences, one NH2- and the other COOH-terminal were found. The former has the features of the cleavable signal sequence, which allows the entry of proteins in the secretory pathway. The latter could be the signal sequence that has to be removed during the addition of glycosylphosphatidylinositol. The predicted amino acid sequence of gp115 shows 10 sequons for N-glycosylation and a high proportion of serine-threonine residues (22%) that could provide several sites for O-glycosylation. The unusual concentration of 27 serines in the COOH-terminal portion of the protein shares homology with a similar polyserine repeat of the serine repeat antigen (SERA protein) of Plasmodium falciparum. A two-dimensional analysis of the "in vitro" translational product of the GGP1 mRNA has been carried out, allowing the identification of the "in vivo" gp115 precursor in a two-dimensional gel.