gebhart/patrepeval huggingface dataset:
Breast cancer during pregnancy (1994)

Breast cancer during pregnancy involves a host of psychosocial, ethical, religious, and legal considerations, as well as medical multidisciplinary decisions. Treatment modalities. Breast or chest wall radiation therapy should be avoided because the fetal dose, regardless of the trimester, can cause permanent complications. In the second and third trimester, chemotherapy is associated with intrauterine growth retardation and prematurity in approximately half of the infants; the risk of birth defects is a concern during the first several weeks. Typical anesthetic agents readily reach the fetus but are not known to be teratogenic. Modified radical mastectomy without delay is the best option in pregnant patients with Stage I or II and some Stage III cancer. Although abortion allows full treatment to the mother, it is not known whether the procedure is therapeutic. Early in pregnancy abortion deserves strong consideration. Prognosis. The poor prognosis of pregnancy-associated breast cancer in the past probably is attributable to a combination of initial delay and possibly to the unfavorable biologic characteristics of pregnancy. When pregnant patients are matched stage for stage with control subjects, survival seems equivalent, although pregnant patients have more advanced stage disease.
ADAMTS1: A Matrix Metalloprotease with Angioinhibitory Properties (2003)

Neovascularization is a hallmark of cancer progression. Suppression of the angiogenic response in tumors has been associated with inhibition and even regression of total tumor mass. Therefore, the derivation of synthetic or natural products that could interfere with proangiogenic signaling pathways can greatly impact cancer therapy. Using the antiangiogenic motifs in thrombospondin-1, we have recently cloned METH1/ADAMTS1, a secreted metalloproteinase with three thrombospondin-1, and shown that the protein inhibits endothelial cell proliferation in vitro and blocks the neovascular response induced by growth factors in vivo. The mechanism of action responsible for these events has not been elucidated. In this report, we present evidence to support two effects of METH1/ADAMTS1 that impact proangiogenic signaling events. ADAMTS1 binds to VEGF and dampens VEGFR2 phosphorylation. The ability of ADAMTS1 to bind VEGF and functionally inactivate VEGFR2 is reversible as dissociation of the complex results in active growth factor. A second activity of ADAMTS1 requires the catalytic domain as a single point mutation in the metalloproteinase domain renders the protein inactive in tumor xenograft assays. The emerging theme is that both domains are likely required for the antiangiogenic/antitumor activities of ADAMTS1.
Optical mouse sensor for detecting height variation and translation of a surface (2008)

A new sensing system based on an optical mouse sensor is developed. The optical mouse sensor is traditionally used as a 2D motion sensor, and in this study it is creatively used for detecting the height variation and translation of the object surfaces at the same time. Based on the experimental characteristics of the sensing system, it can be seen that the sensing system is useful in many fields such as robot odometry. The sensing system is based on a low-cost photoelectric sensor, which is a commercial LED-based optical mouse sensor, and thus it is easily available and generalized. Specially, the outputs of the sensor are intuitively displayed on the computer screen and recorded on the hard disk, which greatly improves the convenience of the system. A periodically-square-shaped rubber surface and a periodically-arc-shaped rubber surface are studied in the experiments. Experiments show that the shape information of the object surfaces and the translation direction of the object surfaces can be obtained at the same time. Besides, in the experiments, it is found that the sensitivity of the optical mouse sensor in different translation direction is different.
Predictions not commands: active inference in the motor system (2012)

The descending projections from motor cortex share many features with top-down or backward connections in visual cortex; for example, corticospinal projections originate in infragranular layers, are highly divergent and (along with descending cortico-cortical projections) target cells expressing NMDA receptors. This is somewhat paradoxical because backward modulatory characteristics would not be expected of driving motor command signals. We resolve this apparent paradox using a functional characterisation of the motor system based on Helmholtz's ideas about perception; namely, that perception is inference on the causes of visual sensations. We explain behaviour in terms of inference on the causes of proprioceptive sensations. This explanation appeals to active inference, in which higher cortical levels send descending proprioceptive predictions, rather than motor commands. This process mirrors perceptual inference in sensory cortex, where descending connections convey predictions, while ascending connections convey prediction errors. The anatomical substrate of this recurrent message passing is a hierarchical system consisting of functionally asymmetric driving (ascending) and modulatory (descending) connections: an arrangement that we show is almost exactly recapitulated in the motor system, in terms of its laminar, topographic and physiological characteristics. This perspective casts classical motor reflexes as minimising prediction errors and may provide a principled explanation for why motor cortex is agranular.
Evaluation of a portable device for diagnosing the sleep apnoea/hypopnoea syndrome (2003)

Waiting times for hospital-based monitoring of the obstructive sleep apnoea/hypopnoea syndrome (OSAHS) are rising. This study tested whether Embletta, a new portable device, may accurately diagnose OSAHS at home. A synchronous comparison to polysomnography was performed in 40 patients and a comparison of home Embletta studies with in-laboratory polysomnography was performed in 61 patients. In the synchronous study, the mean difference (polysomnography-Embletta) in apnoeas+hypopnoeas (A+H) x h(-1) in bed was 2 h(-1). In comparison to the apnoea/ hypopnoea index (AHI) x h(-1) slept, the Embletta (A+H) x h(-1) in bed differed by 8 x h(-1). These data were used to construct diagnostic categories in symptomatic patients from their Embletta results: "OSAHS" (> or = 20 (A+H) x h(-1) in bed), "possible OSAHS" (10-20 (A+H) x h(-1) in bed) or "not OSAHS" (<10 (A+H) x h(-1) in bed). In the home study, the mean difference in (A+H) x h(-1) in bed was 3 x h(-1). In comparison to the polysomnographic AHI x h(-1) slept, the Embletta (A+H) x h(-1) in bed differed by 6 +/- 14 x h(-1). Using the above classification, all nine patients categorised as not OSAHS had AHI < 15 x h(-1) slept on polysomnography and all 23 with OSAHS on Embletta had an AHI > or = 15 on polysomnography, but 18 patients fell into the possible OSAHS category potentially requiring further investigation and 11 home studies failed. Most patients were satisfactorily classified by home Embletta studies but 29 out of 61 required further investigation. The study suggested a 42% saving in diagnostic costs over polysomnography if this approach were adopted.
Assessing Iron Status (2006)

The increasing prevalence of multiple comorbidities among anemic patients with chronic kidney disease has made the use of serum ferritin and transferrin saturation more challenging in diagnosing iron deficiency. Because serum ferritin is an acute-phase reactant and because the inflammatory state may inhibit the mobilization of iron from reticuloendothelial stores, the scenario of patients with serum ferritin >800 ng/ml, suggesting iron overload, and transferrin saturation <20%, suggesting iron deficiency, has become more common. This article revisits the basis for the Kidney Disease Outcomes Quality Initiative recommendations regarding the use of serum ferritin and transferrin saturation in guiding iron therapy, then explores some of the newer alternative markers for iron status that may be useful when serum ferritin and transferrin saturation are insufficient. These newer tests include reticulocyte hemoglobin content, percentage of hypochromic red cells, and soluble transferrin receptor, all of which have shown some promise in limited studies. Finally, the role of hepcidin, a hepatic polypeptide, in the pathophysiology of iron mobilization is reviewed briefly.
Dynamically Specialized Datapaths for energy efficient computing (2011)

Due to limits in technology scaling, energy efficiency of logic devices is decreasing in successive generations. To provide continued performance improvements without increasing power, regardless of the sequential or parallel nature of the application, microarchitectural energy efficiency must improve. We propose Dynamically Specialized Datapaths to improve the energy efficiency of general purpose programmable processors. The key insights of this work are the following. First, applications execute in phases and these phases can be determined by creating a path-tree of basic-blocks rooted at the inner-most loop. Second, specialized datapaths corresponding to these path-trees, which we refer to as DySER blocks, can be constructed by interconnecting a set of heterogeneous computation units with a circuit-switched network. These blocks can be easily integrated with a processor pipeline. A synthesized RTL implementation using an industry 55nm technology library shows a 64-functional-unit DySER block occupies approximately the same area as a 64 KB single-ported SRAM and can execute at 2 GHz. We extend the GCC compiler to identify path-trees and code-mapping to DySER and evaluate the PAR-SEC, SPEC and Parboil benchmarks suites. Our results show that in most cases two DySER blocks can achieve the same performance (within 5%) as having a specialized hardware module for each path-tree. A 64-FU DySER block can cover 12% to 100% of the dynamically executed instruction stream. When integrated with a dual-issue out-of-order processor, two DySER blocks provide geometric mean speedup of 2.1X (1.15X to 10X), and geometric mean energy reduction of 40% (up to 70%), and 60% energy reduction if no performance improvement is required.
Pulmonary surface tension and alveolar stability (1961)

Human and rat lungs were degassed and filled with air and physiological salt solution for determination of pressure-volume relationships. Extracts were prepared from the specimens and examined for their surface film-forming activity. Both the aeration of the alveolar structure of the lungs at functional residual pressure and the surface activity of the extracts showed wide variation. Numerical ratios were defined to express these two properties quantitatively, and a high degree of correlation was observed between them. The range of correlation was extended by treating the rat lungs with nonionic detergents. These findings support the hypothesis that the stability of the pulmonary alveolar structure is dependent on intrinsic surface-active material and have encouraged further attempts at formulating a theory of alveolar mechanics, taking surface forces into account. The theory is presented, and some of its weaknesses are pointed out. Submitted on October 21, 1960
Initial clinical experience with use of CollagraftTM as a bone graft substitute (1992)

Collagraft™(Zimmer, Inc and Collagen Corporation) is a mixture of hydroxyapatite/tricalcium phosphate porous ceramic beads and fibrillar collagen. When mixed with autogenous bone marrow, it serves as an effective bone graft substitute. Since September 1986, this material has been used in a multiclinic prospective trial randomized against cancellous iliac crest autographs in the treatment of long bone fractures. To date, 267 patients have entered this study; 128 patients have received cancellous autograft, and 139 patients have received Collagraft1™. At 6- and 12-month follow up, Collagraft™ appears to function as well as autogenous graft when used in the treatment of acute long bone fractures.
Molecular Cloning and Expression of cDNA Encoding a Galactose/ N-Acetylgalactosamine-Specific Lectin on Mouse Tumoricidal Macrophages1 (1992)

We previously reported that the mouse macrophage galacose and N-acetylgalactosamine-specific lectin (MMGL) may participate in the binding of the macrophages to tumor cells [Oda, S., Sato, M., Toyoshima, S., & Osawa, T. (1989) J. Biochem. 105, 1040-1043]. We now report the cloning and characterization of a cDNA encoding MMGL. The MMGL gene encoded a protein consisting of 304 amino acid residues with a molecular weight of 34,595. The deduced amino acid sequence indicated that MMGL had a single membrane-spanning region, three leucine zipper-like domains, and a carbohydrate recognition domain. Two N-glycosylation sites were found in the extracellular region of MMGL, corresponding to the heavy N-glycosylation in the native MMGL. Comparison of the amino acid sequence of MMGL with those of rat hepatic lectins revealed a high overall sequence homology. The sequence homology was especially high in the putative membrane-spanning region and carbohydrate recognition domain. There was, however, a region of 25 amino acids which did not exist on hepatic lectins. The MMGL cDNA without the region encoding the putative membrane-spanning region and intracellular region was expressed in Escherichia coli. The expressed protein had galactose-binding activity and its sugar-binding specificity was same as that of the native lectin.
Nitrite augments tolerance to ischemia/reperfusion injury via the modulation of mitochondrial electron transfer (2007)

Nitrite (NO(2)(-)) is an intrinsic signaling molecule that is reduced to NO during ischemia and limits apoptosis and cytotoxicity at reperfusion in the mammalian heart, liver, and brain. Although the mechanism of nitrite-mediated cytoprotection is unknown, NO is a mediator of the ischemic preconditioning cell-survival program. Analogous to the temporally distinct acute and delayed ischemic preconditioning cytoprotective phenotypes, we report that both acute and delayed (24 h before ischemia) exposure to physiological concentrations of nitrite, given both systemically or orally, potently limits cardiac and hepatic reperfusion injury. This cytoprotection is associated with increases in mitochondrial oxidative phosphorylation. Remarkably, isolated mitochondria subjected to 30 min of anoxia followed by reoxygenation were directly protected by nitrite administered both in vitro during anoxia or in vivo 24 h before mitochondrial isolation. Mechanistically, nitrite dose-dependently modifies and inhibits complex I by posttranslational S-nitrosation; this dampens electron transfer and effectively reduces reperfusion reactive oxygen species generation and ameliorates oxidative inactivation of complexes II-IV and aconitase, thus preventing mitochondrial permeability transition pore opening and cytochrome c release. These data suggest that nitrite dynamically modulates mitochondrial resilience to reperfusion injury and may represent an effector of the cell-survival program of ischemic preconditioning and the Mediterranean diet.
In vivo imaging and tumor therapy with the sodium iodide symporter (2003)

There has been great progress in the design of vectors for cancer gene therapy. However, it has been difficult to translate success in the laboratory into clinical practice. A major hurdle in understanding these failures has been the relative difficulty in monitoring repeatedly and non-invasively the biodistribution, gene expression and replication of these viral vector systems. With the advent of molecular imaging technology, this deficiency is being rapidly rectified. A number of reporter genes have been used to monitor gene expression. In this review, we discuss the role of the sodium iodide symporter (NIS) as a reporter and therapeutic gene for cancer gene therapy when combined with various radioactive isotopes.
Experiments in morphosyntactic processing for translating to and from German (2009)

We describe two shared task systems and associated experiments. The German to English system used reordering rules applied to parses and morphological splitting and stemming. The English to German system used an additional translation step which recreated compound words and generated morphological inflection.
Confirmation and Control of a Paraquat-Tolerant Goosegrass (Eleusine indica) Biotype1 (2002)

Diminished control of goosegrass was observed in tomato fields located in Manatee County, FL, after years of repeated paraquat use. Tolerance of the Manatee biotype to paraquat was confirmed by its comparison in greenhouse studies with a susceptible biotype from the Alachua County, FL. A 30-fold increase in paraquat rate was required to reach the 50% growth reduction level of the resistant biotype over the susceptible biotype. The Manatee biotype was not tolerant to clethodim, metribuzin, or sethoxydim. These herbicides provided adequate control of all the goosegrass biotypes tested.Nomenclature: Clethodim; metribuzin; paraquat; sethoxydim; goosegrass, Eleusine indica L. #3 ELEIN; tomato, Lycopersicou esculentum Mill.Additional index words: Additive, antagonism, herbicide resistance, synergism.Abbreviations: GR50, herbicide concentration required to inhibit goosegrass aboveground biomass by 50%; WAT, weeks after treatment.
Structural Basis for the Recognition of Blood Group Trisaccharides by Norovirus (2007)

Noroviruses are one of the major causes of nonbacterial gastroenteritis epidemics in humans. Recent studies on norovirus receptors show that different noroviruses recognize different human histo-blood group antigens (HBGAs), and eight receptor binding patterns of noroviruses have been identified. The P domain of the norovirus capsids is directly involved in this recognition. To determine the precise locations and receptor binding modes of HBGA carbohydrates on the viral capsids, a recombinant P protein of a GII-4 strain norovirus, VA387, was cocrystallized with synthetic type A or B trisaccharides. Based on complex crystal structures observed at a 2.0-A resolution, we demonstrated that the receptor binding site lies at the outermost end of the P domain and forms an extensive hydrogen-bonding network with the saccharide ligand. The A and B trisaccharides display similar binding modes, and the common fucose ring plays a key role in this interaction. The extensive interface between the two protomers in a P dimer also plays a crucial role in the formation of the receptor binding interface.
Rapid Identification of Oil‐Contaminated Soils Using Visible Near‐Infrared Diffuse Reflectance Spectroscopy (2010)

In the United States, petroleum extraction, refinement, and transportation present countless opportunities for spillage mishaps. A method for rapid field appraisal and mapping of petroleum hydrocarbon-contaminated soils for environmental cleanup purposes would be useful. Visible near-infrared (VisNIR, 350-2500 nm) diffuse reflectance spectroscopy (DRS) is a rapid, nondestructive, proximal-sensing technique that has proven adept at quantifying soil properties in situ. The objective of this study was to determine the prediction accuracy of VisNIR DRS in quantifying petroleum hydrocarbons in contaminated soils. Forty-six soil samples (including both contaminated and reference samples) were collected from six different parishes in Louisiana. Each soil sample was scanned using VisNIR DRS at three combinations of moisture content and pretreatment: (i) field-moist intact aggregates, (ii) air-dried intact aggregates, (iii) and air-dried ground soil (sieved through a 2-mm sieve). The VisNIR spectra of soil samples were used to predict total petroleum hydrocarbon (TPH) content in the soil using partial least squares (PLS) regression and boosted regression tree (BRT) models. Each model was validated with 30% of the samples that were randomly selected and not used in the calibration model. The field-moist intact scan proved best for predicting TPH content with a validation r2 of 0.64 and relative percent difference (RPD) of 1.70. Because VisNIR DRS was promising for rapidly predicting soil petroleum hydrocarbon content, future research is warranted to evaluate the methodology for identifying petroleum contaminated soils.
Point Mutations in Anthrax Protective Antigen That Block Translocation (2001)

The protective antigen (PA) moiety of anthrax toxin delivers the toxin's enzymatic moieties to the cytosol of mammalian cells by a mechanism associated with its ability to heptamerize and form a transmembrane pore. Here we report that mutations in Lys-397, Asp-425, or Phe-427 ablate killing of CHO-K1 cells by a cytotoxic PA ligand. These mutations blocked PA's ability to mediate pore formation and translocation in cells but had no effect on its receptor binding, proteolytic activation, or ability to oligomerize and bind the toxin's enzymatic moieties. The mutation-sensitive residues lie in the 2beta(7)-2beta(8) and 2beta(10)-2beta(11) loops of domain 2 and are distant both in primary structure and topography from the 2beta(2)-2beta(3) loop, which is believed to participate in formation of a transmembrane beta-barrel. These results suggest that Lys-397, Asp-425, and Phe-427 participate in conformational rearrangements of a heptameric pore precursor that are necessary for pore formation and translocation. Identification of these residues will aid in elucidating the mechanism of translocation and may be useful in developing therapeutic and prophylactic agents against anthrax.
The role of sonic hedgehog in adult neural progenitor cell proliferation in vitro and in vivo (2003)

Neural stem and progenitor cells have significant promise for the regeneration of tissue from the effects of trauma or neurodegenerative disorders, such as Alzheimer's or Parkinson's diseases. However, our understanding of the signaling factors and basic mechanisms that control their behavior must be greatly improved before this promise can be achieved. We have investigated the role of sonic hedgehog (Shh), a signaling protein vital for the development of the nervous system, in regulating adult neural stem cells from the hippocampus. We found high levels of expression of the Shh receptor, Patched, in the dentate gyrus region of adult rat brain, where hippocampal neural progenitor cells are believed to reside, as well as in neural stem cells isolated for the hippocampus. Furthermore, the addition of recombinant Shh to cells in culture elicited a strong time and dose dependent proliferative response. Finally, injection of an adeno-associated viral (AAV) vector carrying Shh cDNA into the hippocampus resulted in a 3.3 fold increase in stem cell proliferation as compared to an AAV-GFP control. This work identifies Shh as a novel regulator of adult hippocampal progenitor cell function and also, to our knowledge, demonstrates the first known role of Shh in adult organisms.
Sildenafil Exposure and Hemodynamic Effect After Fontan Surgery (2013)

After Fontan surgery, sildenafil infusion acutely improves cardiopulmonary hemodynamics, increasing cardiac index. For the range of doses studied, exposure was within the acute safety range reported in adult subjects.