gebhart/patrepeval huggingface dataset:
The Promyelocytic Leukemia Zinc Finger Protein Affects Myeloid Cell Growth, Differentiation, and Apoptosis (1998)

The promyelocytic leukemia zinc finger (PLZF) gene, which is disrupted in therapy-resistant, t(11;17)(q23;q21)-associated acute promyelocytic leukemia (APL), is expressed in immature hematopoietic cells and is down-regulated during differentiation. To determine the role of PLZF in myeloid development, we engineered expression of PLZF in murine 32Dcl3 cells. Expression of PLZF had a dramatic growth-suppressive effect accompanied by accumulation of cells in the G0/G1 compartment of the cell cycle and an increased incidence of apoptosis. PLZF-expressing pools also secreted a growth-inhibitory factor, which could explain the severe growth suppression of PLZF-expressing pools that occurred despite the fact that only half of the cells expressed high levels of PLZF. PLZF overexpression inhibited myeloid differentiation of 32Dcl3 cells in response to granulocyte and granulocyte-macrophage colony-stimulating factors. Furthermore, cells that expressed PLZF appeared immature as demonstrated by morphology, increased expression of Sca-1, and decreased expression of Gr-1. These findings suggest that PLZF is an important regulator of cell growth, death, and differentiation. Disruption of PLZF function associated with t(11;17) may be a critical event leading to APL.
Dynamics of protein secretion during adipocyte differentiation (2016)

The major functions of adipocytes include both lipid storage and the production of secretory factors. However, the type of proteins released from mouse 3T3-L1 cells during adipocyte differentiation remains poorly understood. We examined the dynamics of secreted proteins during adipocyte differentiation using mass spectrometry (MS) combined with an iTRAQ (®) labeling method that enables the simultaneous analysis of relative protein expression levels. A total of 215 proteins were identified and quantified from approximately 10 000 MS/MS spectra. Of these, approximately 38% were categorized as secreted proteins based on gene ontology classification. Adipokine secretion levels were increased with the progression of differentiation. By contrast, levels of fibril collagen components, such as subunits of type I and III collagens, were decreased during differentiation. Basement membrane components attained their peak levels at day 4 when small lipid droplets accumulated in differentiated 3T3-L1 cells. Simultaneously, peak levels of collagen microfibril components that comprise type V and VI collagen subunits were also observed. Our data demonstrated that extracellular matrix components were predominantly released during the early and middle stages of adipocyte differentiation, with a subsequent increase in the secretion of adipokines. This suggests that 3T3-L1 cells secrete adipokines after their ECM is constructed during adipocyte differentiation.
Characterization of Black Chia Seed ( Salvia hispanica L ) and Oil and Quantification of -sitosterol (2013)

The importance of corn, bean, amaranth and black chia seed in the Aztec’s diet is well documented in the historical Florentine Codex. Black chia seed is a good source of omega-3 fatty acid, dietary fiber, proteins, as well as diverse bioelements and antioxidants. The proximal chemical analysis obtained from black chia seed shows 5.15% of moisture, 34.70% of fats, 4.10% of ashes, 17.90% of protein, 40.25% carbohydrates and 17.30% of raw fiber. The extraction technique permitted to obtain a 29% of oil with an iodine value of 197.68 cg/g, peroxides of 2.67 meq/Kg, a refraction index of 1.46 and a density of 0.89 g/mL. The oil’s FTIR spectrum showed a peak at 3010.03 cm -1 characteristic of a =CH stretching mode. Also, the profile of fatty acids performed by, CG-MS, provides evidence of the presence of the (Z.Z.Z) 9,12,15octadecatrienoic acid ( �-linolenic acid, omega-3), �-tocopherol as well as phytosterols: campesterol, stigmasterol and �sitosterol. The latter was quantified obtaining a concentration of 1224.3 mg/L.
Monoclonal antibodies for carcinoembryonic antigen and related antigens as a model system: a systematic approach for the determination of epitope specificities of monoclonal antibodies. (1983)

A systematic approach for the determination of epitope specificities of monoclonal antibodies to a complex antigen system is described. After initial screening to identify antigen-binding monoclonal antibodies, one or more of the clones are isolated by limiting dilution cloning, grown in ascites, and the resulting antibodies secreted into the ascitic fluid are affinity purified on Sepharose-bound protein A, radiolabeled, and cross-compared with antibodies from other clones by a solid-phase competitive immunoassay. In this work, BALB/c mice were immunized with either purified carcinoembryonic antigen (CEA) or the CEA-producing cell line HC 84S. Spleen cells were fused with the mouse myeloma cell line Sp2/0-Ag14. The supernatants from 25 hybrids showed a significant binding of 125I-CEA (greater than or equal to 15%). Nine hybrids were cloned, resulting in 33 different clones. The antibodies produced by the different cloned hybrids and the remaining uncloned hybrids recognized a total of five different epitopes on CEA. All of the epitopes reside on the protein moiety of the molecule as determined by antibody binding to deglycosylated CEA. The monoclonal antibodies with five different epitope specificities were reacted with tissue sections of normal and cancerous tissues and with peripheral blood smears. Each of the five monoclonal antibodies reacted with tissue sections from colonic, gastric, lung, and mammary carcinomas, as well as from a benign colonic polyp and a resection margin from a colonic carcinoma. Four monoclonals reacted with normal liver tissue. Granulocytes in peripheral blood smears bound three antibodies strongly and one antibody weakly, and one antibody was not bound. One monoclonal antibody that reacted with normal liver tissue was not bound by granulocytes. The ability of these five monoclonal antibodies to differentially detect three different CEA-related antigens in normal and malignant tissues may have clinical utility.
Editorial: New analytical and statistical approaches for interpreting the relationships among environmental stressors and biomarkers (2014)

The broad topic of biomarker research has an often-overlooked component: the documentation and interpretation of the surrounding chemical environment and other meta-data, especially from visualization, analytical and statistical perspectives. A second concern is how the environment interacts with human systems biology, what the variability is in "normal" subjects, and how such biological observations might be reconstructed to infer external stressors. In this article, we report on recent research presentations from a symposium at the 248th American Chemical Society meeting held in San Francisco, 10-14 August 2014, that focused on providing some insight into these important issues.
Immunization with Heterologous Flaviviruses Protective Against Fatal West Nile Encephalitis (2002)

Prior immunization of hamsters with three heterologous flaviviruses (Japanese encephalitis virus [JEV] SA14-2-8 vaccine, wild-type St. Louis encephalitis virus [SLEV], and Yellow fever virus [YFV] 17D vaccine) reduces the severity of subsequent West Nile virus (WNV) infection. Groups of adult hamsters were immunized with each of the heterologous flaviviruses; approximately 30 days later, the animals were injected intraperitoneally with a virulent New York strain of WNV. Subsequent levels of viremia, antibody response, and deaths were compared with those in nonimmune (control) hamsters. Immunity to JEV and SLEV was protective against clinical encephalitis and death after challenge with WNV. The antibody response in the sequentially infected hamsters also illustrates the difficulty in making a serologic diagnosis of WNV infection in animals (or humans) with preexisting Flavivirus immunity.
Progress in robot road-following (1986)

We report progress in visual road following by autonomous robot vehicles. We present results and work in progress in the areas of system architecture, image rectification and camera calibration, oriented edge tracking, color classification and road-region segmentation, extracting geometric structure, and the use of a map. In test runs of an outdoor robot vehicle, the Terregator, under control of the Warp computer, we have demonstrated continuous motion vision-guided road-following at speeds up to 1.08 km/hour with image processing and steering servo loop times of 3 sec.
MINI REVIEW Keratan sulfate: structure, biosynthesis, and function (2000)

The last 5 years have seen a marked increase in research on keratan sulfate (KS) and a concomitant increase in our understanding of the range of molecules that carry this adaptable polysaccharide. More than 15 KS-linked proteins have been identified and many of the genes encoding these have been cloned. KS-containing molecules have been identified in numerous epithelial and neural tissues in which KS expression responds to embryonic development, physiological variations, and to wound healing. A corneal cell culture system has been developed in which long-term KS biosynthesis is maintained. Progress has been made toward identification of the glycosyl- and sulfotransferases responsible for KS biosynthesis. A mouse knockout of a corneal KS-proteoglycan has provided the first experimental support for the role of KS in corneal transparency. Evidence has also been presented supporting functional roles of KS in cellular recognition of protein ligands, axonal guidance, cell motility, and in embryo implantation. These findings have served to expand the concept of what keratan sulfate is and the potential roles it may play in the cellular biology of diverse tissues.
Homodimerization and constitutive activation of the erythropoietin receptor. (1992)

The erythropoietin receptor (EPO-R) is a member of the recently described cytokine receptor superfamily. A constitutively active (hormone independent) form of the EPO-R was isolated that has a single amino acid change in the exoplasmic domain, converting arginine-129 to cysteine (R129C). Since EPO-Rs containing R129S, R129E, and R129P mutations are functionally wild type, the presence of cysteine at residue 129, and not the loss of arginine, is required for constitutive activity. Several mutant forms of the EPO-R were analyzed; all constitutively active mutants form disulfide-linked homodimers, whereas EPO-responsive or inactive forms of the receptor do not. Monomers and disulfide-linked dimers of the constitutive receptor are present on the plasma membrane and bind EPO with a single affinity. Homodimerization of the EPO-R is likely to play a role in ligand-induced signal transduction, and disulfide-linked dimerization of the constitutive receptor may mimic this step.
In vitro In vivo comparison of two pH sensitive Eudragit polymers for colon specific drug delivery (2009)

The aim of this study was to develop the polymer coated diclofenac tablet containing superdisintegrant for colonic drug delivery and compare the in vivo performance of two polymers for site specificity. Eudragit FS 3D and Eudragit S100 were used as pH sensitive polymers. Tablets were prepared to give fast release at specific site with the help of sodium starch glycolate as superdisintegrant. Tablets were coated separately with Eudragit FS 30D and Eudragit S100 in various thicknesses and evaluated for in vitro drug release using changing pH method. X ray imaging was used to monitor the placebo tablets throughout the gastrointestinal system. In vitro release studies reveals that Eudragit FS30D coated tablet with 10%w/w coating level start release of drug at pH 6.8 after suitable lag time in the same pH which corresponds to colonic arrival time, as compare to Eudragit S100 coated tablet which release only at higher pH , approximating the transverse colon. In vivo study shows that Tablet coated with Eudragit FS30D with 10%w/w coating level and Eudragit S100 with 10% coating level disintegrated in cecum region. Thus Eudragit FS30D coated tablet may be a promising system for the treatment of colonic disease where pH may decrease and drug also start to release at the same pH after suitable lag time as well as release of drug at the beginning of colon so drug will be available in solution or disperse form for local and systemic effect throughout the colon.
Review Paper: Coding Systems in Health Care (1996)

Computer-based patient data which are represented in a coded form have a variety of uses, including direct patient care, statistical reporting, automated decision support, and clinical research. No standard exists which supports all of these functions. Abstracting coding systems, such as ICD, CPT, DRGs and MeSH fail to provide adequate detail, forcing application developers to create their own coding schemes for systems. Some of these schemes have been put forward as possible standards, but they have not been widely accepted. This paper reviews existing schemes used for abstracting, electronic record systems, and comprehensive coding. It also discusses the remaining impediments to acceptance of standards and the current efforts to overcome them, including SNOMED, the Gabrieli Medical Nomenclature, the Read Clinical Codes, GALEN, and the Unified Medical Language System (UMLS).
Lillie Langtry in Canada and the U.S.A., 1882-1917 (1989)

Lillie Langtry was the most controversial English stage performer to come to North America during the heyday of theatrical touring, c. 1880-1939. She returned frequently, to have her plays and performances almost invariably damned by critics and frequently by mayors. Yet the public was fascinated by Langtry and made her wealthy by crowding into Canadian and American theatres, attracted in part by rumours of her relationship with Edward, Prince of Wales. Langtry's brief visit to Windsor, Ontario, after The Degenerates was banned in Detroit in April 1900, illustrates the kind of controversy that she frequently aroused.
Gnotobiotic Mouse Immune Response Induced byBifidobacteriumsp. Strains Isolated from Infants (2007)

Bifidobacterium, which is a dominant genus in infants' fecal flora and can be used as a probiotic, has shown beneficial effects in various pathologies, including allergic diseases, but its role in immunity has so far been little known. Numerous studies have shown the crucial role of the initial intestinal colonization in the development of the intestinal immune system, and bifidobacteria could play a major role in this process. For a better understanding of the effect of Bifidobacterium on the immune system, we aimed at determining the impact of Bifidobacterium on the T-helper 1 (T(H)1)/T(H)2 balance by using gnotobiotic mice. Germfree mice were inoculated with Bifidobacterium longum NCC2705, whose genome is sequenced, and with nine Bifidobacterium strains isolated from infants' fecal flora. Five days after inoculation, mice were killed. Transforming growth factor beta1 (TGF-beta1), interleukin-4 (IL-4), IL-10, and gamma interferon (IFN-gamma) gene expressions in the ileum and IFN-gamma, tumor necrosis factor alpha (TNF-alpha), IL-10, IL-4, and IL-5 secretions by splenocytes cultivated for 48 h with concanavalin A were quantified. Two Bifidobacterium species had no effect (B. adolescentis) or little effect (B. breve) on the immune system. Bifidobacterium bifidum, Bifidobacterium dentium, and one B. longum strain induced T(H)1 and T(H)2 cytokines at the systemic and intestinal levels. One B. longum strain induced a T(H)2 orientation with high levels of IL-4 and IL-10, both secreted by splenocytes, and of TGF-beta gene expression in the ileum. The other two strains induced T(H)1 orientations with high levels of IFN-gamma and TNF-alpha splenocyte secretions. Bifidobacterium's capacity to stimulate immunity is species specific, but its influence on the orientation of the immune system is strain specific.
Relationships between Shear Wave Velocity and Depth of Overburden (1985)

Relationships between in-situ shear wave velocity and depth of overburden have been derived for various Quaternary age soils encountered primarily in Southern California. The geotechnical parameters found to be significant were geologic age, gravel content, water table depth, and dry density, as well as depth of overburden. The data base for deriving the relationships consists of over 270 shear wave velocity surveys which included refraction, downhole, and cross-hole surveys. The surveys generally provided data to depths of about 100 feet (about 30 meters), however, several of the surveys provided shear wave velocity data to depths of 200 feet (about 60 meters) and greater. Compressional wave velocity data was obtained in many of the same surveys and relationships between compression wave velocity and depth of overburden are also presented.
Single-Mode Monolithic GaSb Vertical-Cavity Surface-Emitting Laser (2012)

We report on the fabrication and performances of an electrically-pumped GaSb monolithic VCSEL, i.e. ,a VCSEL with two epitaxial Bragg mirrors. Selective lateral etching of a tunnel junction is used to provide current and optical confinement. Laser devices with a 6 µm tunnel-junction effective diameter operate at 2.3 µm in CW up to 70 °C, with a threshold current as low as 1.9 mA at 30 °C. The laser emission is single mode with a SMSR near 25 dB and mode-hop-free electro-thermal tunability around 14 nm. This is the first demonstration of a single-mode electrically-pumped monolithic GaSb-based VCSEL.
Membranes as the Energy Source in the Endergonic Transformation of Vitamin A to 11- cis -Retinol (1989)

The eye needs to biosynthesize 11-cis-retinoids because the chromophore of rhodopsin is 11-cis-retinal. The critical metabolic step is the endergonic isomerization of free all-trans-retinol (vitamin A) into 11-cis-retinol. This isomerization process can take place in isolated membranes from the retinal pigment epithelium in the absence of added energy sources. Specific binding proteins probably do not serve as an energy source, and since all of the reactions in the visual cycle are shown here to be reversible, trapping reactions also do not participate in the isomerization reaction. One previously unexplored possibility is that the chemical energy in the bonds of the membrane itself may drive the isomerization reaction. A group transfer reaction is proposed that forms a retinyl ester from a lipid acyl donor and vitamin A. This transfer can drive the isomerization reaction because the all-trans-retinyl ester is isomerized directly to 11-cis-retinol. Thus, the free energy of hydrolysis of the ester is coupled to the thermodynamically uphill trans to cis isomerization. The prediction of an obligate C-O bond cleavage in the vitamin A moiety during isomerization is borne out. Although the natural substrate for isomerization is not known, all-trans-retinyl palmitate is processed in vitro to 11-cis-retinol by pigment epithelial membranes.
Axonal degeneration is an early pathological feature in autoimmune‐mediated demyelination in mice (2001)

Multiple sclerosis (MS) is an inflammatory disorder of the central nervous system (CNS), characterised by focal destruction of myelin. Although it is evident that the immune system contributes to tissue destruction in MS, it is still unclear as to whether this immune response is a cause or a consequence of the disease process. In addition, there is debate over the contribution of axonal damage to clinical progression. We have described a murine model of relapsing-remitting MS (RR-MS), the most common form of the disease, following immunisation with the myelin component, myelin oligodendrocyte glycoprotein (MOG). We showed that a single injection of a MOG peptide (MOG35–55) in NOD/Lt mice induces a paralytic relapsing disease with extensive plaque-like demyelination. This model also mimics many of the immunological features associated with RR-MS. To investigate the relationship between clinical episodes, inflammation, and demyelination/remyelination, we analysed lesions during each attack and remission over the course of the disease, using histological, immunocytochemical, and electron microscopy (EM) techniques. We show that morphological features of lesions in our model resemble those observed in MS. Indeed, severe inflammation and demyelination coincide with the peak of clinical episodes while remissions are characterised by quiescent plaques. Furthermore, axonal damage is evident from the earliest stage of the disease and increases in severity with subsequent relapses. These data establish that in the model of MS-like disease, the peak of clinical episodes coincides with severe inflammation and demyelination and that axonal pathology correlates with clinical progression. Microsc. Res. Tech. 52:731–739, 2001. © 2001 Wiley-Liss, Inc.
Generation of Random Fragments by Sonication (2003)

Except for all but the shortest of sequencing projects, the resolution limits of polyacrylamide gels (being somewhat less than 1 kb) prevents determining the entire sequence in one run. There are several ways to overcome this by subcloning or by primer walking. Each has its advantages and disadvantages. These alternatives should be considered whenever a new project is undertaken. Frequently, the best approach would in fact use more than one method. A high proportion of large-scale sequencing projects use random cloning and sequencing (shotgun sequencing) to produce in excess of 95% of the data, and then employ more directed means to complete it (, , ).
Regulation of myocardial Ca2+-ATPase and phospholamban mRNA expression in response to pressure overload and thyroid hormone. (1989)

The sarcoplasmic reticulum (SR) and the contractile protein myosin play an important role in myocardial performance. Both of these systems exhibit plasticity--i.e., quantitative and/or qualitative reorganization during development and in response to stress. Recent studies indicate that SR Ca2+ uptake function is altered in adaptive cardiac hypertrophy and failure. The molecular basis (genetic and phenotypic) for these changes is not understood. In an effort to determine the underlying causes of these changes, we characterized the rabbit cardiac Ca2+-ATPase phenotype by molecular cloning and ribonuclease A mapping analysis. Our results show that the heart muscle expresses only the slow-twitch SR Ca2+-ATPase isoform. Second, we quantitated the steady-state mRNA levels of two major SR Ca2+ regulatory proteins, the Ca2+-ATPase and phospholamban, to see whether changes in mRNA content might provide insight into the basis for functional modification in the SR of hypertrophied hearts. In response to pressure overload hypertrophy, the relative level of the slow-twitch/cardiac SR Ca2+-ATPase mRNA was decreased to 34% of control at 1 week. The relative Ca2+-ATPase mRNA level increased to 167% of control after 3 days of treatment with thyroid hormone. In contrast, in hypothyroid animals, the relative Ca2+-ATPase mRNA level decreased to 51% of control at 2 weeks. The relative level of phospholamban mRNA was decreased to 36% in 1-week pressure overload. Hyperthyroidism induced a decrease to 61% in the phospholamban mRNA level after 3 days of treatment, while hypothyroidism had virtually no effect on phospholamban mRNA levels. These data indicate that the expression of SR Ca2+-ATPase and phospholamban mRNA may not be coordinately regulated during myocardial adaptation to different physiological conditions.
Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides (2009)

Here it is demonstrated that the yeast Saccharomyces cerevisiae can take up and assemble at least 38 overlapping single-stranded oligonucleotides and a linear double-stranded vector in one transformation event. These oligonucleotides can overlap by as few as 20 bp, and can be as long as 200 nucleotides in length. This straightforward scheme for assembling chemically-synthesized oligonucleotides could be a useful tool for building synthetic DNA molecules.