gebhart/patrepeval huggingface dataset:
Control of Cyclin D1, p27Kip1, and Cell Cycle Progression in Human Capillary Endothelial Cells by Cell Shape and Cytoskeletal Tension (1998)

The extracellular matrix (ECM) plays an essential role in the regulation of cell proliferation during angiogenesis. Cell adhesion to ECM is mediated by binding of cell surface integrin receptors, which both activate intracellular signaling cascades and mediate tension-dependent changes in cell shape and cytoskeletal structure. Although the growth control field has focused on early integrin and growth factor signaling events, recent studies suggest that cell shape may play an equally critical role in control of cell cycle progression. Studies were carried out to determine when cell shape exerts its regulatory effects during the cell cycle and to analyze the molecular basis for shape-dependent growth control. The shape of human capillary endothelial cells was controlled by culturing cells on microfabricated substrates containing ECM-coated adhesive islands with defined shape and size on the micrometer scale or on plastic dishes coated with defined ECM molecular coating densities. Cells that were prevented from spreading in medium containing soluble growth factors exhibited normal activation of the mitogen-activated kinase (erk1/erk2) growth signaling pathway. However, in contrast to spread cells, these cells failed to progress through G1 and enter S phase. This shape-dependent block in cell cycle progression correlated with a failure to increase cyclin D1 protein levels, down-regulate the cell cycle inhibitor p27(Kip1), and phosphorylate the retinoblastoma protein in late G1. A similar block in cell cycle progression was induced before this same shape-sensitive restriction point by disrupting the actin network using cytochalasin or by inhibiting cytoskeletal tension generation using an inhibitor of actomyosin interactions. In contrast, neither modifications of cell shape, cytoskeletal structure, nor mechanical tension had any effect on S phase entry when added at later times. These findings demonstrate that although early growth factor and integrin signaling events are required for growth, they alone are not sufficient. Subsequent cell cycle progression and, hence, cell proliferation are controlled by tension-dependent changes in cell shape and cytoskeletal structure that act by subjugating the molecular machinery that regulates the G1/S transition.
Translational Control of the Abundance of Cytoplasmic Poly(A) Binding Protein in Human Cytomegalovirus-Infected Cells (2010)

Irrespective of their effects on ongoing host protein synthesis, productive replication of the representative alphaherpesvirus herpes simplex virus type 1, the representative gammaherpesvirus Kaposi's sarcoma herpesvirus, and the representative betaherpesvirus human cytomegalovirus [HCMV] stimulates the assembly of the multisubunit, cap-binding translation factor eIF4F. However, only HCMV replication is associated with an increased abundance of eIF4F core components (eIF4E, eIF4G, eIF4A) and the eIF4F-associated factor poly(A) binding protein (PABP). Here, we demonstrate that the increase in translation factor concentration was readily detected in an asynchronous population of HCMV-infected primary human fibroblasts, abolished by prior UV inactivation of virus, and genetically dependent upon viral immediate-early genes. Strikingly, while increased mRNA steady-state levels accompanied the rise in eIF4E and eIF4G protein levels, the overall abundance of PABP mRNA, together with the half-life of the polypeptide it encodes, remained relatively unchanged by HCMV infection. Instead, HCMV-induced PABP accumulation resulted from new protein synthesis and was sensitive to the mTORC1-selective inhibitor rapamycin, which interferes with phosphorylation of the mTORC1 substrate p70 S6K and the translational repressor 4E-BP1. While virus-induced PABP accumulation did not require p70 S6K, it was inhibited by the expression of a dominant-acting 4E-BP1 variant unable to be inactivated by mTORC1. Finally, unlike the situation in alpha- or gammaherpesvirus-infected cells, where PABP is redistributed to nuclei, PABP accumulated in the cytoplasm of HCMV-infected cells. Thus, cytoplasmic PABP accumulation is translationally controlled in HCMV-infected cells via a mechanism requiring mTORC1-mediated inhibition of the cellular 4E-BP1 translational repressor.
Role of Vitamin D Deficiency in Chronic Kidney Disease (2007)

Chronic kidney disease (CKD) has been recognized as a significant public health problem, with approximately 20 million Americans, or approximately 11% of the adult population, currently living with CKD. A significant source of morbidity associated with CKD is the development of disturbances of mineral metabolism, which occurs in virtually all patients during the progression of their disease, and is associated with bone loss and fractures, cardiovascular disease, immune suppression, and increased mortality. As kidney disease develops, there is decreased functional renal mass and a tendency to retain phosphorus. The reduction in functional renal mass and the retained phosphorus act to reduce renal 1alpha-hydroxylase activity and thus the renal production of calcitriol. Further compensation to maintain normal serum calcium and phosphorus homeostasis includes increased production and release of PTH and potentially other phosphaturic factors, such as fibroblast growth factor-23 (FGF23). This increase in FGF23 contributes to maintain normal serum phosphate independent of PTH but may worsen calcitriol deficiency by also inhibiting renal 1alpha-hydroxylase activity. The decrease in calcitriol also results in promoting further hyperparathyroidism and parathyroid gland hyperplasia, because calcitriol normally inhibits the production of prepro-PTH and parathyroid cell proliferation.
Opals: Status and Prospects (2009)

The beauty of opals results from a densely packed, highly ordered arrangement of silica spheres with a diameter of several hundred nanometers. Such ordered nanostructures are typical examples of materials called photonic crystals, which can be formed by known microstructuring methods and by self-assembly. Opals represent a self-assembly approach to these structured media; such an approach can lead to novel materials for photonics, photocatalysis, and other areas. Although self-assembly leads to many types of defects, resulting in the surprising and very individual appearance of natural opals, it causes also difficulties in technological applications of opal systems.
Evaluation of dual-labeled fluorescent DNA probe purity versus performance in real-time PCR (2004)

Real-time PCR technology using dual-labeled fluorescent oligonucleotide probes allows for sensitive, specific, and quantitative determination of mRNA or DNA targets. Historically, dual-labeled probes have been the most expensive reagent in real-time PCR because of the postsynthesis high-performance liquid chromatography (HPLC) and/or gel purification steps required due to limitations in traditional synthesis chemistry. The recent availability of quencher reagents that allow the 3' quencher incorporation as part of the on-machine synthesis has presented the possibility that probes, when carefully synthesized, may be used without extensive postsynthesis purification. This would substantially reduce cost, making the synthesis of dual-labeled fluorescent probes affordable to any DNA synthesis laboratory. The Nucleic Acids Research Group (NARG) of the Association of Biomolecular Resource Facilities (ABRF) (Santa Fe, NM, USA) tested the hypothesis that now any DNA synthesis laboratory is capable of making quality dual-labeled fluorescent probes suitable for real-time PCRs without the need for postsynthesis purification. Members of the DNA synthesis community synthesized dual-labeled human beta-actin probes and submitted them for quality and functional analysis. We found that probes that were at least 20% pure had the same efficiency as those near 100% purity, but the sensitivity of the assay was reduced as the level of purity decreased.
Advances in Chemoprevention of Head and Neck Cancer (2004)

Head and neck squamous cell carcinoma is a devastating disease with a poor outcome in advanced stages, accounting for approximately 3% of all malignancies, with an estimated 37200 new cases and 11000 deaths annually in the U.S. Second primary tumors are estimated to occur at an annual rate of 3%-10% and are significant threats to long-term survivors. Chemoprevention is an appealing strategy, and its success has been demonstrated in breast cancer and familial adenomatous polyposis. High-dose retinoids have been shown to be active against oral premalignant lesions and in prevention of second primary tumors in the head and neck. New targets include the epidermal growth factor receptor, cyclooxygenase-2, and other molecular targets. Challenges in future head and neck cancer chemoprevention investigations include achieving long-lasting efficacy with retinoids and/or new agents, and determining the optimal dose and duration of therapy while maintaining acceptable toxicities.
The right ventricle in pulmonary hypertension (2005)

Pulmonary arterial hypertension (PAH) is a term used to classify a variety of conditions that share in common an injury to the pulmonary vasculature that produces elevations in pulmonary arterial pressure. However, it is the integrity of right ventricular function, rather than the degree of vascular injury, that is the major determinant of symptoms and survival in PAH. The article will review the normal structure and function of the right ventricle and summarize the impact of PAH and its treatments on right ventricular function.
Wnt and FGF signals interact to coordinate growth with cell fate specification during limb development (2008)

A fundamental question in developmental biology is how does an undifferentiated field of cells acquire spatial pattern and undergo coordinated differentiation? The development of the vertebrate limb is an important paradigm for understanding these processes. The skeletal and connective tissues of the developing limb all derive from a population of multipotent progenitor cells located in its distal tip. During limb outgrowth, these progenitors segregate into a chondrogenic lineage, located in the center of the limb bud, and soft connective tissue lineages located in its periphery. We report that the interplay of two families of signaling proteins, fibroblast growth factors (FGFs) and Wnts, coordinate the growth of the multipotent progenitor cells with their simultaneous segregation into these lineages. FGF and Wnt signals act together to synergistically promote proliferation while maintaining the cells in an undifferentiated, multipotent state, but act separately to determine cell lineage specification. Withdrawal of both signals results in cell cycle withdrawal and chondrogenic differentiation. Continued exposure to Wnt, however, maintains proliferation and re-specifies the cells towards the soft connective tissue lineages. We have identified target genes that are synergistically regulated by Wnts and FGFs, and show how these factors actively suppress differentiation and promote growth. Finally, we show how the spatial restriction of Wnt and FGF signals to the limb ectoderm, and to a specialized region of it, the apical ectodermal ridge, controls the distribution of cell behaviors within the growing limb, and guides the proper spatial organization of the differentiating tissues.
Reconstructing Root. An argument for objectivity. (2001)

Substantial evidence suggests that complete rejection of the Root model may be premature, given the inherent logic in an Aristotelian interpretation of its core philosophy. Although critics have focused on a Platonic interpretation of Root's criteria for normalcy and surrounding theories, recent theoretic shifts towards a more flexible view of the factors which can combine to produce pathologic conditions suggest that the Root model retains usefulness. Although it has been suggested that Kuhn's approach may contain a destructive element, one of its propositions--that a phase of normal science is characterized by a common vision of the research required within the paradigm--seems to hold the key to the future success of podiatric biomechanics. The approach of Lakatos seems to provide the required "modicum of self-confidence which enables us to live and practice" to smooth the transition between established and emergent approaches. Although the approaches of Kuhn and Lakatos remain incommensurable, it is certain that Kuhn would agree with one particularly relevant comment by Lakatos, that "blind commitment to a theory is not an intellectual virtue: it is an intellectual crime."
Hydrocarbon emissions characterization in the Colorado Front Range: A pilot study (2012)

The multispecies analysis of daily air samples collected at the NOAA Boulder Atmospheric Observatory (BAO) in Weld County in northeastern Colorado since 2007 shows highly correlated alkane enhancements caused by a regionally distributed mix of sources in the Denver‐Julesburg Basin. To further characterize the emissions of methane and non‐methane hydrocarbons (propane, n‐butane, i‐pentane, n‐pentane and benzene) around BAO, a pilot study involving automobile‐based surveys was carried out during the summer of 2008. A mix of venting emissions (leaks) of raw natural gas and flashing emissions from condensate storage tanks can explain the alkane ratios we observe in air masses impacted by oil and gas operations in northeastern Colorado. Using the WRAP Phase III inventory of total volatile organic compound (VOC) emissions from oil and gas exploration, production and processing, together with flashing and venting emission speciation profiles provided by State agencies or the oil and gas industry, we derive a range of bottom‐up speciated emissions for Weld County in 2008. We use the observed ambient molar ratios and flashing and venting emissions data to calculate top‐down scenarios for the amount of natural gas leaked to the atmosphere and the associated methane and non‐methane emissions. Our analysis suggests that the emissions of the species we measured are most likely underestimated in current inventories and that the uncertainties attached to these estimates can be as high as a factor of two.
Randomized clinical trial of testosterone replacement therapy in hypogonadal men (1988)

We have compared the pharmacokinetics and pharmacodynamics of the three commonly used testosterone formulations in a prospective, randomized cross-over clinical trial. Plasma free and total testosterone and their ratio (proportion of unbound testosterone), sex hormone-binding globulin (SHBG), oestradiol, LH and FSH were measured in 15 hypogonadal men (nine hyper- and six hypogonadotrophic) who underwent, in a randomized sequence, three treatment periods each separated by an intervening washout period. The treatments were: (i) intramuscular injection of 250 mg mixed testosterone esters at 2-weekly intervals, (ii) oral testosterone undecanoate 120 mg bd, and (iii) subcutaneous testosterone pellets (6 x 100 mg). Pellet implantation gave the most prolonged effect with free and total testosterone levels being elevated for up to 4 months. This was accompanied by prompt and sustained suppression of plasma LH and FSH, an increase in plasma levels of oestradiol but no change in SHBG levels. In contrast, intramuscular injections induced marked but reproducible week-to-week fluctuations in free and total testosterone, which resulted in a small decrease in plasma SHBG levels, less marked suppression of LH and FSH and a smaller increase in plasma levels of oestradiol. Oral testosterone undecanoate produced the most variable plasma levels of free and total testosterone with a peak in the first treatment week and a fall thereafter and, despite maintenance of testosterone levels within the physiological range, there was no significant suppression of plasma levels of LH and FSH, and oestradiol levels were unchanged but levels of SHBG and total cholesterol were decreased. Free testosterone levels were increased disproportionately during testosterone treatment as the proportion of unbound testosterone was increased by all three treatments. All three testosterone preparations lowered plasma levels of urea and all were without biochemical or haematological toxicity. Reported sexual function was better maintained and side-effects were fewer with parenteral compared with oral treatments. The marked decrease in SHBG and cholesterol levels during oral testosterone undecanoate, when compared with parenteral treatments, occurred despite lesser androgenic effects (suppression of gonadotrophin levels and reported sexual function), which suggests that the liver is exposed to excessive androgenic load via the portal vein during oral treatment with testosterone esters. It is concluded that testosterone pellets give the closest approximation to zero-order (steady-state) delivery conditions for up to 4 months after a single insertion.(ABSTRACT TRUNCATED AT 400 WORDS)
Procedural Urban Modeling in Practice (2008)

Film and game studios can no longer meet audience demand for visual content by increasing production budgets. Instead they are turning to procedural modeling, particularly for modeling cities. The authors review procedural modeling, examine the CityEngine tool, and study the use of procedural urban modeling in Electronic Arts' Need for Speed games.
The adjuvanticity of interleukin 1 in vivo. (1983)

Interleukin 1 (IL 1) was shown to enhance in vivo secondary antibody responses of mice to a protein antigen. The activity was found to be dose and time dependent. The maximum enhancing effect was obtained with 2000 LAF units of IL 1 given 2 hr after the priming dose of antigen. The observation is consistent with the in vitro immunoenhancing activities of IL 1 and strongly suggests that this protein may be an important mediator of host defense responses, as well as of the stimulatory effects of some adjuvants.
Calcium-sensing receptor abrogates secretagogue- induced increases in intestinal net fluid secretion by enhancing cyclic nucleotide destruction (2006)

The calcium-sensing receptor (CaSR) provides a fundamental mechanism for diverse cells to detect and respond to modulations in the ionic and nutrient compositions of their extracellular milieu. The roles for this receptor are largely unknown in the intestinal tract, where epithelial cells are normally exposed to large variations in extracellular solutes. Here, we show that colonic CaSR signaling stimulates the degradation of cyclic nucleotides by phosphodiesterases and describe the ability of receptor activation to reverse the fluid and electrolyte secretory actions of cAMP- and cGMP-generating secretagogues, including cholera toxin and heat stable Escherichia coli enterotoxin STa. Our results suggest a paradigm for regulation of intestinal fluid transport where fine tuning is accomplished by the counterbalancing effects of solute activation of the CaSR on neuronal and hormonal secretagogue actions. The reversal of cholera toxin- and STa endotoxin-induced fluid secretion by a small-molecule CaSR agonist suggests that these compounds may provide a unique therapy for secretory diarrheas.
Identification of HTLV-III/LAV sor Gene Product and Detection of Antibodies in Human Sera (1986)

The nucleotide sequence of the genome of HTLV-III, the infectious agent etiologically associated with the acquired immune deficiency syndrome, predicts a small open reading frame, termed sor, located between the pol and env genes. A DNA segment containing 82 percent of the sor region was inserted into a prokaryotic expression vector, pJL6, to determine whether sor encodes a viral protein and to gain some insight into its possible function. The bacterially synthesized sor protein reacted with sera from individuals infected with HTLV-III, indicating that sor is expressed as a protein product or products that are immunogenic in vivo. Antibodies to the purified, bacterially synthesized sor protein were found to react specifically with the same protein and also with a protein of molecular weight 23,000 (23K) in HTLV-III-infected H9 cell extracts. The 23K protein comigrated with a protein immunoprecipitated by the serum of a hemophiliac patient with antibodies to HTLV-III, suggesting that this protein is probably the sor gene product.
Open information extraction from the web (2007)

Traditionally, Information Extraction (IE) has focused on satisfying precise, narrow, pre-specified requests from small homogeneous corpora (e.g., extract the location and time of seminars from a set of announcements). Shifting to a new domain requires the user to name the target relations and to manually create new extraction rules or hand-tag new training examples. This manual labor scales linearly with the number of target relations. This paper introduces Open IE (OIE), a new extraction paradigm where the system makes a single data-driven pass over its corpus and extracts a large set of relational tuples without requiring any human input. The paper also introduces TEXTRUNNER, a fully implemented, highly scalable OIE system where the tuples are assigned a probability and indexed to support efficient extraction and exploration via user queries. We report on experiments over a 9,000,000 Web page corpus that compare TEXTRUNNER with KNOWITALL, a state-of-the-art Web IE system. TEXTRUNNER achieves an error reduction of 33% on a comparable set of extractions. Furthermore, in the amount of time it takes KNOWITALL to perform extraction for a handful of pre-specified relations, TEXTRUNNER extracts a far broader set of facts reflecting orders of magnitude more relations, discovered on the fly. We report statistics on TEXTRUNNER’s 11,000,000 highest probability tuples, and show that they contain over 1,000,000 concrete facts and over 6,500,000 more abstract assertions.
Role of leukocyte CD11/CD18 complex in endotoxic and septic shock in rabbits (1992)

Two models of sepsis were investigated using rabbits. In the first model, rabbits given lipopolysaccharide (LPS) were treated with saline (group II) or CD18 monoclonal antibody (MAb) 60.3 (group III). Group I animals received no LPS. Cardiac output was maintained by infusion of lactated Ringer solution with group II (95 +/- 68 ml/kg) requiring significantly more than group I (0 +/- 0 ml/kg) or group III (39 +/- 27 ml/kg). Lung permeability indexes in groups II (median 0.002, range 0.023) and III (median 0.0035, range 0.053) were not different but were significantly greater than group I (median 0.0007, range 0.001). In the second model, peritonitis was produced by devascularizing the appendix, leaving it in situ for 19 h, and then performing an appendectomy. Saline or MAb 60.3 treatment was at appendectomy and every 12 h for 3 days. Survival was significantly greater in the MAb 60.3-treated group at day 10 (90 vs. 40%). Lung permeability was increased at day 2 and was not different between groups. Day 1 fluid requirements were greater in the saline-treated group. These data are consistent with MAb 60.3 protection of systemic but not pulmonary circulation in two models of sepsis.
Evaluation of the microbial growth response to inorganic nanoparticles (2006)

In order to enhance the utilization of inorganic nanoparticles in biological systems, it is important to develop a fundamental understanding of the influence they have on cellular health and function. Experiments were conducted to test silica, silica/iron oxide, and gold nanoparticles for their effects on the growth and activity of Escherichia coli (E. coli). Transmission electron microscopy (TEM) and dynamic light scattering (DLS) were used to characterize the morphology and quantify size distribution of the nanoparticles, respectively. TEM was also used to verify the interactions between composite iron oxide nanoparticles and E. coli. The results from DLS indicated that the inorganic nanoparticles formed small aggregates in the growth media. Growth studies measured the influence of the nanoparticles on cell proliferation at various concentrations, showing that the growth of E. coli in media containing the nanoparticles indicated no overt signs of toxicity.