gebhart/patrepeval huggingface dataset:
Analysis of Chondrex (YKL-40, HC gp-39) in the Cerebrospinal Fluid of Patients With Spine Disease (2002)

In this study, the chondrex concentration was high in spine diseases causing spinal stenosis. The authors believe that chondrex is expressed in cerebrospinal fluid as a result of damage or stress to the neural structure, and that it could be a new marker for spine diseases.
Preanalytical Variables Affecting the Integrity of Human Biospecimens in Biobanking (2015)

The quality of a study will depend on the integrity of the biospecimens. Preanalytical preparations should be planned with consideration of the effect on downstream analyses. Currently such preanalytical variables are not routinely documented in the biospecimen research literature. Future studies using biobanked biospecimens should describe in detail the preanalytical handling of biospecimens and analyze and interpret the results with regard to the effects of these variables.
<title>PRISM: A Practical Mealtime Imaging Stereo Matcher</title> (1984)

A fast stereo-matching algorithm designed to operate in the presence of noise is described. The algorithm has its roots in the zero-crossing theory of Marr and Poggio but does not explicitly match zero-crossing contours. While these contours are for the most part stably tied to fixed surface locations, some fraction is always perturbed significantly by system noise. Zero-crossing contour based matching algorithms tend to I- very sensitive to these local distortions and ar, prevented from operating well on signals with moderate noise levels even though a substantial amount of information may still be present. The dual representationÃ¢â‚¬â€?regions of constant sign in the V2G convolution persist much further into the noise than does the local geometry of the zero-crossing contours that delimit them. The PRISM system was designed to test this approach. The initial design task of the implementation has been to rapidly detect obstacles in a robotics work space and determine their rough extents and heights. In this case speed and reliability are important but precision is less critical. The system uses a pair of inexpensive vidicon cameras mounted above the workspace of a PUMA robot manipulator. The digitized video signals are fed to a high speed digital convolver that applies a 32<sup>2 </sup>VG operator to the images at a 106 pixel per second rate. Matching is accomplished in software on a lisp machine with individual near/far tests taking less than i3luth of a second. A 36 by 26 matrix of absolute height measurements - in mm - over a 100 pixel disparity range is produced in 30 seconds from image acquisition to final output. Three scales of resolution are used in a coarse guides fine search. Acknowledgment: This report describes research done at the Artificial Intelligence Laboratory of the Massachusetts Institute of &apos;Technology Support for the laboratory&apos;s artificial intelligence research is provided in part by the Advanced Research Projects Agency of the Department of Defense under Office of Naval Research contract N00014-80-C-0505 and in part by National Science Foundation Grant 79-23110MCS.
Emerging Role of Endoglin (CD105) as a Marker of Angiogenesis with Clinical Potential in Human Malignancies (2003)

Angiogenesis is crucial for tumor development and progression, and antiangiogenetic therapy represents a promising approach for cancer treatment. Thus, the in-depth understanding of the molecular mechanism(s) regulating angiogenesis, together with the characterization of molecules expressed by endothelial cells and involved in distinct steps of the angiogenetic process, will greatly improve the design of new and more effective therapeutic strategies in human malignancies. Endoglin (CD105), a cell membrane glycoprotein predominantly expressed on cellular lineages within the vascular system, and over-expressed on proliferating endothelial cells, is involved in blood vessels development and represents a powerful marker of neovascularization. CD105 binds several factors of the Transforming Growth Factor (TGF)-beta superfamily, a pleiotropic cytokine that regulates different cellular functions including proliferation, differentiation and migration. In human malignancies of different histotype, CD105 is highly expressed on endothelial cells of both peri- and intra-tumoral blood vessels, while it is weakly expressed or absent on neoplastic cells. This unique tissue distribution strongly suggests for a prognostic, diagnostic and therapeutic potential of CD105 in neoplastic diseases. In this review we will summarize the structural and functional features of CD105, as well as its tissue distribution in normal and neoplastic tissues. Furthermore, the practical implications of CD105 in human malignancies will also be discussed.
Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences (2015)

The software and data are freely available at https://github.com/ypriverol/pIRSupplementary information: Supplementary data are available at Bioinformatics online.
Query decomposition based on ontology mapping in data integration system (2007)

A method of query decomposition based on ontology mapping is proposed. By analyzing the domain models and schemas of data sources, a global ontology and local ontology are established, and the mapping between them are generated as well. During the query process, the query is expressed in the form of a tree, and by taking advantage of mapping rules, the query is decomposed into sub-queries.
Multicomputer architectures for real-time perception (abstract only) (1984)

This paper examines the computing demands that must be met by a system capable of scene description and perception of real-world moving objects. A brief survey is made of the major different kinds of computer systems that have been built, or designed, and of the different sources of potential speed-up of processing that have been exploited. Finally, a number of alternative possible hardware architectures that might be capable of handling real-time perception of moving objects are suggested, and examined.
Immune complex‐induced interleukin‐6, interleukin‐10 and prostaglandin secretion by human monocytes: a network of pro‐ and anti‐inflammatory cytokines dependent on the antigen: antibody ratio (1996)

We have used two experimental models of immune complexes to study the secretion of interleukin (IL)-10, IL-6 and their connection with the immune complex-induced synthesis of prostaglandin (PG) E2 by human monocytes in vitro. Immune complexes formed of tetanus toxoid and polyclonal anti-tetanus toxoid antiserum as well as heat-aggregated human serum immunoglobulins induced the release of IL-6 and IL-10 in a dose- and antigen: antibody ratio-dependent manner. Antigen-antibody complexes formed near equivalence were most effective in induction of a cytokine response. PGE2 could augment the immune complex-induced IL-6 and IL-10 secretion, but alone, did not induce cytokine secretion. IL-10 was capable of down-regulating the release of IL-6 and PGE2. Additionally, we demonstrated that endogenously synthesized IL-10 limited the immune complex-induced secretion of proinflammatory cytokines tumor necrosis factor-alpha and IL-1 beta. All three regulatory factors examined here share anti-inflammatory properties and are closely associated with the T helper type 2 (Th2) immune response. We conclude that immune complexes, besides their well-known ability no cause acute and chronic inflammation, can mediate immunosuppressive effects and influence the balance of Th1/Th2 responses.
Translocation Pathway of the Intratracheally Instilled Ultrafine Particles from the Lung into the Blood Circulation in the Mouse (2006)

Recently, it has been demonstrated that ultrafine particles (UFPs) are able to translocate from the lung into the systemic circulation. Precise mechanisms of the anatomical translocation (crossing the air-blood barrier) of inhaled UFPs at the alveolar wall are not fully understood. In this study, we examined the translocation pathway of the intratracheally instilled ultrafine carbon black (UFCB) from the lung into the blood circulation in mouse. Electron microscopy demonstrated accumulation of intratracheally instilled UFCB in the large-sized gaps developing between the cytoplasmic processes of the alveolar epithelial cells, possibly as a result of shrinkage of cytoplasm, by receiving stimulus/signals generated and released following UFCB attachment on the alveolar epithelial cells. Occasional penetration of the accumulated UFCB into the alveolar basement membrane, exposing to the air space, was observed at the gap. These results suggest that inhaled UFPs may, in part, pass the air-blood barrier through the large-sized gap formed between the alveolar epithelial cells.
Correlation between the effects of polyamine analogues on DNA conformation and cell growth. (1989)

Effects of a number of synthetic analogues of the natural polyamines on the B-Z transition of poly(dG-me5dC) and on the aggregation of calf thymus DNA in solution were studied using circular dichroic and UV spectroscopy. The efficiency of induction of the B-Z transition decreased with a decrease in the length of the central alkyl chain of the analogues, and the ability of analogues to aggregate DNA was markedly reduced for compounds ethylated at the terminal amines. Both structural variations appear to have important effects on the biological functions of polyamines. Most analogues studied depleted intracellular levels of natural polyamines, but only those that did not readily induce the B-Z transition and/or aggregate DNA were good inhibitors of cell growth. All but one of the analogues studied were able to rescue cells--at least in part--from the growth-inhibitory effects of alpha-difluoromethylornithine. The single analogue that was unable to effect rescue also failed to induce both the B-Z transition and the aggregation of DNA.
Masking selected sequence variation by incorporating mismatches into melting analysis probes (2006)

Hybridization probe melting analysis can be complicated by the presence of sequence variation (benign polymorphisms or other mutations) near the targeted mutation. We investigated the use of "masking" probes to differentiate alleles with similar probe melting temperatures. Selected sequence variation was masked by incorporating mismatches (deletion, unmatched nucleotide, or universal base) into hybridization probes at the polymorphic location. Such masking probes create a probe/target mismatch with all possible alleles at the selected polymorphic location. Any allele with additional variation at another site is identified by a lower probe melting temperature than alleles that vary only at the masked position. This "masking technique" was applied to RET protooncogene and HPA6 mutation detection using unlabeled hybridization probes, a saturating dsDNA dye, and high-resolution melting analysis. Masking probes clearly distinguished all targeted mutations from polymorphisms when at least 1 base pair (bp) separated the mutation from the masked variation. We were able to mask polymorphisms immediately adjacent to mutations, except in certain cases, such as those involving single-base deletion probes when both adjacent positions had the same polymorphic nucleotides. The masking probes can also localize mutations to specific codons or nucleotide positions. Masking probes can simplify melting analysis of complex regions and eliminate the need for sequencing.
Antibacterial Effects of the Essential Oils of Commonly Consumed Medicinal Herbs Using an In Vitro Model (2010)

The chemical composition and antibacterial activity of essential oils from 10 commonly consumed herbs: Citrus aurantium, C. limon, Lavandula angustifolia, Matricaria chamomilla, Mentha piperita, M. spicata, Ocimum basilicum, Origanum vulgare, Thymus vulgaris and Salvia officinalis have been determined. The antibacterial activity of these oils and their main components; i.e. camphor, carvacrol, 1,8-cineole, linalool, linalyl acetate, limonene, menthol, a-pinene, b-pinene, and thymol were assayed against the human pathogenic bacteria Bacillus subtilis, Enterobacter cloacae, Escherichia coli O157:H7, Micrococcus flavus, Proteus mirabilis, Pseudomonas aeruginosa, Salmonella enteritidis, S. epidermidis, S. typhimurium, and Staphylococcus aureus. The highest and broadest activity was shown by O. vulgare oil. Carvacrol had the highest antibacterial activity among the tested components.
Hydrogel-coated microfluidic channels for cardiomyocyte culture (2013)

The research areas of tissue engineering and drug development have displayed increased interest in organ-on-a-chip studies, in which physiologically or pathologically relevant tissues can be engineered to test pharmaceutical candidates. Microfluidic technologies enable the control of the cellular microenvironment for these applications through the topography, size, and elastic properties of the microscale cell culture environment, while delivering nutrients and chemical cues to the cells through continuous media perfusion. Traditional materials used in the fabrication of microfluidic devices, such as poly(dimethylsiloxane) (PDMS), offer high fidelity and high feature resolution, but do not facilitate cell attachment. To overcome this challenge, we have developed a method for coating microfluidic channels inside a closed PDMS device with a cell-compatible hydrogel layer. We have synthesized photocrosslinkable gelatin and tropoelastin-based hydrogel solutions that were used to coat the surfaces under continuous flow inside 50 μm wide, straight microfluidic channels to generate a hydrogel layer on the channel walls. Our observation of primary cardiomyocytes seeded on these hydrogel layers showed preferred attachment as well as higher spontaneous beating rates on tropoelastin coatings compared to gelatin. In addition, cellular attachment, alignment and beating were stronger on 5% (w/v) than on 10% (w/v) hydrogel-coated channels. Our results demonstrate that cardiomyocytes respond favorably to the elastic, soft tropoelastin culture substrates, indicating that tropoelastin-based hydrogels may be a suitable coating choice for some organ-on-a-chip applications. We anticipate that the proposed hydrogel coating method and tropoelastin as a cell culture substrate may be useful for the generation of elastic tissues, e.g. blood vessels, using microfluidic approaches.
Resveratrol-induced Apoptosis Is Associated with Fas Redistribution in the Rafts and the Formation of a Death-inducing Signaling Complex in Colon Cancer Cells (2003)

Resveratrol, a polyphenol found in grape skin and various other food products, may function as a cancer chemopreventive agent for colon and other malignant tumors and possesses a chemotherapeutic potential through its ability to trigger apoptosis in tumor cells. The present study analyses the molecular mechanisms of resveratrol-induced apoptosis in colon cancer cells, with special attention to the role of the death receptor Fas in this pathway. We show that, in the 10-100 microm range of concentrations, resveratrol activates various caspases and triggers apoptosis in SW480 human colon cancer cells. Caspase activation is associated with accumulation of the pro-apoptotic proteins Bax and Bak that undergo conformational changes and relocalization to the mitochondria. Resveratrol does not modulate the expression of Fas and Fas-ligand (FasL) at the surface of cancer cells, and inhibition of the Fas/FasL interaction does not influence the apoptotic response to the molecule. Resveratrol induces the clustering of Fas and its redistribution in cholesterol and sphingolipid-rich fractions of SW480 cells, together with FADD and procaspase-8. This redistribution is associated with the formation of a death-inducing signaling complex (DISC). Transient transfection of either a dominant-negative mutant of FADD, E8, or MC159 viral proteins that interfere with the DISC function, decreases the apoptotic response of SW480 cells to resveratrol and partially prevents resveratrol-induced Bax and Bak conformational changes. Altogether, these results indicate that the ability of resveratrol to induce the redistribution of Fas receptor in membrane rafts may contribute to the molecule's ability to trigger apoptosis in colon cancer cells.
Effects of Leptin Deficiency and Short-Term Repletion on Hepatic Gene Expression in Genetically Obese Mice (2001)

By supplying most organs of the body with metabolic substrates, the liver plays a central role in maintaining energy balance. Hepatic metabolism of glucose, fatty acids, and lipoproteins is disrupted in the leptin-deficient obese (Lep(ob)/Lep(ob)) mouse, leading to hyperglycemia, steatosis, and hypercholesterolemia. Microarray expression profiles were used to identify transcriptional perturbations that underlie the altered hepatic physiology of Lep(ob)/Lep(ob) mice. A wide variety of genes involved in fatty acid metabolism are altered in expression, which suggests that both fatty acid synthesis and oxidation programs are activated in obese mice. The expression of a small subset of genes is upregulated by leptin deficiency, not modulated by caloric restriction, and markedly suppressed by short-term leptin treatment. Among these leptin-regulated genes, apolipoprotein A-IV is a strong candidate for mediating the atherogenic-resistant phenotype of Lep(ob)/Lep(ob) mice.
'Fat mass and obesity associated' gene (FTO): No significant association of variant rs9939609 with weight loss in a lifestyle intervention and lipid metabolism markers in German obese children and adolescents (2008)

This study is registered at clinicaltrials.gov (NCT00435734).
Transplantation and Adoptive Cellular Therapy of Cancer: The Role of T-Cell Growth Factors (1993)

The ability to transfer cultured lymphocytes required the availability and the understanding of the use of the T-cell growth factors IL-2, IL-4, IL-7, and IL-12. Application of these cytokines in vitro and in vivo has allowed the modern development of adoptive transfer of tumor reactive lymphocytes to the modern immunotherapy of patients with cancer. In a randomized prospective study of IL-2 administration compared with IL-2 and lymphokine-activated killer (LAK) cells, no increase in response rate was observed. In a total of 90 patients randomized to receive LAK and IL-2 and 91 patients randomized to receive IL-2 alone, there were a total of 24 responses in patients receiving cells and IL-2 and 16 responses in those receiving IL-2 alone (no significant difference). There was some suggestion that complete responses were observed more often in melanoma patients treated with LAK and IL-2. The most interesting aspect of this study is the prolonged duration of responses, lasting for many months or years. Unfortunately, given the large numbers of variables that were examined, it became very difficult to demonstrate a clear-cut association between clinical outcome (response) and any variable that was routinely measured. Significant antitumor responses have been observed greater than expected with IL-2 alone, with the administration of tumor-infiltrating lymphocytes to patients with melanoma. We currently use hollow fiber devices (Cellco, Germantown, MD) to expand cells up through the many doublings required to generate approximately 1-2 × 1011 cells over a period of 6 wk in culture. In a recent review of the results in patients with melanoma treated on such regimens in combination with high-dose IL-2, an approximately 20-50% response rate has been observed. The factors associated with response are still unclear. Although we initially felt that it was associated with specific lysis, subsequent studies from our group suggest that the relevant factor is specific cytokine (INF-γ, GM-CSF, TNF) production upon tumor stimulation. Additional studies will need to be done to clarify these issues.
Matrix-assisted laser desorption/ionisation mass spectrometry of transfer ribonucleic acids isolated from yeast (1997)

tRNATyr and tRNASer purified from bulk brewer's yeast tRNA were subjected to analysis by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Choosing a mixture of 2,4,6- and 2,3,4-trihydroxy-acetophenone and diammonium citrate as matrix a mass resolution of up to 220 (FWHM) was achieved in the linear mode of operation. Cation adduct suppression by addition of cation exchange beads and a chelating agent (CDTA) is shown to substantially improve mass resolution for this class of molecules.
Fluorescence excitation and imaging of single molecules near dielectric‐coated and bare surfaces: a theoretical study (2012)

Microscopic fluorescent samples of interest to cell and molecular biology are commonly embedded in an aqueous medium near a solid surface that is coated with a thin film such as a lipid multilayer, collagen, acrylamide, or a cell wall. Both excitation and emission of fluorescent single molecules near film-coated surfaces are strongly affected by the proximity of the coated surface, the film thickness, its refractive index and the fluorophore's orientation. For total internal reflection excitation, multiple reflections in the film can lead to resonance peaks in the evanescent intensity versus incidence angle curve. For emission, multiple reflections arising from the fluorophore's near field emission can create a distinct intensity pattern in both the back focal plane and the image plane of a high aperture objective. This theoretical analysis discusses how these features can be used to report film thickness and refractive index, and fluorophore axial position and orientation.
From Skin Cells to Ovarian Follicles? (2006)

Generating oocytes from cells derived from skin in vitro may provide a valuable model for identifying factors involved in germ cell formation and oocyte differentiation. In addition, the "oocytes" produced could potentially be useful for therapeutic cloning, and thus offer new possibilities for tissue therapy. We recently reported the differentiation of cells derived from porcine fetal skin into cells resembling germ cells and oocytes. A subpopulation of these cells expressed germ cell markers and formed aggregate like oocyte-cumulus complexes that secreted ovarian steroid hormones and responded to gonadotropin stimulation. Some of these aggregates extruded large oocyte-like cells that expressed markers appropriate to oocytes. We now show further evidence of germ cell marker expression during differentiation. We have also compared the oocyte-like cells with natural oocytes for their expression levels of Oct4, growth differentiation factor-9b (GDF9b), the deleted in azoospermia -like (DAZL) gene, vasa, zona pellucida (ZP), and the meiosis marker synaptonemal complex protein 3 (SCP3), and have revealed interesting similarities and differences.