gebhart/patrepeval huggingface dataset:
Characterization of opioid receptors in intestinal muscle cells by selective radioligands and receptor protection (1992)

Opioid receptors were characterized on muscle cells isolated separately from the circular and longitudinal muscle layers of rabbit intestine. Selective radioligands for kappa- ([3H]U69,593), delta- ([3H][D-Pen2,5]enkephalin, DPDPE), and mu- ([3H][D-Ala2,N-Me-Phe4,Gly5-ol]enkephalin, DAGO) opioid receptors were used in conjunction with a technique of receptor protection designed to enrich cells with a specific receptor type. Binding was observed only in cells from the circular muscle layer. Binding was rapid (peak within 2 min), temperature dependent, and concentration dependent. Dissociation constants (Kd) for high-affinity binding sites derived from saturation curves (1.1 +/- 0.3 nM for U69,593, 0.39 +/- 0.04 nM for DPDPE, and 1.9 +/- 0.3 nM for DAGO) were similar to Kd values derived from competition curves. In competition studies, the order of potency with which opioid ligands inhibited binding depended on the radioligand used: U69,593 (Kd 1.5 +/- 0.2 nM) inhibited preferentially the binding of [3H]U69,593, DPDPE (Kd 0.72 +/- 0.16 nM) the binding of [3H]DPDPE and DAGO (Kd 1.2 +/- 0.3 nM) the binding of [3H]DAGO. In each instance the other two ligands were 400-12,000 times less potent. In cells enriched with one receptor type, binding and contraction were observed only with the corresponding selective ligand. The potency of the ligand was slightly enhanced, whereas the potencies of the other two ligands were further reduced (greater than 10,000-fold). We conclude that distinct kappa-, delta-, and mu-opioid receptors are present on muscle cells of the circular but not longitudinal muscle layer of the intestine.
Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem (2002)

With the consensus human genome sequenced and many other sequencing projects at varying stages of completion, greater attention is being paid to the genetic differences among individuals and the abilities of those differences to predict phenotypes. A significant obstacle to such work is the difficulty and expense of determining haplotypes--sets of variants genetically linked because of their proximity on the genome--for large numbers of individuals for use in association studies. This paper presents some algorithmic considerations in a new approach for haplotype determination: inferring haplotypes from localised polymorphism data gathered from short genome 'fragments.' Formalised models of the biological system under consideration are examined, given a variety of assumptions about the goal of the problem and the character of optimal solutions. Some theoretical results and algorithms for handling haplotype assembly given the different models are then sketched. The primary conclusion is that some important simplified variants of the problem yield tractable problems while more general variants tend to be intractable in the worst case.
DECENTRALIZED MULTI STRING PV SYSTEM WITH INTEGRATED ZVT CELL (2010)

This paper exploits the advantages and limitations of using a cascaded connection of DC-DC step-up stages for a se- ries string of PV panels, in a single-phase residential/commercial grid connected installation. It is demonstrated that when multi- string PV systems are adopted in order to minimize shadowing problems, it is required to employ some approach to reduce the switching losses (turn-on losses of MOSFETs and diode reverse recovery losses) of the DC-DC step-up stages. As a multi-string PV system is normally comprised by several DC-DC step-up stages, integrated soft-switching topologies are attractive due to their compactness, reliability and low cost. Thus, this work proposes the use of an integrated ZVT cell, which assists all the DC- DC step-up stages and employs a very compact circuit, enabling to minimize the switching losses, improving the system effi- ciency. The proposed cell makes use of a magnetically-coupled auxiliary voltage source implemented by adding a secondary winding on the input inductors. In order to validate the proposed topology, experimental results are presented.
Comparison of the abilities of different protein sources of iron to enhance Neisseria meningitidis infection in mice (1989)

This study was done primarily to determine whether the previously observed specificity of the meningococcal transferrin and lactoferrin receptors for human proteins was maintained in vivo during meningococcal infection in mice. Preliminary experiments evaluating the choice of host strain, the age and sex of mice, and the growth conditions of the meningococci indicated that 45-day-old female Swiss Webster mice challenged with meningococci grown on low-pH, low-iron Mueller-Hinton agar plates were appropriate for this study. The comparison of transferrins and lactoferrins from different species demonstrated that only the human forms of these proteins were utilized by meningococci; there was significantly greater mortality among mice treated with iron-saturated human transferrin or lactoferrin (93 and 100%, respectively) than among those not treated or treated with iron-saturated bovine transferrin or bovine lactoferrin (0%). Provision of exogenous hemoglobin also resulted in increased mortality, although not as great as that observed with amounts of transferrin with equivalent iron content, which parallels the more effective utilization of transferrin and lactoferrin in in vitro growth experiments. In addition, unlike with transferrin and lactoferrin, there was no difference in utilization of human and bovine hemoglobin in vitro or in vivo.
Unexpected diversity of RNase P, an ancient tRNA processing enzyme: Challenges and prospects (2009)

For an enzyme functioning predominantly in a seemingly housekeeping role of 5' tRNA maturation, RNase P displays a remarkable diversity in subunit make-up across the three domains of life. Despite the protein complexity of this ribonucleoprotein enzyme increasing dramatically from bacteria to eukarya, the catalytic function rests with the RNA subunit during evolution. However, the recent demonstration of a protein-only human mitochondrial RNase P has added further intrigue to the compositional variability of this enzyme. In this review, we discuss some possible reasons underlying the structural diversity of the active sites, and use them as thematic bases for elaborating new directions to understand how functional variations might have contributed to the complex evolution of RNase P.
Exercise-Induced Asthma (1994)

Exercise-induced asthma is a condition in which vigorous physical activity triggers acute airway narrowing in people with heightened airway reactivity. A more accurate description would be exercise-induced bronchospasm. Long usage, however, has left the former term firmly fixed in the lexicon. To emphasize the underlying pathogenesis, the term “thermally induced asthma” has been proposed1.Exercise-induced asthma is not an isolated disorder or a specific disease. Exercise is but one of many stimuli that result in a limitation of airflow. It is not uncommon for physical exertion to be the first precipitant of asthma. With time, however, others may emerge. . . .
Paracrine Release of Insulin-Like Growth Factor 1 from a Bioengineered Tissue Stimulates Skeletal Muscle Growth in Vitro (2006)

Bioengineered tissues transduced to secrete recombinant proteins may serve as a long-term delivery vehicle for therapeutic proteins when implanted in vivo. Insulin-like growth factor 1 (IGF1) is an anabolic growth factor for skeletal muscle that can stimulate myoblast proliferation and myofiber hypertrophy. To determine whether the release of IGF1 from an engineered bioartificial skeletal muscle (BAM) could stimulate the growth of skeletal muscle in a paracrine manner, we established an in vitro perfusion system for genetically engineered IGF1 BAMs. BAMs were bioengineered from C2C12 murine myoblasts stably transduced with a retroviral vector to synthesize and secrete IGF1 (C2-IGF1 BAMs). C2-IGF1 BAMs or nontransduced control C2 BAMs were cocultured with avian BAMS (ABAMs) in constantly perfused biochambers. During 11 days of perfusion, IGF1 levels in the C2-IGF1 BAM perfusion medium increased linearly from 1 to 20 ng/mL. The ABAMs maintained in biochambers with the C2-IGF1 BAMs had significantly more myofibers (69%, p < 0.005) and larger myofiber cross-sectional areas (40%, p < 0.001) compared to those cocultured with control C2 BAMs. These studies show that levels of IGF1 secreted from the C2-IGF1 BAMs are sufficient to produce an anabolic paracrine effect on nongenetically engineered BAMs, and the in vitro perfusion system provides a model for screening proteins effective in stimulating localized skeletal muscle growth.
Expansion of Polystyrene Using Supercritical Carbon Dioxide:  Effects of Molecular Weight, Polydispersity, and Low Molecular Weight Components (1999)

Closed cell foams of broad molecular weight distribution commercial polystyrene samples, prepared by expansion of supercritical-CO2-swollen specimens, exhibit cell diameters that are ∼3−10 times (19−24 μm) larger than those of foams prepared from polystyrene samples with narrow molecular weight (NMW) distributions (∼2−6 μm). Cell diameters for NMW samples are independent of molecular weight from 147K to 1050K. Simulated polydisperse samples prepared by blending NMW distribution samples ranging from 560 to 1050K and a polydisperse sample prepared by radical polymerization produced foams with cells of the same size as in foams prepared from the NMW distribution samples. These observations suggest that molecular weight and polydispersity are not important factors in determining cell size and are not responsible for the disparity in cell sizes described above. This disparity is due to the presence of a very low molecular weight component (∼270) in the commercial samples. Extraction of this component reduced the cell diameter of resulting foams to that of the NMW distribution samples. Addition of a styrene oligomer (285) to a NMW distribution sample resulted in foams with larger cell diameters. Varying the concentration of this oligomer allows control of cell size in foams. Classical nucleation theory cannot explain these observations, suggesting that an alternative mechanism of cell formation is active.
Microfluidic isolation and transcriptome analysis of serum microvesicles (2009)

Microvesicles (exosomes) shed from both normal and cancerous cells may serve as means of intercellular communication. These microvesicles carry proteins, lipids and nucleic acids derived from the host cell. Their isolation and analysis from blood samples have the potential to provide information about state and progression of malignancy and should prove of great clinical importance as biomarkers for a variety of disease states. However, current protocols for isolation of microvesicles from blood require high-speed centrifugation and filtration, which are cumbersome and time consuming. In order to take full advantage of the potential of microvesicles as biomarkers for clinical applications, faster and simpler methods of isolation will be needed. In this paper, we present an easy and rapid microfluidic immunoaffinity method to isolate microvesicles from small volumes of both serum from blood samples and conditioned medium from cells in culture. RNA of high quality can be extracted from these microvesicles providing a source of information about the genetic status of tumors to serve as biomarkers for diagnosis and prognosis of cancer.
In-Vitro Differentiation of Mature Dendritic Cells From Human Blood Monocytes (1997)

Representing the most potent antigen-presenting cells, dendritic cells (DC) can now be generated from human blood monocytes. We recently presented a novel protocol employing GM-CSF, IL-4, and IFN-gamma to differentiate monocyte-derived DC in vitro. Here, such cells are characterized in detail. Cells in culture exhibited both dendritic and veiled morphologies, the former being adherent and the latter suspended. Phenotypically, they were CD1a-/dim, CD11a+, CD11b++, CD11c+, CD14dim/-, CD16a-/dim, CD18+, CD32dim/-, CD33+, CD40+, CD45R0+, CD50+, CD54+, CD64-/dim, CD68+, CD71+, CD80dim, CD86+/++, MHC class I++/ , HLA-DR++/ , HLA-DP+, and HLA-DQ+. The DC stimulated a strong allogeneic T-cell response, and further evidence for their autologous antigen-specific stimulation is discussed. Although resembling a mature CD11c+ CD45R0+ blood DC subset identified earlier, their differentiation in the presence of the Th1 and Th2 cytokines IFN-gamma and IL-4 indicates that these DC may conform to mature mucosal DC.
Fuzzy-based rate control for real-time MPEG video (1998)

We propose a fuzzy logic-based control scheme for real-time motion picture expert group (MPEG) video to avoid long delay or excessive loss at the user-network interface (UNI) in an asynchronous transfer mode (ATM) network. The system consists of a shaper whose role is to smooth the MPEG output traffic to reduce the burstiness of the video stream. The input and output rates of the shaper buffer are controlled by two fuzzy logic-based controllers. To avoid a long delay at the shaper, the first controller aims to tune the output rate of the shaper in the video frame time scale based on the number of available transmission credits at the UNI and the occupancy of the shaper's buffer. Based on the average occupancy of the shaper's buffer and its variance, the second controller tunes the input rate to the shaper over a much larger time scale by applying a closed-loop MPEG encoding scheme. With this approach, the traffic enters the network at an almost constant bit rate (with a very small variation) allowing simple network management functions such as admission control and bandwidth allocation, while guaranteeing a relatively constant video quality since the encoding rate is changed only in critical periods when the shaper buffer "threatens" to overflow. The performance of the proposed scheme is evaluated through numerical tests on real video sequences.
Parathyroid carcinoma: the relationship of nuclear DNA content to clinical outcome. (1993)

This article reports the use of flow cytometry to determine tumor nuclear DNA content and its correlations with clinical outcome in a series of patients with parathyroid carcinoma. Information concerning nine patients with parathyroid cancer (aged 25 to 88 years) was reviewed. Paraffin-embedded, formalin-fixed archival tissue was used to determine tumor DNA content flow cytometrically. Twenty-five operative procedures were performed in nine patients, including 11 parathyroidectomies, two wide local excisions, six central neck dissections, and four median sternotomies for resection of metastases. With flow cytometry used to determine a tumor DNA index, five patients had evidence of tumor aneuploidy; in two patients two aneuploid peaks were evident. The DNA index ranged from 0.7 (hypodiploid) to 1.92 (mean, 1.31). Follow-up ranged from 1 to 18 years. Four patients died. Five were alive 1 to 13 years after diagnosis of parathyroid disease. Four of the five patients with evidence of tumor aneuploidy had metastatic disease and died, and the fifth has had three local recurrences. The four patients with diploid tumors were alive and free of disease 1, 3, 4, and 8 years after the initial operation. It is concluded that in patients with clinically or pathologically demonstrated parathyroid cancer, flow cytometry may help differentiate those whose cancers are likely to behave indolently (diploid tumors) from those with tumors (aneuploid) more likely to behave aggressively by recurring locally or metastasizing.
Rational Design of CXCR4 Specific Antibodies with Elongated CDRs (2014)

The bovine antibody (BLV1H12) which has an ultralong heavy chain complementarity determining region 3 (CDRH3) provides a novel scaffold for antibody engineering. By substituting the extended CDRH3 of BLV1H12 with modified CXCR4 binding peptides that adopt a β-hairpin conformation, we generated antibodies specifically targeting the ligand binding pocket of CXCR4 receptor. These engineered antibodies selectively bind to CXCR4 expressing cells with binding affinities in the low nanomolar range. In addition, they inhibit SDF-1-dependent signal transduction and cell migration in a transwell assay. Finally, we also demonstrate that a similar strategy can be applied to other CDRs and show that a CDRH2-peptide fusion binds CXCR4 with a K(d) of 0.9 nM. This work illustrates the versatility of scaffold-based antibody engineering and could greatly expand the antibody functional repertoire in the future.
Oral Doxepin Rinse: The Analgesic Effect and Duration of Pain Reduction in Patients with Oral Mucositis Due to Cancer Therapy (2006)

This research expands on our prior study, in which we assessed pain reduction after topical doxepin rinse in patients with oral mucositis resulting from cancer and cancer therapy. We continued to enroll patients with painful oral mucositis attributable solely to cancer therapy and performed further analysis on the duration of pain reduction. Fifty-one patients with oral mucositis were enrolled. Mucositis was scored and oral pain was assessed with a visual analog scale before doxepin oral rinse (5 mg/mL) and at regular intervals up to 4 h after rinsing. Of those who reported pain reduction, 95% did so within 15 min of rinsing with doxepin. In the total sample, the average patient reported a 70% maximum decrease in pain (P < 0.0001). Recurrence of pain was slow and at the conclusion of the study 19 patients (37%) still reported a reduction from baseline pain. With this censored data we used Cox-proportional hazards to determine what variables best explained longer duration of pain reduction. Our final model determined that more severe baseline pain, worse mucosal erythema score, or a larger relative maximum reduction in pain were all associated with a slower rate of pain recurrence after oral rinsing (all P < 0.01).
DNA Gyrase: Structure and Function (1991)

DNA gyrase is an essential bacterial enzyme that catalyzes the ATP-dependent negative super-coiling of double-stranded closed-circular DNA. Gyrase belongs to a class of enzymes known as topoisomerases that are involved in the control of topological transitions of DNA. The mechanism by which gyrase is able to influence the topological state of DNA molecules is of inherent interest from an enzymological standpoint. In addition, much attention has been focused on DNA gyrase as the intracellular target of a number of antibacterial agents as a paradigm for other DNA topoisomerases. In this review we summarize the current knowledge concerning DNA gyrase by addressing a wide range of aspects of the study of this enzyme.
Cloning of the gene coding for a shared human melanoma antigen recognized by autologous T cells infiltrating into tumor. (1994)

By cDNA expression cloning we have isolated a gene encoding a shared human melanoma antigen recognized by HLA-A2 restricted autologous and allogenic tumor-infiltrating lymphocytes (TILs) from patients with metastatic melanoma. By using both transient and stable expression systems, transfection of this gene into non-antigen-expressing HLA-A2+ cell lines resulted in recognition by the antigen-specific TILs. The sequence of this cDNA revealed a previously undescribed putative transmembrane protein whose expression was restricted to melanoma and melanocyte cell lines and human retina but no other fresh or cultured normal tissues tested or other tumor histologies. Thus, we have identified a gene encoding a melanocyte lineage-specific protein (MART-1; melanoma antigen recognized by T cells 1) that is a widely shared melanoma antigen recognized by the T lymphocytes of patients with established malignancy. Identification of this gene opens possibilities for the development of immunotherapies for patients with melanoma.
Transition Metals, Ferritin, Glutathione, and Ascorbic Acid in Parkinsonian Brains (1989)

The regional distributions of iron, copper, zinc, magnesium, and calcium in parkinsonian brains were compared with those of matched controls. In mild Parkinson's disease (PD), there were no significant differences in the content of total iron between the two groups, whereas there was a significant increase in total iron and iron (III) in substantia nigra of severely affected patients. Although marked regional distributions of iron, magnesium, and calcium were present, there were no changes in magnesium, calcium, and copper in various brain areas of PD. The most notable finding was a shift in the iron (II)/iron (III) ratio in favor of iron (III) in substantia nigra and a significant increase in the iron (III)-binding, protein, ferritin. A significantly lower glutathione content was present in pooled samples of putamen, globus pallidus, substantia nigra, nucleus basalis of Meynert, amygdaloid nucleus, and frontal cortex of PD brains with severe damage to substantia nigra, whereas no significant changes were observed in clinicopathologically mild forms of PD. In all these regions, except the amygdaloid nucleus, ascorbic acid was not decreased. Reduced glutathione and the shift of the iron (II)/iron (III) ratio in favor of iron (III) suggest that these changes might contribute to pathophysiological processes underlying PD.
A survey on content-based retrieval for multimedia databases (1999)

Conventional database systems are designed for managing textual and numerical data, and retrieving such data is often based on simple comparisons of text/numerical values. However, this simple method of retrieval is no longer adequate for multimedia data, since the digitized representation of images, video, or data itself does not convey the reality of these media items. In addition, composite data consisting of heterogeneous types of data also associates with the semantic content acquired by a user's recognition. Therefore, content-based retrieval for multimedia data is realized taking such intrinsic features of multimedia data into account. Implementation of the content-based retrieval facility is not based on a single fundamental, but is closely related to an underlying data model, a priori knowledge of the area of interest, and the scheme for representing queries. This paper surveys recent studies on content-based retrieval for multimedia databases from the point of view of three fundamental issues. Throughout the discussion, we assume databases that manage only nontextual/numerical data, such as image or video, are also in the category of multimedia databases.